Search Results for "mass spectrum"
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Showing 16 open source projects for "mass spectrum"
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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AtomProbeLab
Matlab-based analysis of Atom Probe Data
A collection of scripts and functions for the analysis of atom probe tomography data. Currently, this includes: standard file operations, plotting mass spectra, mass spectra analysis and mass peak overlap solving. For more information see the Wiki: https://sourceforge.net/p/atomprobelab/wiki/Home/ Quick overview video: https://youtu.be/8rJHce7M5UU More in-depth video using the APT school demos live script: https://www.youtube.com/watch?v=cyrLHCzZwuw For details of the maximum likelihood... -
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SpecProc
SpecProc is a general processing tool for MassLynx data.
For the new Browser Support and Internet Explorer retirement see https://sourceforge.net/projects/specproc2browser/ NEW! At last, the mighty SpecProc is available to all. This is version 1.14 packed with new features that nobody asked for. This includes tof and quad data, spectrum and chromatogram extraction. Note that methods (olp) files created with earlier versions might throw an error when you try an import them. But hey, a small price to pay. They can only ever have a few things... -
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JSONVisor
Visor for mass spectrometry JSON files generated by Integrator
Visor for mass spectrometry JSON files generated by the Integrator program (Python 3 version). For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/jsonvisor3/code/ci/default/tree/README.md - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). A collection of open source applications for mass spectrometry data mining. PROTEOMICS, 14(20), 2275–2279. https://doi.org/10.1002/pmic.201400124 -
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Although mass spectrometry is well suited to identifying thousands of potential protein post-translational modifications (PTMs), it has historically been biased towards just a few. To measure the entire set of PTMs across diverse proteomes, software must overcome the dual challenges of covering enormous search spaces and distinguishing correct from incorrect spectrum interpretations. Here, we describe TagGraph, a computational tool that overcomes both challenges with an unrestricted string...
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speccy3os
Message passing microkernel-based Operating System for ZX Spectrum +3e
This project is an attempt to design an message passing microkernel-based Operating System for the ZX Spectrum +3e computer equipped with ZXMMC mass storage device. It was made mostly for PoC purpose. -
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zxmmcfid
A ZXMMC mass storage device FID driver for CP/M
CP/M Plus on ZX Spectrum +3 has ability to load device drivers from normal disk files (with .fid extension) on boot. One of the most important devices for any disk operating system is the mass storage drive. Although ZXMMC device is available on the market for years and it works well with +3e firmware, partitions created on MMC cards could not be accessed from CP/M world. At some point it became so frustrating, I decided to write FID driver for it. It's not perfect, but it works surprisingly... -
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The Glycopeptide Spectrum Annotation program (gpAnnotate) is designed to annotate individual glycoproteomics MS/MS spectrum for several established mass spectrometry fragmentation modes: CID: collision induced dissociation HCD: beam-type CID or higher-energy collision dissociation ETD: electron transfer dissociation ETciD: electron-transfer-CID, and EThcD: electron-transfer-HCD. In addition to preset options that are fixed for the above modes, gpAnnotate also allows ‘Custom’ definition...
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SILVER
SILVER: An efficient tool for stable isotope labeling quantification
With the advance of experimental technologies, different stable isotope labeling methods have been widely applied to quantitative proteomics. Here, we present an efficient tool, named SILVER for processing the stable isotope labeling mass spectrometry data. SILVER implements novel methods for quality control of quantification at spectrum, peptide and protein levels respectively. Several new quantification confidence filters and indices are used to improve the accuracy of quantification results... -
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Morpheus search algorithm
a mass spectrometry–based proteomics database search algorithm
Morpheus is a mass spectrometry–based proteomics database search algorithm designed from the ground up for high-resolution tandem mass spectra. We have discovered that for high-resolution MS/MS, simple spectrum preprocessing and scoring performs superior to more complex algorithms originally developed for low-resolution MS/MS, such as Sequest, Mascot, and OMSSA. Morpheus is also very fast—up to nearly 5 times faster than OMSSA for large human datasets. It is written in C# and is available open... -
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QUDeX-MS
Hydrogen/deuterium exchange estimation for isotopic fine structure MS
... of deuterium incorporation from a spectrum with isotopic fine structure resolved. Given a peptide sequence or elemental formula, the distribution of deuterium-associated mass-to-charge ratios is calculated based on a particular charge state corresponding to the molecular species resolved in an input mass spectrum. Peaks in the input mass spectrum fitting within bins corresponding to these values are used to determine the distribution of deuterium incorporated. -
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octave-ms
Collection of routines for manipulation with mass spectrometry data
octave-ms is a collection of IO routines for manipulation with mass spectrometry datasets for octave users. It can handle variety of MS storage file formats including MGF, DTA, PKL, MZXML, MZDATA and MZML, converts MS data from one format to another, extract scans from MS datasets. Combined with octave statistical packages, it can be easy implemented to perform stat tests on various parameters of spectrum. It requires working knowledge in Octave/Matlab. -
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ResCalc3
Spectral resolution calculator for MassLynx
Spectral resolution calculator for MassLynx and now UNIFI. ResCalc3 determines and reports the spectral resolution from a list of mass intensity pairs or MassLynx spectrum. The list can be either in the clipboard or in a text file. It is intended for use with data from either ToF or Quadrupole Instruments and reports the resolution of the most intense peak in the data. The resolution can be optionally compared to a threshold you specify and the result is displayed as Pass/Fail using... -
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Xi Spectrum Viewer
Mass Spectrum Viewer Tool
... to drive functionality. It comprises 3 parts: (1) the core Spectrum Viewer displays peptide-spectrum matches and implements zooming, mouse-over peaks to highlight matching parts of peptide, mouse-over parts of peptide to highlight matching peaks, export SVG, and API; (2) the Auxiliary Annotator matches peptide to spectrum for given parameters and prepares the data for the Viewer; (3) these reside on a web page that provides the user control over peptides, spectra and other parameters e.g. linker mass. -
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iPiG
Integrating PSMs into Genome browser visualisations
iPiG targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser (http://genome.ucsc.edu/). iPiG takes PSMs from the MS standard format mzIdentML (*.mzid) or in text format and provides results in genome track formats (BED and GFF3 files), which can be easily imported into genome browsers. For more details about iPiG and it's functionallity, please... -
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It's a project to predict peptide fragmentation of mass spectrometry. Check the detail at Anal Chem. 2011 Feb 1;83(3):790-6. On the accuracy and limits of peptide fragmentation spectrum prediction. Li S, Arnold RJ, Tang H, Radivoja
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