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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 a 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 - Protein identification by amino acid composition
  • AACompSim - Compare the amino acid composition of a UniProtKB/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. This tool takes advantage of Hough transformation for spectra recalibration and outlier exclusion is now available as a stand-alone version.  Click here.
  • 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 UniProtKB/Swiss-Prot or UniProtKB/TrEMBL entry or 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. Labkey Software - builds and customizes LabKey Server (formerly CPAS), a free and open source platform for processing, analyzing, storing and securely sharing high volumes of mass spectrometry data using a variety of popular search engines including Mascot™, Sequest™, and X-Tandem™.

  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. NIST Peptide Mass Spectral Libraries - a growing, community-based database of MS peptide fragmentation patterns derived from empirical data. The authors encourage the use of the database for software development as a replacement to methods that predict MS patterns based computer algorithms.

  5. 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

  6. PepBank - a sequence searchable database of peptides compiled from text mining and public peptide data sources - only peptides less than 20 amino acids and with available sequences are stored.

  7. 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.

  8. Phenyx - a software platform for the identification and characterization of proteins and peptides from mass spectrometry data

  9. Protein Prospector - proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments from UCSF

  10. ProteinCenter - ProteinCenter allows import of protein data including peptides with PTM, mapping peptides on protein sequences, and clustering based on shared peptide evidence

  11. ProteoIQ - software developed for comparative proteomic analyses, where spectral counting-based quantification is combined with protein validation and data mining functions to find differences and similarities between multiple proteomic data sets.

  12. 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

  13. Scaffold 3 - software which produces a confidence level for protein identification from one or more Mascot, Sequest, X! Tandem, or Phenyx searches. It can be used in conjunction with a MS/MS search engine in order to validate/visualize data across multiple experimental runs as well as provide a more accurate protein probability.

  14. 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.

  15. 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.

  16. Sequit! - software for de novo sequencing of peptides by ESI and MALDI tandem mass spectrometry

  17. 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.  You can read more about this software here.
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