MS/MS

PeptideSieve

It has been noted [1] that only a handful of a protein’s possible tryptic peptides are consistently observed in proteomics experiments. We denote these consistently observed peptides to be proteotypic peptides. Such peptides have a variety of potential applications in proteomic research including improving protein identification scoring functions of database search software, providing a panel of reagents for protein quantification as well as the annotation of genomes for coding sequences of e.g.

UniPep

Unipep is a project to provide access to proteomics data from the Serum Biomarker group at the Swiss Federal Institute of Technology (ETH) in Zurich Switzerland, and the Institute for Systems Biology (ISB) in Seattle, Washington USA.

PhosphoPep

PhospoPep version 2.0 is a project to support systems biology signaling research by providing interactive interrogation of MS-derived phosphorylation data from 4 different organisms. Currently there is data from the fly (Drosophila melanogaster), human (Homo sapiens), worm (Caenorhabditis elegans), and yeast (Saccharomyces cerevisiae).

PeptideAtlas

PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.

Libra

Libra is a module within the trans-proteomic pipeline to perform quantification on MS/MS spectra that have isobaric multi-reagent labeled peptides. More specifically, at ISB we use Libra on MS/MS spectra of iTRAQ labeled samples; it can also be used on TMT labeled samples. There is no limitation to the number of channels that Libra can quantitate against.

ASAPRatio

Automated Statistical Analysis on Protein Ratio (ASAPRatio) accurately calculates the relative abundances of proteins and the corresponding confidence intervals from ICAT-type ESI-LC/MS data.

SpectraST

SpectraST (short for "Spectra Search Tool" and rhymes with "contrast") is a spectral library building and searching tool designed primarily for shotgun proteomics applications. It is developed at the Institute for Systems Biology (ISB), in the research group of Professor Ruedi Aebersold. The main developer is Henry Lam.

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