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PROTEOMICS DATA ANALYSIS


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Mascot logo

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 tool logo

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 - Functional site prediction logo

ELM(Eukariotic Linear Motif)is a resource for predicting functional sites in eukaryotic proteins.

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OMSSA logo
Subcategories: ncbi

The Open Mass Spectrometry Search Algorithm [OMSSA] is an efficient search engine for identifying MS/MS peptide spectra by searching libraries of known protein sequences.You may also download OMSSA and use it as a command line executable on your own machine. OMSSA was developed by the NIH and is completely free.

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Hydrophobicity Profiler logo

Hydrophobicity Profiler allows you to upload a FASTA-formatted protein sequence and calculate its hydrophobicity profile using one of five different hydrophobicity scales. This is useful to verify that the peptides identified are eluting in a reasonable order because the retention time of the reverse phase liquid chromatography commonly used with electrospray ionization depends upon the hydrophobicity of the peptide.

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GenPattern Proteomics logo
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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ProteinProspector logo

Proteomics tools for mining sequence databases in conjunction with mass spectrometry experiments.

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Protein Digestor logo

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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PepArML logo

The PepArML Meta-Search Engine provides a unified interface for running tandem mass spectrometry searches with Mascot, Tandem, OMSSA, KScore (Tandem with the K-Score scoring plugin), SScore, Myrimatch, and InsPecT on a heterogeneous grid of computers locally on the Edwards Lab cluster and remotely using Amazon Web Services or NSF's TeraGrid infrastructure.

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X! TANDEM logo

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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MRMaid logo

MRMaid helps you design SRM assays by suggesting peptides and product ions to monitor based on millions of experimental spectra from the public data repository known as PRIDE database (PRoteomics IDEntifications; www.ebi. ac.uk/pride). This Web-based application developed suggests SRM transitions based on the peptides and fragment ions that have been detected previously in shotgun proteomics experiments stored in PRIDE.MRMaid also provides information that can aid in the design of a targeted as

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MRMPath logo

MRMPath is an online tool that predicts suitable peptides for multiple-reaction monitoring (MRM) mass spectrometry assays based on protein sequence. Users first enter the accession number or sequence of their protein of interest. Alternatively, users can choose a particular biological pathway and species, and MRMPath generates a list of all the proteins involved in the chosen pathway using information stored in the Kyoto Encyclopedia of Genes and Genomes database (KEGG).

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PEPTIDEPICKER logo

PeptidePicker is a Web-based application that integrates information from a variety of different data sources to compile a list of optimal peptides for an SRM/MRM mass spectrometry assay.

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SRMAtlas logo

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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