A Practical Guide to working

with AlphaScreen
Table of Contents

I. Overview Of AlphaScreen™ .................................................... 1

Introduction and Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

What is AlphaScreen? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

Unique features: Comparison to other HTS technologies . . . . . . . . . . . . . . . . . . . . . .3

How to measure AlphaScreen: plates and instrumentation . . . . . . . . . . . . . . . . . . . .4

II. AlphaScreen – Assays and Applications ................................... 5

Ready-to-use assay kits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5

Generic reagent detection kits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6

Custom conjugation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6

Assay formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6

Available reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8

III. How to work with AlphaScreen— a general guide ..................... 13

Getting Started . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13

Environment and placement of instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13

Use and storage of reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14

Experimental protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14

Assay Design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14

Signal reduction or signal increase? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14

Choosing the best combination of assay components . . . . . . . . . . . . . . . . . . . . . . . .16

Biology and chemistry considerations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17

Plate Choice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18

Initial Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18

Determining optimal reagent concentrations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18

Generating data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19

Interpreting data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20

w w w. p e r k i n e l m e r. c o m i
 Optimizing your assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20

Assay format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20

Order of addition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21

Reagent choice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22

Buffer choice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22

Salts, detergents and ions (Transition Metals such as Al2+, Fe2+, Fe3+, Cu2+, Ni2+ and Zn2+) . . . . . . .23

Cell culture media and sera . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23

Liquid handling and dispensing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23

Miniaturization and reagent concentration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23

IV. Taking AlphaScreen from assay development to high

throughput screening . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24

Initial experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24

Wet runs of liquid handling instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24

Assay equilibrium time course . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24

Choosing an optimal experimental environment . . . . . . . . . . . . . . . . . . . . . . . . . .25

Lighting considerations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25

Temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .26

Other recommendations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27

Miniaturization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27

Compound interference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .28

V. Troubleshooting guide ........................................................ 29

VI. Literature available by application ......................................... 32

Appendix I: Fusion-Alpha™ Quick Start guide ............................... 36

Appendix II: AlphaQuest® HTS Quick Start guide .......................... 42

Appendix III: EnVision™ Multilabel Plate Reader

with AlphaScreen module Quick Start guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .50

ii
List of Tables

Table 1: AlphaScreen reagents and part numbers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9

Table 2: What types of assays can I set up and how? . . . . . . . . . . . . . . . . . . . . . . . . . . . .11

Table 3: Plate choice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18

List of Figures

Figure 1: AlphaScreen binding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2

Figure 2: No binding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2

Figure 3a: Direct format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7

Figure 3b: Direct format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7

Figure 4: Indirect format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8

Figure 5: The hooking effect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15

Figure 6: IgG detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16

Figure 7: Optimization of c-Src Tyrosine Kinase Enzyme

and Biotin-Poly-(Glu, Tyr) Substrate Concentrations . . . . . . . . . . . . . . . . . .19

Figure 8: Optimization of buffer conditions and Mouse-IgG Biotin-Tracer . . . . . . .22

Figure 9: Experiment to determine incubation time required to reach
assay equilibrium . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24
Figure 10: Light transmittance spectrum for rosco filter . . . . . . . . . . . . . . . . . . . . . . . . . .25

Figure 11: Light exposure time course . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .26

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iv
I. Overview of AlphaScreen
Introduction and background
What is AlphaScreen?
AlphaScreen™ is a bead-based chemistry used to study biomolecular interac-
tions in a microplate format. The acronym ALPHA stands for Amplified
Luminescent Proximity Homogeneous Assay. As the name implies, some
of the key features are that it is a non-radioactive, homogeneous proximity
assay. Binding of molecules captured on the beads leads to an energy transfer
from one bead to the other, ultimately producing a luminescent/fluorescent
signal. AlphaScreen was originally developed under the name LOCI®
(Luminescent Oxygen Channeling Immunoassay) by Dade Behring, Inc. of
Germany. Originally published in 19941, the paper outlining the method
describes a chemistry that is at once fast, homogeneous, sensitive and easy
to use. LOCI is sold and used by clinical diagnostic labs, while PerkinElmer
possesses the rights to manufacture and distribute beads and reagents under
the name AlphaScreen for drug discovery purposes.

To understand how a signal is produced, one must begin with an under-

standing of the beads. Every AlphaScreen assay contains two bead types,
Donor beads and Acceptor beads. Both bead types are coated with a hydrogel
which minimizes non-specific binding and self-aggregation, and provides
reactive aldehyde groups for conjugating biomolecules to the bead surface.
Beads are latex-based and approximately 250 nm in diameter. They are much
smaller than those of other bead-based assays such as SPA beads (2–10 µm)
and FMAT (6–20 µm). This feature represents significant advantages. The
beads are too small to sediment in biological buffers and bead suspensions
can be easily dispensed using automated liquid handling devices without
clogging small tips. They possess a relatively large surface area for conjuga-
tion of biomolecules and are typically used at much lower concentration
(µg/mL) than that of SPA beads (mg/mL), for example. Yet, they are large
enough to be centrifuged and/or filtered, thus no chromatographic separa-
tion is needed for purification following bioconjugation, resulting in high
yield and ease of use. The beads are very stable in suspension, even at high
temperatures (ex.: 95°C for PCR), as well as in lyophilized form.

Each bead type contains a different proprietary mixture of chemicals, which

are key elements of the AlphaScreen technology. Donor beads contain a photo-
sensitizer, phthalocyanine, which converts ambient oxygen to an excited form
of O2, singlet oxygen, upon illumination at 680 nm. Please note that singlet
oxygen is not a radical; it is molecular oxygen with a single excited electron.
Like other excited molecules, singlet oxygen has a limited lifetime prior to
falling back to ground state. Within its 4 µsec half-life, singlet oxygen can
diffuse approximately 200 nm in solution. If an Acceptor bead is within that

1. Luminescent oxygen channeling immunoassay: Measurement of particle binding kinetics by chemi-

luminescence. Ullman, EF, et al. Proc. Natl. Acad. Sci. USA, Vol. 91, pp. 5426–5430, June 1994.

w w w. p e r k i n e l m e r. c o m 1
 proximity, energy is transferred from the singlet oxygen to thioxene derivatives
within the Acceptor bead, subsequently culminating in light production at
520– 620 nm. In the absence of an Acceptor bead, singlet oxygen falls to
ground state and no signal is produced. This proximity-dependent chemical
energy transfer is the basis for AlphaScreen’s homogeneous nature.

Proximity of Acceptor to Donor beads depends on the biological interaction

of the molecules bound to them. The most common AlphaScreen assay is
constructed by capturing one binding partner, such as a receptor, onto the
Donor beads and the other partner, such as the ligand, onto the Acceptor
beads. When the partners interact, chemical energy is transferred from Donor
to Acceptor beads and a signal is produced (Figure 1). Alternatively, compe-
tition or cleavage assays can be read as signal reduction (Figure 2). Donor beads
are typically sold as streptavidin (SA) conjugates, since biotinylation of one
binding partner provides efficient capture onto the Donor bead. Acceptor
beads come in a variety of conjugates, primarily to antibodies (anti-species
IgG, anti-His, anti-FLAG®, anti-phosphopeptide, etc.); the second binding
partner would then need to have the corresponding antigen attached. Both
beads are also available unconjugated and may be coated directly to the
binding partners via a simple reductive amination protocol.

Excitation
680 nm
1
O2 Emission
520-620 nm

AlphaScreen A AlphaScreen
Donor Bead B
Acceptor Bead

Figure 1: AlphaScreen Binding

Binding of biological “partners” brings Donor and Acceptor beads into close
proximity (≤200 nm) and thus a fluorescent signal between 520–620 nm is produced.

Excitation
680 nm 1
O2

C AlphaScreen
Acceptor Bead
AlphaScreen A
Donor Bead

Figure 2: No Binding
When there is no binding, Donor and Acceptor beads are not in close proximity.
Singlet oxygen decays and no signal is produced.

2
Unique features: comparison to other HTS Technologies
AlphaScreen offers many advantages to the user. It has unique features
over alternative technologies, including:

• Very high sensitivity

The signal (in counts per second, or cps) is a cascade reaction which occurs
due to the high concentration of photosensitizer inside the Donor beads
and the high density of thioxene derivative and fluorophores inside the
Acceptor beads. Upon excitation at 680 nm, each Donor bead can release
up to 60,000 singlet oxygen molecules per second resulting in a very high
signal amplification. Due to the strong signal produced by the signal
amplification cascade reaction, AlphaScreen is capable of detecting
molecular interactions occurring down to femtomolar concentration of
binding partners.

• Very low backgrounds

Backgrounds are really low (ex.: empty well ~ 100– 200 cps; dependent
on the plates and the reader). There are three reasons for this: First,
we are measuring in a time-resolved mode (20 msec) which eliminates
virtually all fluorescent background from assay components and plates.
Second, the wavelength at which the signal is read is lower than the
excitation wavelength, where most of the background counts are found.
Third, since the illumination wavelength is very long at 680 nm, very
few biological or assay substances will interfere. There is virtually no
auto fluorescence from plates and assay components making AlphaScreen
a highly sensitive and robust assay technology.

• High signal/Background ratios

Because of this combination of strong signal and low background,
AlphaScreen S/B ratios tend to be outstanding, some assays reaching
S/B ratios of several hundreds.

• True miniaturization
AlphaScreen assays can be easily miniaturized to 5 µL or less with no
change in reagent concentration, no need for assay re-optimization, and
no sacrifice in assay robustness. Simply reduce the absolute amount of all
reagents by the same percentage and transfer it into a smaller well.

• Cost effective
Because of the tremendous S/B ratios and the fact that true miniaturization
allows reagent “stretching” AlphaScreen is competitive in terms of cost.
Generally speaking, AlphaScreen can be performed at pennies per well,
with some assays at less than 1 cent per well.

w w w. p e r k i n e l m e r. c o m 3
 • Optimal versatility in assay design
Extreme versatility in assay design is achievable with AlphaScreen.
Enzyme activity, receptor-ligand interactions, low affinity interactions,
second messenger levels, functional GPCR studies, DNA, RNA, proteins,
peptides, carbohydrates, small molecules, large molecules, or binding
partners of greatly disparate size can all be measured with AlphaScreen.
If you can bind, label, or cleave, you can measure with AlphaScreen.

• Low affinity to high affinity interactions

AlphaScreen can measure virtually any strength of biological interaction.
Unlike alternative technologies, AlphaScreen is suitable for low affinity
binding assays. This is possible because the signal produced by Donor/
Acceptor bead pairs results from the binding of dozens, or even hundreds
of biopartners, rather than just one. Each Donor bead carries up to 3,000
streptavidin molecules, and each Acceptor bead is coated with up to 300
antibodies. Bead proximity, and resulting signal generation, is maintained
by the interaction of these many possible biopartners. With alternative
chemistries, each binding partner carries a single label so that if some beads
are unbound, less signal is generated. AlphaScreen conveniently sidesteps
the issue by having many binding reactions per bead pair.

In summary, AlphaScreen is the most flexible assay technology ever offered

by any company to date. No other system offers such a combination of great
results, cost effectiveness, versatility and ease of use.

How to measure AlphaScreen: plates and instrumentation

AlphaScreen assays are always performed in white opaque plates to produce
as strong a signal as possible. Assays may be performed in 96-, 384- or
1536-well formats.

AlphaScreen can be measured on the EnVision™ Multilabel Plate Reader

with AlphaScreen technology, the Fusion-Alpha™ Multilabel Reader, or the
AlphaQuest® HTS Microplate Analyzer.

The EnVision Multilabel Plate Reader with AlphaScreen technology is espe-

cially suitable for medium throughput screening as well as assay development,
measuring a 384-well plate in typically 5 minutes or even less, providing
1.5 times more throughput than the Fusion-Alpha. The Fusion-Alpha provides
performance as superior as the EnVision at a moderate throughput. AlphaQuest
HTS is a dedicated AlphaScreen reader with two laser diodes and four read
heads, designed for high throughput demands in the HTS environment.
1536-well plates can be read in typically 9 minutes or even less on an
AlphaQuest HTS.

All three instruments use the same principles for measuring AlphaScreen,
with optics designed to ensure smooth transfer from 96- to 1536-well formats.
Thus, moving from assay development to high throughput screening is quick
and easy, regardless of the detection platform used.

4
II. AlphaScreen – Assays and Applications
This section of the guide summarizes the types of AlphaScreen products
available and many applications they enable.

PerkinElmer’s objective is to offer products of the highest quality that

simplify experimental research, yet maintain superior performance.
To best meet the diverse needs of our customers, we have developed
four basic families of AlphaScreen products:

• Ready-to-use Assay Kits

• Generic Detection Kits

• Unconjugated

• Custom-labeled

Ready-to-use assay kits

G-protein coupled receptor (GPCR) and cell signaling studies are quite
prevalent in today’s research environment. To meet the needs of this current
trend, PerkinElmer has developed a series of ready-to-use detection kits.
These kits include:

• cAMP quantification

• IP3 quantification

• Tyrosine Kinase assays (PY20, P-Tyr-100, or PT66 detection antibody)

• TNFα

The robustness of AlphaScreen chemistry allows freedom in defining

experimental set up of assays, even when using one of these very specific
ready-to-use kits. For example, the cAMP kit may be used in studying
functional GPCR activation, in identifying the ligand of an orphan receptor,
in screening for an agonist of a Gαs- or Gαi-coupled receptor, in whole cell
and membrane preparation studies, and more. In addition, our kinase kits
have the versatility to study a number of different kinases. The combination
of a user-defined kinase substrate and the choice of three detection antibodies
against tyrosine kinases (see above) as well as the use of Protein A indirectly
capturing specific antibodies against phospho-serine and phospho-threonine,
opens the doors to study any kinase of interest.

Each ready to use kit contains all the necessary components to perform
a successful AlphaScreen assay. For example, the cAMP competitive assay
kit contains streptavidin-coated Donor beads, anti-cAMP antibody-coated
Acceptor beads, and biotinylated cAMP. Kit-specific suggested protocols
are supplied with each kit. While these protocols can be used as general
starting guides, we highly recommend assay optimization for your assay
samples. Please refer to pages 20–23 of this guide to learn more about
optimizing an assay. PerkinElmer prides itself on developing products that

w w w. p e r k i n e l m e r. c o m 5
 fulfill the most current application needs. Therefore, our product line of
ready-to-use kits is ever increasing. Please contact your local representative for
the most up-to-date list of detection kits. If one of these kit types, for any reason,
does not satisfy your requirements, there is the option of either designing an
assay scheme using our generic reagents or custom labeled beads.

Generic reagent detection kits

An even greater level of assay versatility is seen when working with
AlphaScreen generic detection kits. They can be divided into three general
categories: epitope-tag detection kits, chemical label detection kits and primary
antibody recognition kits. The above-mentioned detection kits are all supplied
with streptavidin-coated Donor beads, Acceptor beads coated with a specific
antibody and a positive control. Because the Donor beads are coated with
streptavidin, one assay component must be biotinylated. This is the only
requirement for use of this type of reagent system. Consequently, the flexibility
of the generic detection kits is tremendous.

Custom conjugation
If during assay design, a specific reagent (i.e. DNA, antibody, protein)
conjugated to either the Donor or Acceptor bead is required, two options
are available. The first option is to order unconjugated Acceptor beads and
perform the conjugation. Conjugation is a simple reductive amination reac-
tion that is easily performed. Please remember that the size of AlphaScreen
beads allows for centrifugation, which simplifies the conjugation procedure.
A protocol for bioconjugation of antibodies is provided upon purchase of
unconjugated beads. Should one decide to create their own Acceptor beads,
streptavidin-coated Donor beads are available for purchase. The second option
is to send the custom reagent to PerkinElmer’s custom services (for more
information please contact [email protected]) for Donor and/or
Acceptor bead conjugation. This service will be performed under a strict
confidentiality agreement. Both these options provide the user with yet
another avenue of freedom in designing an assay scheme.

The task of designing an assay scheme from scratch can seem daunting. We
believe an understanding of a few key pieces of information will greatly aid
you in designing your assay. First and foremost you need to understand types
or assay formats that are possible. Second, you need to establish what reagents
you have available at your disposal, not only from PerkinElmer, but also from
other commercial sources and from within your own facility.

Assay formats
There are two potential assay formats — direct and indirect. Choosing which
assay format to use is most often dictated by the assay-specific reagents that
are available. While the direct assay format allows for the greatest level of

6
control over stoichiometry of the binding partners, it can be difficult to
acquire the necessary amounts of reagents for Acceptor bead coupling. As a
result, indirect assay formats are often used with the generic detection kits.

Excitation
680 nm

Emission
520-620 nm
biotinylated-cAMP

Streptavidin-coated
Donor Beads
anti-cAMP conjugated
Acceptor Beads

Figure 3a: Direct Format

Direct Format:
In general, it involves a biotinylated component that binds to an antibody
directly coated onto the Acceptor beads or to a protein that is captured by
such an antibody. The direct format is advantageous because of its simple
design and the ease of control of the stoichiometry of the binding partners.
However, small quantities of a particular antibody, while potentially accept-
able when using the indirect assay formats, may limit the use of the direct
assay format. An example of a direct assay format is the competitive cAMP
detection kit (see Figure 3a). cAMP is labeled with biotin, the Donor beads
are streptavidin-coated and the Acceptor beads are coated with an anti-cAMP
antibody. Because the biotin-streptavidin interaction is very high affinity
(fM range), the proximity of the two beads in reality is determined by a
single binding event, cAMP and anti-cAMP antibody.

Emission
Excitation 520-620 nm
680 nm

anti-TNFR1 IgG

biotin-TNFα sTNFR1

Streptavidin-coated anti-TNFR1 IgG conjugated

Donor Beads Acceptor Beads

Figure 3b: Direct Format

w w w. p e r k i n e l m e r. c o m 7
 The second example illustrated is a receptor-ligand interaction such as TNFR1
and TNFα (see Figure 3b). The soluble TNFR type I (sTNFRI) used in this assay
is the 55 kDa truncated form of the receptor TNFR-60 type B. The AlphaScreen
signal is generated via two binding events, capture of sTNFRI by anti-sTNFRI
coated Acceptor beads and binding of biotinylated TNFα to sTNFR1.

Indirect Format:
In this format, the biotinylated component binds to a protein or antibody
that is not directly coated onto the Acceptor beads but is recognized by a
secondary antibody or Protein A. The beads must be within 200 nm for the
transfer of energy to occur. This is small enough to limit signal generated in
the absence of binding, while allowing freedom to use several generic
reagents in a single assay scheme. As in the example shown in Figure 4, the
biotinylated peptide substrate is bound by anti-phosphoserine antibodies
when phosphorylated by Akt. The anti-phosphoserine antibody is captured
by Protein A coated onto the Acceptor beads.

Emission
Excitation 520-620 nm
680 nm

anti (pS) GSK3

IgG

P
Protein A conjugated
n Acceptor Beads
biotin GSK3

Streptavidin-coated
Donor Beads

Figure 4: Indirect Format

Other common applications, using the direct or indirect format are listed
in Table 2, including assays such as protease assays, immunoassays,
protein-protein and protein-DNA interaction assays and others.

Available reagents
The generic reagents that our kits will recognize are as follows:

• Biotinylated component

• Chemical labels (FITC and digoxigenin)

• Epitope tags (HA, His, c-myc, GST, FLAG)

• Primary antibodies via capture by Protein A or anti-species antibodies

(rabbit and mouse)

As mentioned earlier, one component must be biotinylated. Because most

peptides or proteins, including antibodies, and DNA can be biotinylated,
this requirement does not limit the development of an assay.

8
Chemical labels, such as FITC and digoxigenin, can be conjugated to a variety
of biologicals. Epitope tag usage is confined to protein or peptide components.
Please note, as with other methodologies, epitope tags as well as chemical
labels may alter the biological parameters of the expressed fusion protein,
including the primary binding reaction of interest.

Table 1 lists available reagents that can be used for various applications.
The list is by no means inclusive. If you would like to use a primary antibody
in designing an assay scheme, but have not developed one in-house, bear in
mind that there are many commercial sources of antibodies. In many cases,
antibodies (both primary and anti-species) are available labeled with biotin
or FITC.

Table 1: AlphaScreen Reagents and Part Numbers

AlphaScreen Reagent Quantity Part No.

AlphaScreen Conjugation Kit 6760000K

• Streptavidin-coated Donor beads 2 mg
• Unconjugated Acceptor beads 2 mg

Biotinylated-GST 1.5 mL @ 500 nM 6760305M

Biotinylated-HIS 150 uL @ 5 uM 6760303M

cAMP-biotin Supplement* 10,000 pts 6760301M

50,000 pts 6760301R

1000 pts 6760625D

cAMP Assay Kit† 10,000 pts 6760625M
50,000 pts 6760625R

500 pts 6760611C

c-Myc Detection Kit† 10,000 pts 6760611M
50,000 pts 6760611R

500 pts 6760604C

DIG (Digoxin/Digoxygenin) Detection Kit† 10,000 pts 6760604M
50,000 pts 6760604R

500 pts 6760605C

FITC (Fluorescein) Detection Kit† 10,000 pts 6760605M
50,000 pts 6760605R

500 pts 6760613C

FLAG® (M2) Detection Kit† 10,000 pts 6760613M
50,000 pts 6760613R

500 pts 6760603C

GST (Glutathione-S-Transferase) Detection Kit† 10,000 pts 6760603M
50,000 pts 6760603R

500 pts 6760612C

HA (Hemagglutinin) Detection Kit† 10,000 pts 6760612M
50,000 pts 6760612R

(continued)

w w w. p e r k i n e l m e r. c o m 9
 AlphaScreen Reagent Quantity Part No.
500 pts 6760619C
HIS6 (6-Histidine-Nickel Chelate) Detection Kit 10,000 pts 6760619M
50,000 pts 6760619R

IP3 Assay Supplement** 500 pts 6760621C

10,000 pts 6760621M

500 pts 6760606C

Mouse IgG Detection Kit† 10,000 pts 6760606M
50,000 pts 6760606R

500 pts 6760602C

Phosphotyrosine (PT66) Assay Kit† 10,000 pts 6760602M
50,000 pts 6760602R

500 pts 6760620C

Phosphotyrosine (P-Tyr-100) Assay Kit† 10,000 pts 6760620M
50,000 pts 6760620R

500 pts 6760601C

Phosphotyrosine (PY20) Assay Kit† 10,000 pts 6760601M
50,000 pts 6760601R

Protein A Acceptor Beads 5 mg 6760137M

25 mg 6760137R

500 pts 6760617C

Protein A General IgG Detection Kit 10,000 pts 6760617M
50,000 pts 6760617R

500 pts 6760607C

Rabbit IgG Detection Kit† 10,000 pts 6760607M
50,000 pts 6760607R

1 mg 6760002S
Streptavidin-Coated Donor Beads 5 mg 6760002
50 mg 6760002B

500 pts 6760622C

TNFα Receptor Binding Kit† 10,000 pts 6760622M
50,000 pts 6760622R

1 mg 6762003
Unconjugated Acceptor Beads 5 mg 6762001
50 mg 6762002

1 mg 6762013
Unconjugated Donor Beads 5 mg 6762011
50 mg 6762012

All kits contain both strepdavidin-Donor beads and the respective Acceptor bead type.
† Acceptor beads are coated with antibody conjugate with specificity for detection of respective epitope.
* To perform a cAMP assay the AlphaScreen cAMP Assay Kit is also required.
** To perform an IP3 assay the AlphaScreen GST Detection Kit is also required.

10
 Table 2: What Types of Assays Can I Set Up and How?

Acceptor beads -
Assay Type Proposed set-up Alternative set-up

Receptor-Ligand
TNFα-sTNFR1 anti-TNFR1 IgG
(indirect)

biotin-TNFα sTNFR1
Protein A conjugated
Streptavidin-coated Acceptor Beads
Donor Beads

Functional assays
cAMP (direct) biotinylated-cAMP

Streptavidin-coated
Donor Beads
anti-cAMP conjugated
Acceptor Beads

IP3 (direct)

biotinylated
IP3 analog

anti-GST conjugated
Acceptor Beads

Streptavidin-coated GST-tagged
Donor Beads IP3 binding protein

Kinase Direct format

Acceptor:
EGFR (direct) • PY20, PT66 Ab

P-Tyr-100 conjugated
biotinylated Acceptor Beads
polyGT
Streptavidin-coated
Donor Beads

Akt (indirect) Indirect format

Indirect capture of Acceptor:
primary IgG using anti (pS)GSK3 IgG • Anti-species* to capture
Protein A primary Ab for detection
of P-serine or P-threonine
Protein A conjugated
biotinylated GSK3
Acceptor Beads • Protein A to capture pri-
mary Ab for detection of
Streptavidin-coated
Donor Beads P- serine or P- threonine

Protein-protein Indirect format

Acceptor:
p53/HDM2 (direct) GST-tagged
HDM2 • Anti-species*/label**
Please note that proteins
• Primary Ab
are expressed with tags
for ease of purification. biotinylated anti-GST conjugated • Protein A to capture
Acceptor Beads
p53 primary Ab
Streptavidin-coated
Donor Beads

w w w. p e r k i n e l m e r. c o m 11
 Acceptor beads -
Assay Type Proposed set-up Alternative set-up

Immunoassay biotinylated
TNFα detection anti-TNFα
(monoclonal)
TNFα
Sandwich format
(direct)
anti-TNFα (polyclonal) conjugated
Acceptor Beads
Streptavidin-coated
Donor Beads

TNFα detection Indirect format

Sandwich format Acceptor:
biotinylated
(indirect) anti-TNFα anti-TNFα • Anti-species*/label**
(monoclonal) TNFα (polyclonal)
Please note that you • Primary Ab
need to use either a bio-
tinylated goat or mouse
IgG1 anti-TNFα antibody Protein A conjugated
Streptavidin-coated
to avoid interference Donor Beads Acceptor Beads
with Protein A

Protease
Cathepsin D (direct) biotinylated and digoxigenin
labeled substrate
Cleavage of the specific
substrate by cathepsin EE
D results in a signal KP KK
IMF FRLL G
decrease anti-digoxin IgG conjugated
Streptavidin-coated Acceptor Beads
Donor Beads

ACE Indirect format using

(direct) ACE unlabeled peptide
biotin-DRVYIHPFHL biotin-DRVYIHPF
Angiotensin I Acceptor:
is cleaved to • Anti-species*/label**
Angiotensin II by • Primary Ab: anti-
the action of ACE. Angiotensin I/II IgG
biotinylated
(polyclonal)
Angiotensin II Donor:
DRVYIHPF • biotinylated anti-
anti-Angiotensin II Angiotensin II IgG
IgG (monoclonal) conjugated
Acceptor Beads (monoclonal)
Streptavidin-coated Note: use either a biotinylated
Donor Beads
goat or mouse IgG1 anti-Ang II
antibody to avoid interfer-
ence with Protein A

Protein-DNA
digoxigenin
Interaction ERE

ERE-ERα biotinylated
ERα
interaction (direct)
Biotinylated protein anti-digoxin IgG conjugated
Acceptor Beads
Streptavidin-coated
Donor Beads

12
 Acceptor beads -
Assay Type Proposed set-up Alternative set-up
Generic example Digoxigenin-DNA
duplex (3’ overhang)
Helicase (direct) Helicase

unwinding
Biotinylated capture annealing
oligo

Anti-tag IgG conjugated

Acceptor Beads

Streptavidin-coated
Donor Beads

* Anti-species = anti-mouse IgG and anti-rabbit IgG

** Label = anti-FITC, anti-digoxin/digoxigenin
*** Epitope-tag = anti-c-myc, anti-6-Histidine, anti-Glutathione-S-transferase,
anti-Hemagglutinin, anti-FLAG

The above options have been used in various combinations, both by customers
and PerkinElmer, to develop a wide range of assays including tyrosine and
serine/threonine kinase assays, protease assays, helicase assays, low and high
affinity protein-protein binding assays, cytokine quantification assays, SNP
detection, phage display assays, protein-DNA binding assays, antibody
detection, cell membrane and whole cell-based second messenger assays,
Gαs and Gαi cAMP regulation, nuclease activity, and DNA quantification.

III. How to work with AlphaScreen —

a general guide
Getting started
Environment and placement of instrument
Upon initial installation of the EnVision with AlphaScreen module, Fusion-
Alpha Multilabel Reader or AlphaQuest HTS instrument, choose an envi-
ronment that is least prone to dramatic temperature fluctuations. Avoid
placing the instrument directly under intense fluorescent lighting fixtures or
exposing it to direct sun light. If possible, choose a location with dim light-
ing (under 100 Lux) and/or apply green filters to light fixtures. Likewise, pro-
tect the pipetting station/liquid handling robot from direct white fluorescent
light. Please refer to section IV page 24 for environment considerations for
HTS applications. However, for lower throughput and assay development
needs, the day to day running of AlphaScreen experiments can be done in
any normal laboratory environment.

w w w. p e r k i n e l m e r. c o m 13
 Use and storage of reagents
AlphaScreen reagents are produced to the highest industry standards. The
reagents should be stored at 4°C unless specified otherwise and protected
from exposure to light (the plastic container in which the beads are supplied
is quite adequate for this purpose). The beads are designed to stay in suspen-
sion and come supplied with Proclin 300 (Preservative, Sigma-Aldrich) to
prevent microbial growth. To avoid any loss of materials, it is recommended
to centrifuge (pulse) the beads and resuspend them by pipetting before use.
Keep away from sources of heat. [N.B. The beads themselves, the dyes and
hydrogel coating are all very heat stable even up to temperatures of 95°C as
illustrated by using the beads for SNP typing with PCR (Beaudet et al.,
Genome Res. 2001; 11(4); 600-8). As may be expected, when using pro-
tein-coated AlphaScreen beads, the quality of the product may be compro-
mised by exposure to excessive heat due to bio-molecule denaturation.]

Experimental protocol
Most AlphaScreen assays are simple indeed. For example, many assay formats
permit simultaneous mix and read of all components. Others may require an
initial incubation, such as for an enzymatic reaction, followed by a detection
step prior to analysis. The protocol adopted is determined by the biochem-
istry of the interacting binding partners and the method that yields a suitable
signal window and background.

Assay design
Signal reduction or signal increase?
Careful consideration of assay design and format will significantly reduce
assay development time and minimize inherent inaccuracies in assay
performance. In choosing between a signal reduction or signal increase type
of assay, one must take into account the various parameters of the assay such
as lower limit of detection, range of sensitivity, detection instrument, source
and composition of assay components and samples as well as liquid handling
capability. A signal increase type assay offers benefits over a signal reduction
or competitive type assay. This type of assay is often less prone to yielding
false positive results as careful selection of assay components ensures
specificity. Another advantage of the signal increase type assay is that it is
often more sensitive. The sensitivity is influenced by choosing binding partners
or antibodies of different affinities for the target molecules. In the event that
a suitable tagged intermediary (ex.: biotinylated tracer) is not available for
use in a signal reduction type assay, the signal increase format may be a
viable option if antibodies are available to at least two epitopes on the target
molecule(s). There are an increasing number of modified antibodies available
on the market today that are pre-conjugated with AlphaScreen compatible
tags such as biotin or FITC.

14
On the other hand, a signal reduction assay is not subject to the ‘hooking
effect’, an effect common to many immunoassays relying on antibody
recognition and binding of target molecule. A signal increase assay may be
affected by this phenomenon as signal will increase with increasing target
molecule concentration up to a point, after which the target molecule will
become inhibitory to the production of signal. The reason is saturation of the
available binding sites on one or both of the AlphaScreen beads (see Figure 5).

The ‘Hooking Effect’

Variation of Signal with Target Molecule Concentration
in a Signal Production Type Assay

60000
AlphaScreen Counts

Streptavidin-Donor
Bead
45000
Biotinylated Target
30000 Molecule

Anti-Target Molecule
15000
Antibody Coated
Acceptor Bead
0
10 9 8 7 6 5 4 3 2 1
[Target Molecule] (log M)

Low target molecule conc. Optimal target molecule conc. Excess target molecule conc.
(some binding sites occupied) (optimal # binding sites occupied) (all binding sites occupied)
= = =
signal production maximum signal production reduced signal production
above background

Limited Optimal Bead association

bead association bead association inhibited

Figure 5: The Hooking Effect

w w w. p e r k i n e l m e r. c o m 15
Choosing the best combination of assay components
For many AlphaScreen assays there are various possible formats that can be
chosen. Careful consideration must be given to numerous parameters such
as the desired assay functionality, sensitivity range, specificity and nature
of the samples to be analyzed. Cost, ease of reagent production, reagent avail-
ability, affinities of interacting assay components, stability/lability of bind-
ing partners will all influence the performance of the assay. In addition, the
versatile nature of the AlphaScreen technology often permits the choice of
various AlphaScreen reagents for a given assay. For example, the signal
increase assay for detection of IgG concentrations may be run in two formats
using either Protein A Acceptor beads (A) or anti-species IgG Acceptor
beads (B) (see Figure 6).

Excitation
No Signal Excitation Signal
680 nm Emission
680 nm
520-620 nm

biotin-anti hlgG biotin-anti hlgG

Fab specific Fab specific
Protein A conjugated Streptavidin-coated Protein A conjugated
Streptavidin-coated Acceptor Beads Donor Beads Acceptor Beads
Donor Beads

A. Generic IgG Detection using Protein A

Excitation
No Signal Signal
Excitation
680 nm 680 nm
Emission
520-620 nm

biotin-anti hIgG biotin-anti hlgG

Fab specific Fab specific
Streptavidin Polyclonal anti-species IgG Streptavidin Polyclonal anti-species IgG
Donor bead conjugated Acceptor Beads Donor Bead conjugated Acceptor Beads

B. Specific Detection using Anti-IgG Antibodies

Figure 6: IgG Detection

16
Kinase assays are an increasingly important area of focus for the fields of drug
discovery, therapeutics and R&D. There are a plethora of different formats one
can consider for running tyrosine, serine and threonine kinase assays using
AlphaScreen. There are three separate choices of detection kit for phospho-
tyrosine assays (see Table 1; page 9). If these reagents do not provide a
suitable solution, one could construct a novel tyrosine kinase assay using
a separate anti-phosphotyrosine antibody of choice, which can be captured
by using Protein A beads or anti-IgG species beads. A kinase assay may be
performed using one of several different substrates depending upon the assay
screen requirements and/or the specificity and activity of the enzyme. For
example, one can use an artificial biotinylated substrate such as biotin-poly-
(Glu,Tyr) or biotin-poly-(Glu,Ala,Tyr). These generic substrates are often more
efficiently phosphorylated than a specific biological substrate in vivo. A
synthetic biotinylated peptide derived from an endogenous protein sequence
may also be chosen, lending a higher degree of specificity to the assay. It may
even be necessary to use a full-length protein as substrate. There are essen-
tially two approaches to add biotin to a full-length protein, either by chemical
reaction (such as biotinylation using NHS-biotin), or by engineering a
recombinant form of the protein encoding a biotinylation sequence that may
be labeled in vivo or in vitro (ex.: the Biotin Avi Tag system from Avidity,
LLC). The latter choice offers a more specific labeling of the binding partner
and may ultimately give a better signal in the assay.

Ultimately, the best choice of reagents for constructing an assay is the one
that is the most practical to use.

Biology and chemistry considerations

It is not always feasible to directly measure or quantitate the primary mole-
cule of interest or interactions with such molecules. Take the example of a cell
surface receptor with a very low abundance. Measuring ligand interaction with
a low abundance receptor is extremely difficult even when using high levels
of high-energy 125I radiolabeled ligand. A suitable compromise may be
attained if a specific downstream product of a receptor-ligand interaction
is measured. Look for relatively high levels of a target molecule that can easily
be measured in a specific manner. Examples of such are PerkinElmer’s cAMP
and IP3 detection assays, both methods being used for quantitation of second
messenger production arising from GPCR stimulation in whole cells.

In addition, ensuring conditions that maintain stability of assay components

is crucial for successful assay design. One must choose buffer conditions that
are compatible with maintaining the integrity of the specific interaction of
interest (see buffer choice section on page 22). For many proteins and other
biological molecules, optimal integrity, conformation and biological activity
is dependent on various factors such as pH, ionic concentration or presence
of co-factor.

w w w. p e r k i n e l m e r. c o m 17
 Plate choice
White opaque plastic plates are required for reading AlphaScreen. Black
plates will absorb light and lead to greatly reduced signals. Table 3 lists
recommended plate types for use with AlphaScreen.

Table 3: Plate Choice

Plate Type Supplier Maximum Working Cat. No.

Volume Capacity
1536-well OptiPlate™ PerkinElmer 10 µL 6005228

384-well OptiPlate PerkinElmer 80 µL 6007290

™
384-well CulturPlate PerkinElmer 80 µL 6007680
™
384-well ProxiPlate PerkinElmer 20 µL 6006280

96-well OptiPlate PerkinElmer 350 µL 6005290

96-well CulturPlate PerkinElmer 350 µL 6005680

96-well ProxiPlate PerkinElmer 100 µL 6006290

Initial experiments
Determining optimal reagent concentrations
Choose a suitable buffer system and titrate each binding partner to ascertain
the optimal concentration. It may also be necessary to vary the order of ad-
dition of the components to permit the most efficient interactions. For initial
experiments it is recommended that a final bead concentration of 20 µg/mL
be adhered to with respect to both Donor and Acceptor beads. Subsequent
‘stretching’ of the beads may be assessed once it is known that a sufficiently
high signal/background can be achieved. Typically, most AlphaScreen assays
will utilize a final biotinylated binding partner concentration in the nanomolar
range (ex.: 0.5 nM – 30 nM with 20 µg/mL of beads). Concentration ranges
for each binding partner that interact directly with the capture molecule on
the AlphaScreen beads are usually between the low nanomolar range up
to mid-micromolar range (ex.: 0.1 nM–300 nM) depending on the affinity of
the binding partners and the efficiency of labeling and/or stoichiometry of
the capture tag/epitope (again working with 20 µg/mL of beads). An example
of an optimization experiment for a tyrosine kinase assay, using
AlphaScreen PY20 anti-phosphotyrosine Acceptor beads, is depicted in
Figure 7. In this instance only the enzyme concentration and biotinylated
substrate components are optimized. Metal co-factor and ATP concentrations
are also critical for optimization of kinase assays. Typically one would
choose the lowest concentration of reagent that gives a good signal/back-
ground. For example, from the data below, as little as 0.5 nM final biotin-
poly-GT and as little as 0.01 U/well c-Src enzyme were sufficient to achieve
a robust signal with an S/B ratio of 143. This kinase assay is a signal increase
type assay, and as such, sensitivity is governed by the number of interactions

18
 that occur between the beads due to phosphotyrosine capture by the anti-
phosphotyrosine Acceptor beads and the biotin-substrate capture by the
streptavidin Donor beads. In general, a signal increase assay benefits from
having a high number of higher affinity interactions between the Acceptor
and Donor beads. On the other hand, the sensitivity of a signal reduction
type assay may benefit from having fewer interactions of lower affinity
occurring between the beads.

200000
AlphaScreen Signal

Enzyme Conc
150000
1 U/well
0.3 U/well
100000 0.1 U/well
0.03 U/well
50000 0.01 U/well
0
0
50.0 10.0 5.0 1.0 0.5 0.0
[Biotin-pGT] (nM)

Figure 7: Optimization of c-Src Tyrosine Kinase Enzyme

and Biotin-Poly-(Glu, Tyr) Substrate Concentrations

Generating data
Assay development times for AlphaScreen assays are typically very short due
to the rapid speed with which one can generate data. It is not uncommon to
have the basic format and preliminary conditions for a new assay determined
within a day or two using AlphaScreen. In part this is possible due to the
very high signal/background ratios which are typical for many AlphaScreen
assays, and hence the wide range of suitable conditions with which to gen-
erate a signal. In addition, most assays may be prepared and ready to read
within 3 hours. For example, a cAMP detection assay involves the following
steps; (i) aliquot drug or receptor ligand, (ii) add cells plus Acceptor beads
in stimulation buffer, (iii) incubate for 10–30 minutes (depending upon opti-
mal stimulation time required), (iv) add Donor beads plus biotin-cAMP in
lysis buffer, (v) incubate for 1 hour and read plate. This may all be achieved
within 2 hours from start to finish.

Following initial reagent component optimization and buffer selection, EC50

values for effectors and IC50 values for inhibitors of molecular interactions
can be determined very easily.

Data output from the EnVision with AlphaScreen module, AlphaQuest HTS or
Fusion-Alpha Multilabel Reader can be generated in various formats which are
easily transferred to data analysis programs such as Excel® or GraphPad Prism®.

w w w. p e r k i n e l m e r. c o m 19
 Interpreting data
Analysis and interpretation of data should be done with the analysis
program of choice such as the examples given in the previous section.

AlphaScreen assays are typified by having very low variability between

replicate sample wells. It is often enough to run assays in duplicate.
Indeed AlphaScreen technology is ideal for screening samples in singlicate,
as required by today’s ever cost-conscious HTS departments. Most
AlphaScreen applications will yield S/B and S/N ratios that exceed other
assay technologies. A telling attribute of AlphaScreen assays are the
extremely high Z’ factor values that are typical of the technology (Zhang
et al., 1999, J. Biomol. Screen., 4, 67-73). The Z’ factor is a dimensionless
parameter that allows for comparison and evaluation of the performance
of different assay technologies that use different reagents, formats and
instruments. The Z’ factor takes into account the standard deviations of
two count populations, and hence gives a more useful estimate of assay
signal window than do either S/B or S/N alone. Z’ factor values for many
AlphaScreen assays may be as high as 0.8 – 0.9, where a value in excess
of 0.5 indicates that an assay is suitable for screening in singlicate.

Optimizing your assay

Assay format
Assay format is an important consideration and can greatly impact the
performance of the assay, the throughput and the cost per well. The
number of additions, the time taken to aliquot the reagents, the capacity
and speed of the automated liquid handling robot (if the assay is ultimately
intended for HTS) should all be taken into account in choosing the optimal
assay format. Assay development procedures are frequently run using
96-well microplate formats, often with the use of a multi-channel pipette.
This does not preclude the use of 384-well formats for assay development.
Indeed, there are several good reasons for using 384-well instead of 96-
well plates. The observed AlphaScreen signal will be influenced by the
following:

• Some plates, such as ProxiPlate (PerkinElmer) or 1536-well plates are

designed to place the sample closer to the AlphaScreen plate reader
detector and therefore will give an increased signal.

• Excitation and signal measurement are both accomplished from the

top of the plate within the plate reader. The measured signal is in part
dependent upon reflected light, therefore the reflective properties of
the plate influence signal. Higher density plates possess narrower
wells that more efficiently reflect the emitted light back to the PMT
(PhotoMultiplier Tube).

20
• The width of the excitation laser beam is 1 mm, the same for all plate
densities. Therefore there is an ‘effective’ reaction volume, the one hit by
the laser light directly, and a total well volume. Higher density
microplates allow for a higher proportion of the total well volume to be
illuminated with the laser beam (most of the reagents get excited), hence
greater signal generation proportionately.

• Due to the reasons given above, signals are commonly greater in higher
density microplates.

• AlphaScreen is highly amenable to miniaturization. Unlike some assay

technologies, reagent concentration does not have to be re-optimized when
transitioning to higher plate densities and lower assay volumes. Hence
there are significant cost savings attained by using higher density plates.

AlphaScreen is intended to be used as an homogeneous assay and does not

require wash steps. However, this does not preclude the user from running
a non-homogeneous formatted AlphaScreen assay (ex.: run an enzymatic
assay at a high substrate concentration due to Km restraints, followed by
diluting a small aliquot of the reaction mixture into an AlphaScreen reaction
well). This may be necessary if the sensitivity of the assay far exceeds the
range in which the biological reaction must be run.

Order of addition
Order of addition can influence the signal generated to a large extent. The
optimal order in which assay components interact should always be deter-
mined empirically. It must be borne in mind that some binding partners may
abrogate the association of other binding partners if allowed to interact in
the wrong order. This might be especially true in the example of an immuno-
sandwich type assay using two different antibodies recognizing separate
epitopes on a relatively small molecule. Steric hindrance by one antibody
may prevent the other antibody from binding. In general, one nearly always
gives the advantage to an antibody-antigen interaction over the biotin-strepta-
vidin association. One notable exception to this rule is in the case of the
cAMP assay. The principle of this assay is a signal reduction, competitive
assay type where endogeneous cAMP produced in whole cells competes
with biotinylated cAMP for binding to an anti-cAMP antibody conjugated to
the Acceptor beads. Biotinylated cAMP is a relatively small molecule and if
exposed to the antibody before being bound to the streptavidin Donor bead,
a noticeable reduction in signal will be observed due to a proportion of the
biotin molecules being ‘smothered’ by the antibody. In addition, biotinylated
cAMP is pre-bound to the streptavidin-Donor beads as free streptavidin can
interact with components of lysed cells to reduce the AlphaScreen signal.
Furthermore, free biotin present in cell culture media or bacterial culture can
also lead to reduction of the AlphaScreen signal. In this case, pre-incubation
of biotinylated substrate with Donor beads prior to adding medium or bacterial
culture will strongly improve signal quenching.

w w w. p e r k i n e l m e r. c o m 21
 Reagent choice
Reagent choice is critical. Where possible, using purified binding partners
is always preferable. Affinity purified polyclonal (pre-adsorbed if necessary)
and/or monoclonal antibodies should be considered first. Importantly, the
method of assay component capture to the AlphaScreen beads has to be
selected with the molecules of interest in mind. One should choose a suitable
method of assay component capture, compatible with the nature of the assay
and the required dynamic range of the assay. For example, an especially high
affinity antibody should not be chosen for a signal reduction type assay if
the highest degree of sensitivity is required. The target molecule IgG would
have to be present at a relatively high concentration in order to displace
biotinylated IgG, hence lowering sensitivity for target molecule detection.

Buffer choice
Buffer choice can be very important. Choose pH, buffering capacity and
salt concentration that will facilitate the desired interactions between the
components of your assay. If metal co-factors are needed for correct conforma-
tional integrity or enzymatic activity, it is best to titrate these components
appropriately. In the case of excessive non-specific binding being observed,
a variety of different detergents may be used such as Tween 20 (ex.: 0.01–0.1%),
Triton-100 (ex.: 0.01–0.1%), CHAPS (0.1% or less). For most AlphaScreen
applications, a BSA concentration of 0.1% (w/v) is sufficient to minimize
non-specific interactions. Some assays may require slightly higher concen-
trations of BSA or even the use of an alternate ‘blocking’ reagent such as low
molecular weight dextran or gelatin. Try to avoid azide as a preservative
as this is a potent scavenger of singlet oxygen and will inhibit the
AlphaScreen signal. Proclin 300 (Sigma-Aldrich) is recommended as a
preservative and anti-microbial agent.
AlphaScreen Signal

400000
Buffer A
300000 Buffer B
S/B = 483 Buffer C

200000

100000

0
50.0 10.00 5.00 1.00 0.50 0.10 0.00
[Biotin-mlgG] (nM)

Figure 8: Optimization of Buffer Conditions and Mouse-IgG Biotin-Tracer.

Note: It is recommended to work with buffers with pH within physiological range for optimum
AlphaScreen signal.

22
For the buffer optimization of a human IgG detection assay shown below in
Figure 8, it is clear that different buffer components can influence the optimal
binding partner concentration. Buffer C yields the highest signal and also
permits the use of a lower concentration of biotin-mouse-IgG compared to
buffer A. Buffer conditions will certainly affect S/B but can also significantly
influence the sensitivity and dynamic range of an assay.

Salts, detergents and ions

(Transition metals such as Al2+, Fe2+, Fe3+, Cu2+, Ni2+ and Zn2+)
The use of different salts and detergents in assay buffer systems can affect
the specific biological interactions of interest and the performance of the assay
significantly. If a low maximum signal window or high background is
apparent, consider trying an alternative buffer, type of salt, salt concentration,
a reducing reagent or detergent.

We strongly recommend avoiding the use of the following transition metal ions:
Al2+, Fe2+, Fe3+, Cu2+, Ni2+ and Zn2+. These metals have been shown to be potent
singlet oxygen quenchers in the mM and sub-mM ranges (100 µM for Fe2+).

Cell culture media and sera

The culture medium RPMI 1640 does not interfere with the AlphaScreen
system when used at 1%. However, the presence of 10% culture medium
leads to a signal quenching of about 30%. Biotin in the medium is most
probably the main culprit for quenching. This problem can be solved by
pre-incubating the biotinylated binding partner with the streptavidin coated
Donor beads. We have also tested MEM and DMEM and obtained comparable
results to the data presented for RPMI 1640.

Similarly, fetal calf serum reduces total signal by about 25% when used up
to a concetration of 10%, presumably because of its iron content. Rinsing cells
grown in serum with an appropriate buffer such as PBS is recommended.

Liquid handling and dispensing

Use of either a single or multi-channel electronic hand held pipette is
recommended for dispensing of reagents for R&D and assay development.
Low retention, fine point pipette tips permit greater pipetting precision.
See page 24 for recommendations on use of automated liquid handling
instruments.

Miniaturization and reagent concentration

AlphaScreen is highly amenable to miniaturization. Unlike most other assay
technologies, reagent concentration does not have to be re-optimized when
transitioning to higher plate densities and lower assay volumes. Hence there
are significant cost savings attained by using higher density plates.

w w w. p e r k i n e l m e r. c o m 23
IV.Taking AlphaScreen from assay
development to high throughput
screening
Initial experiments
Wet runs of liquid handling instrument
It is recommended to perform ‘wet runs’ using the AlphaScreen assay buffers
(without AlphaScreen beads), and the intended choice of tips and plates, as
well as the automated robotic dispensing program. This will help determine
potential errors that may arise during the liquid handling steps. Inappropriate
dispense height, reagent reservoir, plate and tip choice can impact the
AlphaScreen signal significantly. This experiment may be performed for
2–3 plates using an inexpensive fluorescent dye to monitor the CVs
incurred during liquid dispensing.

Assay equilibrium time course

Most AlphaScreen assays involve the use of various biological binding
partners and/or antibodies. Each system has an intrinsic time that will be
needed for the bead association reaction to come to equilibrium. Therefore,
it is recommended to run a time-course experiment with separate wells for
each time-point to determine the length of time taken for the AlphaScreen
reaction to reach equilibrium (Figure 9). (This of course will be temperature
dependent, with cooler temperatures requiring longer to reach equilibrium.)
When running multiple plates, ensure that all plates are incubated for the
minimum time period determined, so that all plates are equivalent.

90000 6 hr
AlphaScreen Signal

75000
2 hr
60000

45000

30000 Assay # 1
Assay # 2
15000

0
0 2 4 6 8 10 12

Incubation Time (hr)

Figure 9: Experiment to Determine Incubation Time Required

to Reach Assay Equilibrium
Note: In order to detect a suitable level of signal, we recommend incubating the cAMP assay at least
one hour after the last reagent addition. It is worth mentioning that maximal counts are typically
obtained after 14–16 hours incubation at room temperature, which corresponds to the time needed
for this assay to reach equilibrium. As equilibrium is reached, the local concentration of biotin-
cAMP between the donor and acceptor beads will increase, resulting in a standard curve (competition
with unlabeled cAMP) with a higher IC50 (ex.: IC50 shift from 5 to 15 nm). To avoid this phenomenon
when prolonged incubation times are used, we recommend using a lower concentration of biotin-
cAMP (ex.: 2 nM instead of 10 nM).

24
Choosing an optimal experimental environment
Lighting considerations
The absolute ideal environment for all light sensitive chemistries such as
AlphaScreen, is to run the assay under subdued light conditions (under 100
Lux). However, given the varied nature of HTS laboratories, and often times
the necessity to run multiple assay types simultaneously in the same envi-
ronment, this is usually not practical. If possible, consider outfitting an
enclosed room with green filtered lighting, place both the liquid handling
robot and AlphaScreen plate reader within and also aliquot AlphaScreen
beads within this room (Figure 10 — Recommended filter: Roscolux Chroma
Green #389 from Rosco; fluorescent tube sleeves, Cat. #: 4812-389; or filter
roll, Cat. #: R389. Rosco Labs: www.rosco.com).

The use of green filters has been shown to be almost as effective as running
the assay in the dark (Figure 11). In the event that an enclosed environment
is not available, consider covering light fixtures with green filters in the
immediate vicinity of the liquid dispenser and plate reader. It is most
important to control the area around the liquid handling robot. Some LH
stations are fitted with plastic casing which may be in turn covered with
green filter roll to permit dispensing of reagents in normal laboratory lighting.
Alternatively a black cloth may be used to cover the liquid handling robot
and AlphaScreen reader plate stacker.

If incubating stacks of plates for extended periods, which may be exposed

to ambient laboratory lighting conditions, consider covering plates with
either aluminum foil or a black cloth, or even a cardboard box.

#389 Chroma Green

TRANS. = 40%
420 500 580 660

90
80
70
% Transmission

60
50
40
30
20
10
0
380 460 500 580 660 700
Wavelength N.M.

Figure 10: Light Transmittance Spectrum for Rosco Filter

w w w. p e r k i n e l m e r. c o m 25
 % Initial AlphaScreen Signal
100

75

50

25

0
0 10 20 30 40 50 60
time (minutes)

700 lux
700 lux + green filter

Figure 11: Light Exposure Time Course

Light exposure time course to determine time window for bead dispensing. The time course experi-
ment was done in the immediate vicinity of the liquid handling robot being used to dispense the
AlphaScreen beads. This experiment helps to determine if it is necessary to implement further
precautions to lower the level of incident light during the time taken to dispense the beads.

Temperature
Chemiluminescent reactions such as those involved during the AlphaScreen
signal generation are temperature dependent. Typically, the AlphaScreen
signal variation is 8% per °C. Temperature fluctuations prevailing in the
room where the AlphaScreen plate reader is located will thus affect the
AlphaScreen signal intensity. For example, an assay normally read at 23°C
will produce 16% more signal if the ambient temperature increases to 25°C.
Conversely, if the temperature drops to 20°C, the same assay will yield 24%
less signal.

It is also important that the temperature of the reagents and plate are in
equilibrium with the ambient temperature around the plate reader to ensure
accurate measurement of the AlphaScreen signal. Failure to allow the plate
to attain ambient instrument temperature may lead to gradients of counts
across the plate as it warms up or cools down while being read. Each
AlphaScreen plate reader is equipped with a Peltier cooling device that cor-
rects the plate holder and plate to ambient instrument temperature. Given
that a typical 384-well plastic plate filled with reagents (and only 3 – 4°C dif-
ferent from ambient) may take from 15–30 minutes to equilibrate to the instru-
ment, it is important that equilibrium has been attained before the plate is
entered into the reader. This can be achieved easily by incubating the plate
or plates either next to the instrument or in the plate reader stacker, if fitted.

Finally it is worth mentioning that the dark noise of the PMT (photomultiplier
tube) used to read the AlphaScreen signal is sensitive to high temperatures.
High background counts in the order of 5,000–10,000 cps can be observed
if the PerkinElmer AlphaScreen reader is located in rooms where the
temperature is reaching 30°C.

26
Other recommendations
• Every HTS environment can be different with respect to available instru-
mentation and robotics, temperature control and lighting fixtures, and
preferred or required assay format. For example, an integrated robotic
platform with liquid handling stations and inline plate readers may be
obligatory for all assay types. Obviously it may be more difficult to control
the ambient lighting in this case as the sample plates are run in a conveyor
belt fashion and are usually not stacked as per a batch analysis mode.
The degree to which the environment has to be controlled with respect to
lighting and temperature homeostasis should be determined empirically
and will depend upon the specific circumstances.

• In order to ensure that all plates yield consistent and equivalent results,
it is important to ensure all plates are treated equally.

• If running in batch mode, following dispensing of reagents to a fresh

batch of plates, transfer in batches of 40 plates to Packard plate stacker
with a black plate covering the uppermost white plate containing samples.

• In order to maintain the lowest dead volume and wastage of AlphaScreen

reagents, consider the use of a low dead volume reagent reservoir for auto-
mated liquid dispensing.

Miniaturization
Development of new assays and optimization of existing assays using
AlphaScreen is characterized by having markedly short timeframes to
completion, with concomitant man hour and cost savings. In addition to
AlphaScreen being highly suited for a multitude of R&D applications and
lower throughput assays, the technology has been designed specifically
with HTS in mind. Following initial assay optimization at a particular final
reaction volume, assay volumes are easily miniaturized without the need
for re-optimization or increased reagent concentrations. One can simply
reduce all volume additions proportionately without loss in sensitivity or
assay performance. Indeed, higher signal and S/B ratios are often achieved
with higher density microplates. Using low volume assay formats in 384-well
(shallow well/ProxiPlate) or 1536-well plates can yield significant savings
in cost per well and help preserve precious and scarce reagents. It is recom-
mended to use a plate seal cover to prevent evaporation of samples and
subsequent signal inconsistencies. PerkinElmer TopSeal™-A (PerkinElmer
Cat. #: 6005185) is ideal for this purpose and does not interfere with the
AlphaScreen signal permitting the plate to be read without first removing
the plate seal.

Compared to radioisotopic assays and many fluorescence-based assays,

AlphaScreen has a distinct advantage in displaying lower cross-talk between
adjacent wells in higher density microplates. This ensures improved efficiency
for detection of positive hits in the screening process at uHTS capacities.

w w w. p e r k i n e l m e r. c o m 27
 Compound interference
As with other screening technologies, some compounds from HTS libraries
may interfere with the AlphaScreen signal. The main mechanisms of
compound interference on the AlphaScreen signal are 1) by singlet oxygen
quenching, 2) by competition against the interaction between biotin and
streptavidin, and 3) by acting as an inner filter. Strong singlet oxygen
quenchers are transition metals (Al2+, Fe2+, Fe3+, Cu2+, Ni2+ and Zn2+) when
used in the µM range, anti-oxydants such as azide and ascorbate, com-
pounds with structures based on thiophene (100 µM – 10 mM), and heme-
containing transition metals (ex.: hemoglobin). Competitors against the interac-
tion between biotin and streptavidin are biotin-like structures, while inner
filters are compounds that will absorb light at 520–620 nm (emission)
and/or at 680 +/- 5 nm (excitation). Thus, blue/green compounds will act
as inner filters. Other mechanisms of compound interference on the
AlphaScreen signal are by compounds that act as Donor or Acceptor analogs.
Donor analogs are structures capable of generating singlet oxygen and stimu-
lating Acceptor beads in the absence of Donor beads. These are usually
aromatic structures such as porphyrins (ex.: phthalocyanine). Acceptor
analogs are compounds capable of absorbing singlet oxygen and emitting
light between 520–620 nm. These are usually aromatic heterocyclic com-
pounds (ex.: nodulisporic acid derivatives) and may be present in soluble
natural extracts as well. Donor and acceptor analogs were shown to have a
limited activity relative to Donor and Acceptor beads, respectively (less than
1% for donor analogs and up to 10% for acceptor analogs) and hence, these
are uncommon. As well, structures based on imidazole were shown to
interfere with the AlphaScreen 6-histidine-nickel chelate kits.

The most recommended tool used for trouble-shooting high hit rates with
AlphaScreen is the positive control that comes with the kit used in the assay
or one’s own positive control that is more related to the assay. This control
can be used to assess compound interference from an HTS library on all assay
components except targets. Other HTS tools used for characterizing the mech-
anism of compound interference are biotinylated-Acceptor beads, as well as
unibeads (all available as custom made products: for more information please
contact [email protected]). Pre-incubation of compounds with
the streptavidin-Donor beads followed by addition of the biotinylated-
Acceptor beads will determine whether a compound acts as a competitor of
the interaction between biotin and streptavidin. On the other hand, addition
of compounds to pre-bound biotinylated-Acceptor and streptavidin-Donor
beads will determine whether a compound acts as a singlet oxygen
quencher. Unibeads contain all the chemicals normally embedded in both
the Donor and Acceptor beads so that all of the chemical processes occur
within this single bead. The unibeads are thus used to determine whether a
compound acts as an inner filter. Such controls are necessary for screens gen-
erating high hit rates in order to prove whether these hits are false positives
or not. The data generated with these compounds on the assay and on the
control can then be correlated in order to define real positives.

28
V. Troubleshooting guide
Problem Cause Effect/Remedy
No signal Reagent Donor beads have been exposed to light/photobleached.
Use another lot of beads.
No biotinylated binding partner. Check the extent of
biotinylation of binding partners by ex. HABA test
(Pierce) or by competition with the AlphaScreen kit
positive control (this AlphaScreen test can only be
performed if the biotinylated binding partner is not
recognized by the acceptor beads).
Binding partners do not interact. Check for potential
steric hindrance. Re-optimize the assay by changing
the order of addition.
Buffer Inhibitor or quenching component in buffer. Avoid use of
components that quench singlet O2 ex.: azide, transition
metals (Al2+, Fe2+, Fe3+, Cu2+, Ni2+ and Zn2+); avoid use of com-
ponents that absorb light strongly in the 520-680 nm range.
Instrument/Plates Incompatible microplate choice, ex.: use of black
plates. Use standard solid opaque white microplates ex.:
PerkinElmer, Costar, Greiner or Nunc.
Plate reader error or failure. Consult instrument manual
or call PerkinElmer Service. When setting up the
instrument please ensure that the AlphaScreen mode
is selected.
Lower signal Reagent Concentration of Acceptor or Donor beads is too low.
than expected Initially use the recommended bead concentration of
20 µg/mL.
Wrong concentration of biotin-binding partners or
Acceptor bead-captured binding partners. Titrate binding
partners to determine optimal concentration.
Degradation of bead conjugates due to incorrect or
prolonged storage. Beads should be stored at 4ºC
in the dark.
Assay Non-optimal order of addition of binding partners or
AlphaScreen beads.
Inappropriate assay buffer composition. Check for
correct pH, buffering capacity and salt concentrations,
as well as for requirements for reducing reagents,
detergents, chelators, metal-cofactors, blocking
reagents or enzyme inhibitors.
Incubation time too short ex.: enzyme reaction time,
cell stimulation time, or pre-incubation time of binding
partners.
Instrument/Plates Incompatible microplate choice, ex.: use of black, clear
bottom plates or plates made of polypropylene. Use
standard solid opaque white microplates ex.:
PerkinElmer, Costar, Greiner or Nunc.
Plate reader error or failure. Consult instrument manual
or call PerkinElmer Service. When setting up the
instrument please ensure that the AlphaScreen mode
is selected.

w w w. p e r k i n e l m e r. c o m 29
Problem Cause Effect/Remedy
Lower signal than Temperature Abnormally low temperature prevaling in the room
expected (con’t) where the reader is located will result in decreased
signal (see page 26).
Signal Plates Warped or distorted plates. Avoid storage of microplates
inconsistency under heavy objects or next to sources of heat.

Uneven plate molding or tissue culture treatment.

Light penetrating edges of plate. Ensure use of black

cover plate during bead incubation; incubate plate in
darkened environment such as inside a drawer or cover
plate entirely with foil or material impenetrable to light.

Poorly fitted plate seal; especially on shallow well

384- or 1536-well plate types.

Assay Differential evaporation from wells around plate

edges. Use a plate seal cover to minimize evaporation
of sample; avoid incubation of plates at elevated
temperatures.

Degradation of buffer components, especially BSA

blocking reagent. Prepare fresh buffer; store buffer
without BSA at 4°C and use within 3–4 days. Ensure
that you add BSA powder, 0.1% (w/v) usually sufficient.

High background Assay Non-specific interaction between assay components.

signal Use blocking agents, BSA at higher concentration (>
0.1% w/v) or detergent such as Tween-20 (up to 3%).

Plate Inappropriate dark adaptation. Incubate plates with

black top cover plate; incubate inside drawer or covered
from exposure to light ex.: use foil.

Use of white top plate cover. Use black top cover plate.

Detection Unsuitable laboratory lighting conditions; avoid use of

‘simulated daylight’ type fluorescent tubes. Use alter-
native location or cover light source with green filter.

Accidental exposure of beads to light just prior to

reading; Acceptor beads will auto-fluoresce for 2–3
min. Re-dark adapt for at least 5 min prior to reading
of plate.

Air bubbles trapped in some wells. Using electronic multi-

pipettes or automated liquid handling dispensers, ensure
sufficient dead volume in tips to minimize bubbling.

Temperature Abnormally high temperature prevailing in the room

where the reader is located will lead to higher background
(see page 26).

30
Problem Cause Effect/Remedy
High degree of Assay Differences due to transfer from assay development to
signal variability HTS lab. Often there are different operators from assay
development to HTS; ensure operators are trained
adequately; refer to HTS recommendations on page
24; consult PerkinElmer applications specialists.

Differential liquid evaporation from wells. Use a plate

seal such as a PerkinElmer TopSeal-A.

Mixing problems. For 96-well plates, use a shaker during

incubations; for higher density plates, try to add aliquots
of no lower than 5 µL or ensure liquid expulsion speed
from tip is sufficient to promote adequate mixing.

Day to day Inappropriate standard operating procedures. Ensure

variability experimental procedure is the same from day to day;
prepare the beads in the same area, ensure incubation
times are constant and temperature does not fluctuate
greatly — if the latter is a problem, consider using an
incubator to control ambient temperature.

Instrumentation Pipetting or dispensing errors. Ensure all manual and

automated pipettes, and liquid handling systems are
calibrated accurately; use suitable tips, optimize dispense
height and programming of automated dispensers.

Temperature difference between the plate and the detector

chamber within the plate reader; on the 4-detector
AlphaQuest, this will manifest itself as 4 separate apparent
signal gradients for the four quadrants or the plate.
Incubate the plate next to the instrument or in the plate
stacker if fitted; check for correct operation of instrument
plate cooling device—consult PerkinElmer Service.

Unexpected Instrument/Plates Uneven microplates.

gradient of signal Plate is kept at a too low temperature prior to reading.
across entire plate Chemistry designed to give best results at room tem-
perature (ex.: 20–25°C); do not chill plates or incubate
on ice before reading.

Temperature of plate not equilibrated to instrument

ambient temperature. Incubate plate for at least
30 minutes next to instrument or in plate stacker if fitted;
a larger number of stacked plates may require longer to
reach instrument ambient temperature.

Robotic liquid Inconsistent placing of aliquots in wells, clogged liquid

dispensing head dispenser; uneven placing of plate on dispenser
platform; incorrect tip choice; automated dispenser
program error/inaccuracy.

w w w. p e r k i n e l m e r. c o m 31
VI.Literature by application
Please visit www.perkinelmer.com/alphascreen to download
available PDFs

AlphaScreen general
Articles
• Bossé R., Illy C., Elands J. and Chelsky D. Miniaturizing screening: how
low can we go today? Drug Discovery Today. 2000 Jun: 1(1): 42-7.

• Seethala R. and Prabhavathi F. Homogeneous Assays: AlphaScreen.

Handbook of Drug Screening. Marcel Dekker Pub., 2001. pp. 106-110.

Enzyme assays
Application Notes
• Map Kinase Assay.

• P-Tyr-100 Insulin Receptor Tyrosine Kinase Assay.

Scientific Posters
• AlphaScreen to Monitor Protein Ubiquitination on Proteome Scale.
6th MipTech-ICAR. (2003).

• Comparison of Kinase Assay Technologies for High Throughput

Screening. SBS 8th Annual Conference. (2002).

• Development of a Homogenous p38 Kinase Assay using AlphaScreen

Technology. SBS 8th Annual Conference. (2002).

• Development of a miniaturised non-radioactive assay for the Ser/Thr

kinase, JNK-1, using AlphaScreen. Coldwell M., Fowler A., Hill S.,
Rawlins P., Swift D., Illy C., Pedro L. and Sullivan E. AstraZeneca.
SBS 6th Annual Conference. (2000).

• Reverse-Proteomic Analysis of Rho GTPase Regulation by PhoGAPs

using AlphaScreen. 6th MipTech-ICAR. (2003).

• Serine-Threonine kinase assays: an evaluation of currently available

technologies. Hill S., Drayton K., Fowler A., Rawlins P., Swift D., Harper
P., Dale I., Carey C., Hemsley P., Unitt J., Sullivan E. and Coldwell M.
AstraZeneca. SBS 6th Annual Conference. (2000).

• Ultra-Sensitive Detection of Akt Kinase Activity Using AlphaScreen.

SBS 7th Annual Conference. (2001).

32
Articles
• Gray A., Olsson H., Batty I.H., Priganica L., Peter Downes C.
Nonradioactive methods for the assay of phosphoinositide 3-kinases and
phosphoinositide phosphatases and selective detection of signaling lipids
in cell and tissue extracts. Anal Biochem. 2003 Feb 15;313(2):234-45.

• Peppard J., Glickman F., He Y., Hu S.I., Doughty J., Goldberg R.

Development of a high-throughput screening assay for inhibitors of
aggrecan cleavage using luminescent oxygen channeling (AlphaScreen).
J Biomol Screen. 2003 Apr;8(2):149-56.

• Warner G., Illy C., Pedro L., Roby P. and Bossé R. AlphaScreen Kinase
HTS Platforms. Current Medicinal Chemistry, 2004, 11, 719-728.

GPCRs
Scientific Posters
• Comparison of cAMP Assay Technologies for High Throughput Screening.
SBS 8th Annual Conference. (2002).

• New and Highly Sensitive AlphaScreen cAMP Assay to Measure

Femtomol cAMP Variants in Cell and Membrane Based Assays.
SBS 9th Annual Conference. (2003).

Ligand-receptor binding assays

Application Notes
• ERα Binding Assay.

• Screening for Inhibitors to TNFα/sTNFR1 Binding Using AlphaScreen

Technology.

Scientific Posters
• AlphaScreen TNFα Binding Assay Kit: A Homogeneous, Sensitive and
High-Throughput Assay for Screening TNFα Receptors. SBS 8th Annual
Conference. (2002).

• Development of a homogeneous non-radioactive HTS platform for

detection of nuclear receptor modulators using the AlphaScreen
Technology. Keystone Symposium on Nuclear Receptor Superfamily. (2002).

w w w. p e r k i n e l m e r. c o m 33
 Articles
• Glickman J.F., Wu X., Mercuri R., Illy C., Bowen B.R., He Y. and Sills M.
A Comparison of AlphaScreen, TR-FRET, and TRF as Assay Methods for
FXR Nuclear receptors. J. Biomol. Screening. 2002, 7(1): 3-10.

• Wu X., Glickman F., Bowen B., Sills M. Comparison of Assay

Technologies for a Nuclear Receptor Assay Screen Reveals Differences in
the Sets of Identified Functional Antagonists. Journal of Biomolecular
Screening. 2003, 8(4): 381-392.

• Xu H.E., Stanley T.B., Montana V.G., Lambert M.H., Shearer B.G., Cobb
J.E., McKee D.D., Galardi C.M., Plunket K.D., Nolte R.T., Parks D.J., Moore
J.T., Kliewer S.A., Willson T.M. and Stimmel J.B. Structural basis for
antagonist-mediated recruitment of nuclear co-repressors by PPARalpha.
Nature. 2002 Feb 7;415(6873):813-817.

Protein interaction assays

Application Note
• Gβγ-GIRK1 Interaction Assay.

Scientific Posters
• Detection of low affinity interaction occurring between complex protein
structures using AlphaScreen. 4th Miptech-ICAR. (2001).

• Experience with AlphaScreen for High Throughput Screening of Low

Affinity SH2 Domain Protein-Peptide Interactions. Hill S., Allenby G.,
Boissonneault M., Bossé R., Botterell S., Dale I., Dodgson K., Hemsley P.,
Holford R., Murray C., Rawlins P., Unitt J. and Coldwell M. AstraZeneca.
SBS 7th Annual Conference. (2001).

• Homogenous detection and measurement of micromolar affinity

interactions using AlphaScreen. SBS 6th Annual Conference. (2000).

Phage display
Scientific Poster
• Highly sensitive detection of the interaction occurring between phage
displayed peptides and their target using AlphaScreen. Cambridge
Health Institute on Phage Display. (2002).

34
ELISAs
Application Note
• Comparison of ELISA and AlphaScreen Assay Technologies for
Measurement of Protein Expression Levels.

Other references
• Dafforn A., Kirakossian H. and Lao K. Miniaturization of the luminescent
oxygen channeling immunoassay (LOCI®) for use in multiplex array for-
mats and other biochips. Clin Chem. 2000 Sep;46(9):1495-7.

• Lishanski A. Screening for single-nucleotide polymorphisms using branch

migration inhibition in PCR-amplified DNA. Clin Chem. 2000
Sep;46(9):1464-70.

• Liu Y.P., Behr M.A., Small P.M. and Kurn N. Genotypic Determination of
Mycobacterium tuberculosis Antibiotic Resistance Using a Novel
Mutation Detection Method, the Branch Migration Inhibition M. tubercu-
losis Antibiotic. J Clin Microbiol. 2000 Oct; 38 (10):3656-3662.

• Liu Y.P., de Keczer S., Alexander S., Pirio M., Davalian D., Kurn N.
and Ullman E.F. Homogeneous, rapid luminescent oxygen channeling
immunoassay (LOCI®) for homocysteine. Clin Chem. 2000 Sep;46(9):1506-7.

• Patel R., Pollner R., de Keczer S., Pease J., Pirio M., DeChene N., Dafforn
A. and Rose S. Quantification of DNA using the luminescent oxygen
channeling assay. Clin Chem. 2000 Sep;46(9):1471-7.

• Ullman E.F., Kirakossian H., Singh S., Wu Z.P., Irvin B.R., Pease J.S.,
Switchenko A.C., Irvine J.D., Dafforn A., Skold C.N., et al. Luminescent
oxygen channeling immunoassay: measurement of particle binding kinet-
ics by chemiluminescence. Proc. Natl. Acad. Sci. USA. 1994 Jun
7;91(12):5426-30.

• Ullman E.F., Kirakossian H., Switchenko A.C., Ishkanian J., Ericson M.,
Wartchow C.A., Pirio M., Pease J., Irvin B.R., Singh S., Singh R., Patel R.,
Dafforn A., Davalian D., Skold C., Kurn N. and Wagner D.B. Luminescent
oxygen channeling assay (LOCI®): sensitive, broadly applicable homoge-
neous immunoassay method. Clin Chem. 1996 Sep;42(9):1518-26.

w w w. p e r k i n e l m e r. c o m 35
Appendix I: Fusion-Alpha™
Quick Start guide
A. How to define a new AlphaScreen assay
1. Starting the system
a) Turn on the instrument by pressing the “On/Off” switch located in the
right rear of the Fusion Multilabel Reader instrument, then turn on the
computer and monitor.

b) Access the instrument control module software from the Windows NT

desktop by selecting start (bottom left corner), scrolling and selecting
programs, scrolling and selecting Fusion and then scrolling and select-
ing Fusion instrument control.

c) The Fusion instrument control window will be displayed.

d) The message “connecting to instrument” will appear. When communica-

tions are established a “downloading” window will appear. When down-
loading is complete the message “initializing instrument” will appear
and will then be followed by an instrument self test. The self test window
will appear and the instrument will execute the tests displayed. If all
tests are passed, the instrument displays an “initialization complete”
message and the system status bar changes to a green bar with “normal”
displayed. If the status bar does not turn green, use the details button for
access to the error log.

Note: If the system does not initialize, verify that the excitation and
emission filter wheels are in place.

2. Defining an assay
a) From the Fusion instrument control window select file in the toolbar
menu, scroll down to new and select to open the new assay definition
window.

The following parameters must be selected before the assay definition

window can be opened:

Assay name
Detection mode = Alpha
Number of labels = one
Plate density = 96, 384, 1536
Copy settings from assay = optional – can use settings from another
already created assay

When finished select OK to open the assay definition window.

The assay definition window is divided into the following tabs:

 Assay properties

 Sample map

36
  Alpha parameters

 Sample handling

 External programs

For each tab select and/or fill the following parameters:

Assay properties
Plate type

Automatic report generation = (1)-enable printed report options (if the data
is to be printed and if printer is connected) and (2)-enable file report
options

Ad(1)- Next to the enable printed reports select edit definition and select
the following parameters (if the data is to be printed and if printer is con-
nected):

Report style = well single-line matrix

Report content = counts
Generate report = by plate

Select OK to return to the assay definition window.

Ad(2)- Next to the enable file reports select edit definition and select the
following parameters:

Report style = well single line matrix

Report content = counts
Data labels = no labels

Report output = generate by plate, file format CSV (for being able to open
the data in Excel), filename will go in c:\fusion\reports if left as is or can
be directed to a newly created folder within the reports folder in the c:\
drive.

It is recommended to use $s as part of the file name: this sign uses plate
sequence number as file extention (this option makes traking plates easier:
e.g. First plate read with a particular assay will have plate seq. no. 001).

Select OK to return to the assay definition window.

Assay description = optional

Assay bar code = optional (if enabled, assay bar code ID and plate
orientation must be entered)

w w w. p e r k i n e l m e r. c o m 37
 Sample map
It is not necessary to create a sample map for plate reading since a default
map is already set up in the system. The default map reads an entire plate
from the last column (top to bottom). Selecting control in the toolbar menu
from the Fusion instrument control window and then stop reading can stop
plate reading. Once stopped, the stop counting window will open: select
stop or resume. Please note that all data will be saved whether the instrument
is stopped or not.

To create a new sample map, select create new sample map to open the save
sample map window. Add sample map name, description (optional) and
select OK to open the sample mapping window. From the sample mapping
window select wells to be read and then the assign labels button to assign
unknowns to the selected wells. Please note that the selected wells do not
have to be in reading sequence. Select unknowns if more than one label is
available. Close the sample mapping window and then select yes when the
“save changes” message appears. The assay definition window will now
show the new sample map.

Alpha parameters
Count time = 1 second
Delay before reading a new plate = 0 minutes
Delay before reading a new batch = 0 minutes

Sample handling
It is not necessary to shake the plates or to change the temperature of the
instrument in order to read AlphaScreen. Please refer to operation manual
for more information.

External programs
The Fusion instrument can be connected to external programs. Please refer
to operation manual for more information on this topic.

When finished select OK to close the assay definition window.

Note:

1. Edits can be made to an assay by selecting edit in the Fusion instrument

control window and then assay definition to open the assay definition
window. Select OK when finished to close the assay definition window.

2. It is also possible to obtain a detailed list of assay parameters by selecting

tools in the Fusion instrument control toolbar menu and then launch
assay definition editor. The assay that is opened in the Fusion instru-
ment control will automatically be shown. To view another assay select
file from the assay definition editor window, then open to open the open
assay definition window. From the open assay definition window select
the assay name and then select OK. When finished, close this window to
return to the Fusion instrument control window.

38
B. How to run an assay
a) From the Fusion instrument control window select file from the toolbar
menu, scroll down to open assay definition/sample map window and
select to open this window. Select the assay/sample map to be used and
then OK to return to the Fusion instrument control window.

b) From the Fusion instrument control window select control in the toolbar
menu, scroll down to load/eject and select to eject the plate carrier.

c) Place plate in the plate carrier with well A1 at the upper left corner.

d) From the Fusion instrument control window select control in the toolbar
menu, scroll down to start reading and select to read the assay.

e) When the instrument is done reading a counting complete window will

appear.

From the counting complete window select and/or fill the following para-
menters:

Plate comment = optional

End batch will close the window and return to the Fusion instrument con-
trol window.

C. Useful tricks
1. Deleting an assay
a) Not recommended when data has been generated since it will not be pos-
sible to open it from the results viewer when necessary. However, the
Excel files will still be available from the data folder if the assay from
which the data was generated was deleted.

b) From the Fusion instrument control window select tools in the toolbar
menu, scroll down to launch assay definition editor and select to open
the assay definition editor window.

c) From the assay definition editor window select file from the toolbar
menu, scroll down to delete assays and select to open the delete assay
window.

From the delete assay window select the following parameters:

Assay

All data and assay definition or data only (please note that the Excel files
in the reports folder will still be available)

Delete assay

Select delete and then are you sure: yes and close the delete assay
window and then the assay definition editor window to return to the
Fusion instrument control window.

w w w. p e r k i n e l m e r. c o m 39
 Note: It will not be possible to delete an assay that is already opened
in the Fusion instrument control window. It must be closed from this
window before deleting. If the assay to be deleted was closed from the
Fusion instrument control window and still cannot be deleted, close the
Fusion instrument control window (not the instrument) and re-open it.

2. Locating generated data when enable file reports and/or

enable printed reports are not selected from the assay
definition window
a) Generated data will not be available from the reports folder
(c:\fusion\reports directory) if enable file reports is not selected from
the assay definition window. It will also not be printed if enable printed
reports is not selected. However, the data can be located by using the
results viewer.

b) First, the assay definition should be edited in order to include the miss-
ing information: please refer to Note no. 1 on page 38 of the Defining an
assay section.

c) From the Fusion instrument control window select tools in the toolbar
menu, scroll down to launch results viewer and select to open the open
assay window.

d) From the open assay window select the assay for which reports were not
generated and then select OK to open the results viewer window. The
results viewer contains all results associated with a particular assay.

e) From the results viewer window select the plate data of interest, then
select file from the toolbar menu, scroll down to edit printed reports
and/or edit file reports and select to open the printed report definition
and/or file report definition windows.

f) From the printed report definition and/or file report definition windows
select the same parameters as in the edit definition sections within the
assay properties tab of the assay definition window on page 37 (for
enable file reports and/or printed reports).

g) Close the results viewer window to return to the Fusion instrument control
window. The data will now be found in the report folder and/or will be
printed.

40
w w w. p e r k i n e l m e r. c o m 41
Appendix II: AlphaQuest HTS
Quick Start guide
A. How to define a new assay
1. Starting the system
a) Turn on the instrument by pressing the switch located on its left side to
the “On” position.

b) When the instrument is started the system is initialized. When the initial-
ization is complete, access the instrument control module software from
the Windows NT desktop by selecting start (bottom left corner), scroll-
ing and selecting programs, scrolling and selecting AlphaQuest and then
scrolling and selecting AlphaQuest.

c) The AlphaQuest instrument control window will be displayed.

d) When communication is established between the instrument and the

computer, the AlphaQuest instrument control window will display an
instrument status of “normal”. This status indicates that the AlphaQuest
instrument control window can be used to run an assay.

2. Defining an assay
a) From the AlphaQuest instrument control window select application in
the toolbar menu, scroll down to assay definition and select to open the
assay definition window.

b From the assay definition window select file from the toolbar menu,
scroll down to new and select to open the new assay window.

From the new assay window fill out the following parameters:

Assay name
Assay #/Bar code (has to be filled even if not using bar codes on plates)
Assay type = Alpha
Plate type = either 96, 384 or 1536
Description (optional — for informational purposes only)

Script
Alpha.srp

When finished select OK. The assay information will be displayed in sum-
mary form in the assay definition window. The information in this win-
dow cannot be edited.

c) To change assay information select parameters from the toolbar menu in

the assay definition window, scroll down to assay and select to open the
assay parameters window.

In the assay parameters window the bar code, description and script
name can be changed, but not the name of the assay and the plate type.

42
 Select for key samples required by plate.

When finished select OK to return to the assay definition window.

d) From the assay definition window select parameters from the toolbar
menu, scroll down to screening ranges and select to open the screening
ranges window.

This window enables the user to define primary fields and screening
ranges for each primary field. These settings are not necessary for plate
reading and therefore can be left blank. Please refer to user manual for
more information.

e) From the assay definition window select parameters from the toolbar
menu, scroll down to sample type and select to open the sample type
selection window.

Only the unknowns sample type is needed as selected samples for plate
reading. Please refer to user manual for more information on how to
define other sample types.

When finished select OK to return to the assay definition window.

f) From the assay definition window select parameters from the toolbar
menu, scroll down to report definition and select to open the report def-
inition window.

The report definition window is divided into the following tabs:

 Printer output

 ASCII file output

 Printer output screening

 ASCII file screening

For each tab select the following paramenters:

Printer output
Sample types = unknown
Data groups = leave as is
Report layout = matrix single line
Data alignment = justify full
Include/exclude items = sample well counts only

ASCII file output

Sample types, data groups, included/excluded items as above (2.f)
Data layout = matrix (single line)
File format = Excel import if working with Excel

w w w. p e r k i n e l m e r. c o m 43
 Directory = can be left as is so that data will be imported directly in the
data folder or in a newly created folder within the data folder (the data
folder can be found in the c:\ drive)

Filename = recommended to use the same name as the assay name—

this is the name that is recorded in the data folder so it is easier to
associate with its corresponding assay if it has the same name

It is recommended to select for: Use plate sequence number as file exten-

tion (this option makes traking plates easier: e.g. First plate read with a
particular assay will have plate seq. no. 001)

No need to label columns and to save assay definition to disk

Printer output screening and ASCII file screening

Enables the user to control screening for printed reports and for the
ASCII output files. No need to enable these options for plate reading.
Please refer to user manual for more information.

When finished select OK to return to the assay definition window.

3. Defining instrument parameters

a) From the assay definition window select parameters from the toolbar
menu, scroll down to instrument and select to open the instrument
parameters window.

The instrument parameters window is divided into the following tabs:

 General

 Automatic reporting

 User programs

For each tab select the following paramenters:

General
Count time = 1 sec

Disable: barcoding active, apply crosstralk correction factors, perform

normalization on next plate counted (this option is selected only when
normalization is performed— recommended to perfom normalization for
newly created assays: please refer to section E2.)

Well read order = by row

Position A1 = upper left

Automatic reporting
Enable printed report options (if printouts of results are needed and
if printer is connected)

44
Enable ASCII data files (this has to be selected or files will not be saved to
the data folder)

Select generate output at end of computational group

User programs
To be filled only if the user wants to load and run an application pro-
gram. No need to work with this option for plate reading. Please refer to
user manual for more information.

When finished select OK to return to the assay definition window.

b) Close the assay definition window to return to the AlphaQuest instru-

ment control window.

B. How to run an assay

a) Select an assay name (this is the name given for the assay definition cre-
ated) in the AlphaQuest instrument control window.

b) Eject the plate carrier by selecting eject in the AlphaQuest instrument

control window.

c) Place plate in the plate carrier with well A1 at the upper left corner.

d) Select start from the AlphaQuest instrument control window for reading
the plate.

e) The entire plate will be read since the sample map selected at this point
is the default map. However, selecting pause in the AlphaQuest instru-
ment control window will stop the instrument. Once paused, reading
can be resumed or stopped. Please note that all data will be saved
whether the instrument is stopped or not.

f) Please note that it is not necessary to set a sample map for plate reading.
If interested, please refer to instructions below on how to create a sample
map.

C. How to create a sample map

a) From the AlphaQuest instrument control window select application in
the toolbar menu, scroll down to sample mapping and select to open the
sample map window.

b) From the sample map window select file from the toolbar menu, scroll
down to new and select to open the new sample map window.

From the new sample map window select and fill out the following
parameters:

Assay (select name of assay for which a sample map is to be created)

Map name (create new name)

w w w. p e r k i n e l m e r. c o m 45
 When finished select OK to go back to the sample map window. An
empty plate will now appear. Wells can be selected with the mouse and
these can be assigned by double-clicking on the available unknown label
in the same window (unknowns should be the one chosen if more than
one label appear on the list).

When finished select file from the toolbar menu, scroll down to save and
close to return to the AlphaQuest instrument control window. The
sample map can then be selected for the particular assay it was created
for in the AlphaQuest instrument control window prior to plate reading
(please refer to the section B).

D. Useful tricks
1. Deleting an assay
a) Not recommended when data has been generated since it will not be possible
to open it from the results analysis module when necessary. However,
the Excel files will still be available from the data folder if the assay
from which the data was generated was deleted.

b) From the AlphaQuest instrument control window select application in

the toolbar menu, scroll down to assay definition and select to open the
assay definition window.

c) From the assay definition window select file from the toolbar menu,
scroll down to delete and select to open the delete assay window.

From the delete assay window select the following parameters:

Assay
Can select for delete acquired data only (only data generated with the
selected assay will be deleted and not the assay definition itself —
please note that the Excel files in the data folder will still be available)

d) Select delete and then are you sure: yes and close the window to return
to the AlphaQuest instrument control window.

2. Locating generated data when enable ASCII data files

and/or enable printed reports are not selected from the
automatic reporting tab in the instrument parameters window
a) Generated data will not be available from the data folder if the enable
ASCII data files parameter is not selected. It will also not be printed if
enable printed reports is not selected. However, the data can be located
by using the results analysis module.

b) First, the assay definition should be edited in order to include the

missing information:

From the AlphaQuest instrument control window select application in

the toolbar menu, scroll down to assay definition and select to open the
assay definition window. Select the assay to be edited and then follow
the instructions for defining instrument parameters in section B 3.)

46
c) From the AlphaQuest instrument control window select application in
the toolbar menu, scroll down to results analysis and select to open the
results analysis window.

d) From the results analysis window select file from the toolbar menu,
scroll down to print assay and select to open the print assay window.

From the print assay window select the following parameters:

Assay = the assay from which data is to be located

Select contents (data) to be printed and/or saved
Select send to printer if the data is to be printed (and if printer is
connected)
Select enable ASCII file reports so that the data can be transferred to
the data folder

When finished select OK.

E. How to run IPA and normalization

1. Instrument performance assessment (IPA)
 Evaluates the performance of the AlphaQuest instrument.

 IPA measures and stores results for specific performance parameters.

 Recommended to run IPA at least once per week. This way it is

possible to track instrument performance against historical data.

a) Place the IPA plate onto the carrier. Make sure that the words “right
front” appear in the lower right corner of the plate as it sits on the carrier.

b) Slide the switch (middle of the plate) to “On” (the IPA plate uses 2
commercially available lithium batteries — Duracell® DL2430 — each
battery lasts ~60 hours).

c) Select IPA from assay name in the AlphaQuest instrument control

window.

d) Select start from the AlphaQuest instrument control window for reading
the IPA plate.

e) Look at the IPA status in the AlphaQuest instrument control window

after IPA plate reading: if the test is successful an “IPA status: pass”
message will appear.

Please refer to user manual for more information on looking at

IPA results.

w w w. p e r k i n e l m e r. c o m 47
 2. Normalization
 Normalization is important for multi-detector systems (it is not
needed for single detector systems).

 It ensures that the instrument’s detectors are producing equivalent

results.

a) The IPA must be run first to ensure the instrument performs properly
(please refer to section E 1).

b) A new assay must be defined (please refer to section A).

c) From the AlphaQuest instrument control window select application in

the toolbar menu, scroll down to assay definition and select to open the
assay definition window.

d) From the assay definition window select parameters in the toolbar

menu, scroll down to instrument and select to open the instrument
parameters window.

e) Select the general tab in the instrument parameters window.

f) Select “perfom normalization on next plate counted” in the instrument

parameters window.

When this selection is made, the system will count the normalization
plate the next time the assay is run. All other plates that are counted
subsequent to the normalization plate for that assay will have the new
normalization factors applied to them.

When finished select OK.

g) Prepare the normalization plate. The normalization plate that is prepared

must match the normalization sample map (please refer to how to view
the normalization map below). The samples used should be as similar as
possible to those in the assay. The following variables should be consid-
ered when choosing samples for normalization: assay type, plate type,
sample volume, bead/reagent concentration.

How to view the normalization map:

 From the AlphaQuest instrument control window select application

in the toolbar menu, scroll down to sample mapping and select to
open the sample map window.

 From the sample map window select file from the toolbar menu,
scroll down to open and select to open the open sample map window.

48
 From the open sample map window select the following parameters:

Assay name to be normalized

Normalization map (from the sample maps list)

When finished select OK to go back to the sample map window, where

the normalization map will be displayed. Once viewed, close the
window to return to the AlphaQuest instrument control window.

h) Normalize the assay by running the assay from the AlphaQuest

instrument control window. Select the assay and normalization
sample map and then start.

w w w. p e r k i n e l m e r. c o m 49
Appendix III: EnVision™ Multilabel
Plate Reader with AlphaScreen module
Quick Start guide
A. How to define a new AlphaScreen assay
1. Starting the System
a) Turn on the instrument by pressing the On/Off switch located on the
back top corner on the left side of EnVision.

b) If you have a control unit, switch it on. The control unit is a separate
CPU used to run the instrument software in some configurations of
EnVision. In other configurations the job is handled by the workstation
PC.

c) Wait until the red light on the EnVision panel is steady (not blinking).
(This takes a couple of minutes.)

d) Switch on the user computer and monitor.

e) Start the EnVision Manager by clicking the EnVision icon on the

Windows desktop. Click the I Agree button to accept the Limited
Warranty Agreement. The EnVision Manager will then start loading.
When it is complete the Reader Control window will appear.

Note: If you are running in Enhanced Security mode you will have to give
your user name and password. There maybe certain features of the software
that you do not have permission to use. This will depend on the rights
given to you by the system administrator. Contact your administrator or see
the EnVision Enhanced Security manual for details about Enhanced
Security.

2. Defining an assay
a) Check that there is a suitable AlphaScreen mirror module loaded.

Click Mirrors. If the AlphaScreen mirror module is not available (i.e. not
physically loaded in the instrument) you must load it as described in the
Instrument manual (Routine maintenance - “Changing a mirror module”).

b) Check that there is a suitable AlphaScreen emission filter

Click Filters. If the AlphaScreen emission 570 filter is not available

available (i.e. not physically loaded in the instrument) you must load
it as described in the Instrument manual (Routine maintenance —
“Changing filter slides”).

c) Set the AlphaScreen Label parameters

Click Labels.

50
 Select the AlphaScreen label.
If you want, you can copy this default label and edit its parameters.
Make sure the Mirror module and Filter are the same as the ones loaded
in the instrument.
If you want to change the Total measurement time and the Excitation
time you can do this. The software will keep the values within accept-
able limits.

d) Set the Plate parameters

Click Plates.
Choose the plate. You should select OptiPlate from PerkinElmer.
You can use any of the well densities: 96, 384 or 1536.

e) Optimize the chosen Label and Plate combination

Click the Optimize button on the toolbar.

Choose the plate and label combination to be the same
as you have just selected.
Load an empty plate of the type you selected.
Select to Optimize plate dimensions.
Run the plate optimization following the steps shown by the wizard.
When the optimization is complete, start a new optimization.
Select the same plate and label combination.
Select to Optimize crosstalk corrections.
Load samples as required by the wizard.
Load the plate and run the optimization.

f) Set the measurement parameters

Click Protocols. Select the User folder for your protocol.

Click the New protocols button on the toolbar.
Give a name for the new protocol.

Click the Plate tab and set the plate parameters:

Choose the plate type first. This should be the same
as the one you just optimized.
Define the sample area and select the sample type— Measured.
Samples should run from top to bottom starting from the top
right hand corner.

Optional: Click ID to add text with the protocol.

Click the Operation tab.

Click the down arrow by the Measurement button.
Select Measurement.
Select the AlphaScreen label.
The Calculation for AlphaScreen (Crosstalk) will be selected
automatically.

Click the Output tab.

Select how results are output.

w w w. p e r k i n e l m e r. c o m 51
 B. How to run an assay
a) Run samples
Choose manual or stacker loading.
If you are using barcodes, define them in Barcode settings and
Reader Settings.
Click Reader control.
Choose the measurement protocol made for AlphaScreen.
Click Start.
Live results will be shown in the Reader control window (Plate view).

Optional: Display results as numeric values (Grid view).

b) View results

Click the Latest button.

The Result viewer will open to show the latest results.
or
Click Results.
Select the results you want displayed.
The Result viewer will open to show selected results.

Select the type of results you want displayed

(use the Navigation Tree in the Result viewer).

Click the Export button.

Define the output format and content.
Click the Export button to send results to File or Printer depending
on the choice you have made.

52
PerkinElmer Life and
Analytical Sciences
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Phone: (800) 762-4000 or
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©2004 PerkinElmer, Inc. All rights reserved. The PerkinElmer logo and design are registered trademarks of PerkinElmer,
Inc. AlphaQuest, AlphaScreen, EnVision and Fusion-Alpha are trademarks or registered trademarks of PerkinElmer, Inc.
or its subsidiaries, in the United States and other countries. AlphaScreen chemistry is based on patented LOCI® technology
developed by Dade Behring, Inc. PerkinElmer, Inc. holds the exclusive license for this technology in the life science
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