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Peptide Related Proteomics Software and Tools
A variety of online tools and commercially available software exist that allow for protein identification from peptide sequences determined by mass spectrometry (or other sequencing techniques). If you are interested in finding software to calculate the physico-chemical or biochemical properties of peptide, see our other section on peptide software.
  1. The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE. Their section on ExPASy proteomics and sequence analysis tools contains a variety of useful online programs. A list of their peptide related tools can be found below:
  • AACompIdent - Identify a protein by its amino acid composition
  • AACompSim - Compare the amino acid composition of a Swiss-Prot entry with all other entries
  • MultiIdent - Identify proteins with pI, Mw, amino acid composition, sequence tag and peptide mass fingerprinting data
  • Aldente - Identify proteins with peptide mass fingerprinting data. A new, fast and powerful tool that takes advantage of Hough transformation for spectra recalibration and outlier exclusion
  • PeptIdent - Identify proteins with peptide mass fingerprinting data, pI and Mw. Experimentally measured, user-specified peptide masses are compared with the theoretical peptides calculated for all proteins in Swiss-Prot, making extensive use of database annotations
  • TagIdent - Identify proteins with pI, Mw and sequence tag, or generate a list of proteins close to a given pI and Mw
  • FindMod - Predict potential protein post-translational modifications and potential single amino acid substitutions in peptides. Experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified Swiss-Prot entry or from a user-entered sequence, and mass differences are used to better characterize the protein of interest.
  • FindPept - Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artificial chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage
  • PeptideMass - Calculate masses of peptides and their post-translational modifications for a Swiss-Prot or TrEMBL entry or for a user sequence
  • MALDIPepQuant - Quantify MALDI peptides (SILAC) from a Phenyx output

    Other sections include tools that will translate nucleotide sequences to peptide sequences and tools to predict sites of glycosylation, phosphorylation, or myristoylation.

  1. Mapper - a University of Manchester protein search tool which uses mass spectrometry data produced by the digestion of a protein to identify a match to a protein from a database.
  2. Mascot - a search engine that uses mass spectrometry data to identify proteins from primary peptide sequence databases. As a software package, the Mascot server can be in-licensed for in-house use.
  3. MASPIC - an intensity-based tandem mass spectrometry scoring scheme that improves peptide identification at high confidence
  4. PEAKS - de novo sequencing and protein identification software: auto/manual de novo and database searching tools for MS/MS spectra and a fully automatic high throughput, command line auto de novo tool for ms/ms spectra capable of batch processing
  5. PeptideAtlas - multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Some of the experimental data have been already published; many are still unpublished.
  6. PeptideSearch - a tool for database searching by mass spectrometric data, such as peptide mass maps or (partial) amino acid sequences. PeptideSearch is also available as a standalone Macintosh application.
  7. Phenyx - a software platform for the identification and characterization of proteins and peptides from mass spectrometry data
  8. Protein Prospector - proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments from UCSF
  9. ProteinCenter - ProteinCenter allows import of protein data including peptides with PTM, mapping peptides on protein sequences, and clustering based on shared peptide evidence
  10. PROWL/ProFound - a tool for searching a protein sequence collections with peptide mass maps. A Bayesian algorithm is used to rank the protein sequences in the database according to their probability of producing the peptide map
  11. Sequence V1.5 - software for collision induced dissociation mass spectrometric sequencing of peptides prepared by combinatorial split-and-pool methodology. The software works for both cyclic and linear peptides, and combines library enumeration and sequencing into one package. Any number of mass spectra may be supplied, with arbitrary MSn steps. Common peptide fragmentations are understood, and the user may specify unnatural residues and end groups.
  12. SEQUEST - software that correlates uninterpreted tandem mass spectra of peptides with amino acid sequences from protein and nucleotide databases. SEQUEST will determine the amino acid sequence and thus the protein(s) and organism(s) that correspond to the mass spectrum being analyzed. SEQUEST is distributed by Thermo Scientific.
  13. Sequit! - software for de novo sequencing of peptides by MALDI and ESI tandem mass spectrometry
  14. Sherpa - (Macintosh only) - designed to be a robust, easy to use aide-de-camp in the correlation and interpretation of LC/MS and MS/MS spectra to a known protein sequence or sequences. Native files from Sciex APIIII, Sciex 100/300, and Finnigan SSQ/TSQ electrospray mass spectrometers are currently supported. Some features include: calculation of protein molecular weight, digest fragments, digest fragment charge state m/z values; user definable termini, amino acids, and modifications; comparison of two LC/MS files