Mascot is a powerful and widely used search engine that uses mass spectrometry data to identify proteins from primary sequence databases.
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Compute pI/Mw is a tool which allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of Swiss-Prot entries or for a user entered sequence of aminoacids. The resulting theoretical values check the consistency of the position on a 2D PAGE gel of the identified and unmodified proteins.
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ELM(Eukariotic Linear Motif)is a resource for predicting functional sites in eukaryotic proteins.
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Category: Proteomics data analysis, Gene expression
GenPattern Proteomics allows: Broad
GenePatern allowr various data analyses for proteomics: MRM-MS; peptide signature prediction; PEPPeR algorhitms; detection and alignment features across runs in LC-MS; support for SELDI/MALDI data.
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The standard MS/MS experiment starts by digesting the proteins into peptides with an enzyme such as trypsin. USe Protein Digestor to see what peptides will result from digesting a protein.
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Proteomics tools for mining sequence databases in conjunction with mass spectrometry experiments.
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X!Tandem is a very fast seach engine which searches for matches of MS/MS spectra to a protein database. X!Tandem is free to use on the web or to download. X!Tandem works in conjunction with thegpm.org and can take advantage of the information gleaned from previous searches. It has an option, PPP, which searches first only the peptides that have been found most frequently for each protein
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SRMAtlas is a database of selected reaction monitoring (SRM) transitions and mass spectra derived from synthetic peptides created for SRM assay development and analyzed on the types of mass spectrometers most frequently used for SRM/MRM experiments— triple quadrupole, Orbitrap, and quadrupole–time-offlight instruments. Users can search SRMAtlas using a protein accession number or peptide sequence, or by uploading a text file containing a list of protein names or peptide sequences
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