Software

Proteomics Tools and Resources

Trans-Proteomic Pipeline

The Trans-Proteomic Pipeline (TPP) is a complete and mature suite of free and open-source software tools for MS data representation, MS data visualization, peptide identification and validation, protein identification, quantification, and annotation, data storage and mining, and biological inference.

TPP is available on Linux and Windows systems and builds on Mac OS X as well, and supports a well-established worldwide user community, and can be downloaded from our SourceForge site.

TPP is comprised of dozens of individual tools. Some (as well as a few which are not included in the TPP distribution), are listed below:

• Input Processing / Data Handling
  • mzML – standard format for mass-spectrometry data
  • msconvert – native data to mzML converter (and many other formats)
  • mzXML2Search– convert mz[X]ML to other open formats
  • readmzXML – mz[X]ML parser/reader
• Database and Spectral Library Search
  • SpectraST^TM – spectral library search engine provided by TPP
  • Comet – open-source database search engine provided with TPP
  • X!Tandem – open-source database search engine provided with TPP
  • Magnum – perform open-modification database searching
• Cross-linking Analysis
  • Kojak – identified cross-linked peptides; supports virtually any cross-linker chemistry
• Probability Assignment and Validation
  • PeptideProphet^TM – validation of peptide identifications made by tandem mass spectrometry (MS/MS) and database searching; probabilities are assigned to the peptide identifications made by search engines
  • iProphet^TM – validation of distinct peptide sequences; can also combine search results of multiple search engines
  • PTMProphet – validation of post-translational modification sites
  • ProteinProphet^TM – statistical model for validation of peptide identifications at the protein level
• Peptide and Protein Quantification
  • XPRESS – software to calculate the relative abundance of proteins in the sample; may also be run in label-free mode
  • ASAPRatio – Automated Statistical Analysis on Protein Ratios
  • Libra – N-channel quantification software for isobaric labeling (TMT, iTRAQ, IBT, etc)
  • StPeter – Label-free protein quantification
• Visualization and Interfaces
  • Pep3D – viewer for LC-MS and LC-MS/MS runs
  • ShowXIC – view extracted (or total) ion chromatograms
  • PepXMLViewer – peptide dataset interaction
  • ProtXMLViewer – protein dataset interaction
  • MADCAPS – protein sequence alignment, mapping of identified peptides, and in-silico digestion
  • CUVALibRe – examine isobarically labelled data analyzed by Libra
• Miscellaneous
  • ProteoMapper – map peptide sequences to proteins; supports variants via PEFF format, and wildcards
  • SubsetDB – FASTA manipulation
• Interpretation
  • SBEAMS – Systems Biology Experiment Analysis Management System
  • Cytoscape – platform for visualizing and integrating molecular interaction networks

PeptideAtlas

PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several dozen other organisms and tissues, and searched using the latest search engines and protein sequences. All results of sequence and spectral library searching are subsequently processed through the Trans Proteomic Pipeline to derive a probability of correct identification for all results in a uniform manner to insure a high quality database, along with false discovery rates at the whole atlas level. Results may be queried and browsed at the PeptideAtlas web site. The raw data, search results, and full builds can also be downloaded for other uses.

SRMAtlas

The SRMAtlas is a compendium of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. It results from high-quality measurements of natural and synthetic peptides conducted on a triple quadrupole mass spectrometer, and is intended as a resource for selected/multiple reaction monitoring (SRM/MRM)-based proteomic workflows.

SWATHAtlas

The SWATHAtlas project makes available spectral libraries that are designed to aid in SWATH™ data processing for several species. It enables the ability to query and explore a set of seed datasets on-line, custom analysis of SWATH™ datasets in the repository. Users have the option to analyze and repair spectral ion libraries using the DIALib-QC tool.

Quetzal

Quetzal is a peptide fragment ion spectrum annotation tool to assist researchers in annotating and examining tandem mass spectra to ensure that they correctly support study conclusions. Quetzal annotates spectra using the new Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) mzPAF standard for fragment ion peak annotation. Quetzal includes a Python-based codebase, a web-service endpoint that provides annotation services, and a user-friendly web-based application for annotating spectra and producing publication-quality figures.