Proteomics Tools

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This is a list of Proteomics tools created by the NBIC BioAssist task force

Please feel free to add your tools and your experiences! You can make a new page about a tool if you want to describe it in some detail.

Category Package Description Performance/experience
Peptide identification (DB) Peppy Peppy performs all necessary tasks of six-frame proteogenomic searches of LC-MS/MS data on a genome. This includes genome segmentation, translation and FDR analysis -- all done automatically with no need for intervention. Six-frame searches allow the discovery of novel proteins or protein forms that are specific to disease. None
Infrastructure Data Analysis Framework DAF or Data Analysis Framework is a software package developed in the NBIC BioAssist Proteomics task force to enable transparent distributed computations on the grid or a cluster. This Analysis Framework was developed to fulfill the computational and data analysis requirements of life science data in general and proteomics in particular. None
Framework msCompare MS-compare is a framework that can run multiple tools from different sources in a multiplicative comparison so that you can find the combination that gives the best results for your data. The framework contains a system of file conversion programs. Written by Berend Hoekman (NBIC BioRange)
Conversion Expecter A graphical user interface for the conversion of MS/MS spectra and peptide identifications into PrideXML None
Identification Phenyx MS/MS protein identification software, available for Linux and Windows, Phenyx is scallable in terms of computing nodes and supports many input data formats. Search results can be exported from MS Excel to XML formats
Framework TPP The Trans-Proteomic Pipeline (TPP) includes all of the steps of the ISB MS/MS analysis pipeline, after the database search. Most users will only need to download the TPP distrubtion. None
Framework CPAS Computational Proteomics Analysis System. CPAS is a suite of database and analysis tools, originally developed in the FHCRC CPL, that manages proteomics experimental workflows and integrates database search algorithms (X!Tandem, Mascot, and Sequest) and Institute for Systems Biology (ISB) data management tools. None
Framework Labkey Server Derived from CPAS. LabKey Server incorporates a robust data pipeline for importing and processing mass spectrometry data from raw and mzXML data files. The pipeline manages the chain of processing steps needed to infer protein identifications and expression levels from the output of a mass spec machine. The pipeline integrates with leading search engines including X!Tandem™, Mascot™, and Sequest™. The pipeline also integrates PeptideProphet™, ProteinProphet™ , and XPRESS™, all components of the Trans Proteomic Pipeline™ from the Institute for Systems Biology. None
Framework Prequips a Java-based, modular software platform for integration, visualization and analysis of complex proteomics mass spectrometry data sets. The software has a graphical user interface and provides access to data produced by data analysis pipelines such as the Trans-Proteomic Pipeline. It bridges the gap between data processing pipelines and high-level analysis tools used in Systems Biology. None
Framework OpenMS/TOPP OpenMS is an open-source software C++ library for LC/MS data management and analyses. It offers an infrastructure for the development of mass spectrometry related software. OpenMS is free software available under the LGPL. OpenMS will be compatible with the upcoming Proteomics Standard Initiative (PSI) formats for MS data. We also try hard to keep up to date with code documentation and making it easy to use OpenMS. None
Framework ProteoWizard ProteoWizard is a modular and extensible set of open-source, cross-platform tools and software libraries for proteomics data analysis. The libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations. None
Framework XCMS XCMS is an LC/MS-based data analysis approach which incorporates novel nonlinear retention time alignment, feature detection, and feature matching. Without using internal standards, the method dynamically identifies hundreds of endogenous metabolites for use as standards, calculating a nonlinear retention time correction profile for each sample. Following retention time correction, the relative metabolite ion intensities are directly compared to identify changes in specific endogenous metabolites, such as potential biomarkers. Written in R. None
Framework Mass++ Mass++ is software for mass spectrometer. The software can read and process various MS data format. Mass++ is a plug-in style software. So users can customize Mass++ depending on their purposes such as addition of new functions and deleting unnecessary functions to increase pefomance without editing Mass++ source code. mail list None
Framework mspire mspire - 'Mass Spectrometry Proteomics in Ruby' is a collection of tools for working with MS proteomics data in ruby. It seeks to provide support for open standards (e.g., parsers for mzData, mzXML, Peptide/Protein Prophet and the TPP) and contribute other useful functionality for working with mass spectrometry data in ruby. None
Framework proteios A multi-user platform for analysis and management of proteomics data. Licensed under GPLv2 None
Framework msInspect sInspect allows you to process and view mass spectrometry (MS1) data in an mzXML file. You can use msInspect's built-in tools to inspect data, identify peptide features, generate peptide arrays using data from multiple runs, and export data to external applications for further analysis and collaboration. msInspect is an open source application written in Java. None
Framework Insilicos Proteomics Pipeline The Insilicos platform is a flexible, high-throughput system for analysis of biological samples and identification of biomarkers. Uniquely, the Insilicos platform can achieve nearly complete coverage of biomarker proteins in complex samples. None
Framework PatternLab a “simple to use” yet efficient and panoptic software to addresses shotgun proteomic data analysis that was initialy published in BMC Bioinformatics in 2008. None
Framework Corra s a single, user-friendly, informatic framework, that is simple to use and fully customizable, for the enabling of LC-MS-based quantitative proteomic workflows of any size, able to guide the user seamlessly from MS data generation, through data processing, visualization, and statistical analysis steps, to the identification of differentially abundant or expressed candidate features for prioritized targeted identification by subsequent MS/MS (also in SourceForge) Conclusion
Framework TIQAM TIQAM (Targeted Identification for Quantitative Analysis by MRM) is developed as a suite of software tools to support targeted indentification and quantification using multiple reaction monitoring (MRM) mass spectum technology. More specifically, TIQAM software provided user friendly interfaces to assist process of peptide selection, transition generation and validation. (See also poster) None
Framework Scaffold Visualize and Validate Complex MS/MS Proteomics Experiments
Framework PEAKS PEAKS is a suite of tools, each specifically designed to solve a unique problem. One tool, or a selection of tools from the PEAKS family will suit your environment.
Framework Rosetta Biosoftware The Rosetta Elucidator® system is a data management and analysis solution for mass spectrometry data, and supports multiple workflows (label-free, SILAC, and shotgun proteomics and metabolomics), data from different instruments, and integration with different search engines for accurate peptide and protein identifications.
Framework ProteinPilot For ABI
Framework ProteinCenter From Proxeon (formerly Protana). ProteinCenter™ is a web-based data interpretation tool that enables scientists to compare and interpret data sets in minutes instead of months.
Framework ViPDAC Virtual Proteomics Data Analysis Cluster. It runs on Amazon Elastic Cloud, have to run an instance in Amazon but the source code is available
Mass Accuracy MaxQuant MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high resolution MS data. None
Mass Accuracy VIPER VIPER (Visual Inspection of Peak/Elution Relationships) can be used to visualize and characterize the features detected during LC-MS analyses. It is primarily intended for processing deisotoped data from high mass measurement accuracy instruments (e.g. FT, TOF, or Orbitrap) and comparing the features found to a list of expected peptides (aka mass and time (MT) tags), as practiced by the AMT tag approach. None
Mass Accuracy DTASuperCharge A component of MSQuant. It creates MGF peak lists from raw files, retaining the retention time and scan number information required by MSQuant. It requires Xcalibur (including the XDK) and Microsoft .NET 2.0 or later to be installed. It is not clear whether it can be made to run stand-alone, on a system without a full installation of Xcalibur. None
Peptide identification (DB) Mascot Mascot is a mass spectral search algorithm that uses mass spectrometry data to identify proteins from primary sequence databases.
The most popular search engine.
Peptide identification (DB) Sequest SEQUEST 3G is the latest, next-generation SEQUEST standard specifically developed and optimized for translational proteomic applications involving phosphorylation and other post-translational modifications (PTMs). SEQUEST 3G defines a single common standard for similarity scores, search parameters and statistics, and input/output file formats and is ideal for noisy and poor quality spectra.
Peptide identification (DB) Phenyx henyx enables proteomics scientists to 1) submit MS/MS data and identify peptides and proteins 2) visualize and evaluate results using various dynamic views, 3) manually validate results and compare Phenyx runs and those of other database search engines (like Mascot, SEQUEST and X!Tandem), 4) perform quantitative analysis with the Phenyx quantitation module, and 5) export results and generate reports into various formats and integrate Phenyx into your laboratory workflow.
Peptide identification (DB) Paragon
Peptide identification (DB) Byonics combines traditional MS/MS matching with de novo sequencing.
Peptide identification (DB) X!Tandem This software has a very simple, sophisticated application programming interface (API): it simply takes an XML file of instructions on its command line, and outputs the results into an XML file, which has been specified in the input XML file. Unlike some earlier generation search engines, all of the X! Series search engines calculate statistical confidence (expectation values) for all of the individual spectrum-to-sequence assignments. None
Peptide identification (DB) OMSSA 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. OMSSA scores significant hits with a probability score developed using classical hypothesis testing, the same statistical method used in BLAST. OMSSA is free and in the public domain. None
Peptide identification (DB) InsPecT None
Peptide identification (DB) SpectrumMill None
Peptide identification (DB) Crux None
Peptide identification (DB) MyriMatch None
Peptide identification (DB) PepSlice None
Peptide identification (De novo) PEAKs
Peptide identification (De novo) Lutefisk Lutefisk is software for the de novo interpretation of peptide CID spectra None
Peptide identification (De novo) MSNovo None
Peptide identification (De novo) EigenMS None
Peptide identification (De novo) NovoHMM None
Peptide identification (De novo) Audens None
Peptide identification (De novo) RAId None
Peptide identification (lib match) SpectraST (part of TPP) SpectraST (short for "Spectra Search Tool" and rhymes with "contrast") is a spectral library building and searching tool designed primarily for shotgun proteomics applications. None
Peptide identification (lib match) BiblioSpec BiblioSpec is a suite of software tools for creating and searching MS/MS peptide spectrum libraries. BiblioSpec is available free of charge for noncommercial use through an interactive web-site None
Raw Data Xcalibur Thermo. Windows application to control the instrument and basic data processing. Plays well with Sequest and TPP None
Raw Data Bioworks Thermo. Based on Xcalibur. More advanced data processing. New version is called ProteomeDiscoverer. None
Raw Data Analyst. ABI None
Raw Data MassLynx. Waters None
Raw Data MassHunter. Agilent None
Raw Data DataAnalysis. Bruker None
Raw Data ProteomeDiscoverer Thermo. New version of Bioworks None
Raw Data / Conversion X2XML converts different RAW files to mzXML None
Results processing Pride Converter Converts different peak list files and results different search engine results files to PRIDE XML. None
Results processing Mascot parser From matrix science None
Results processing OMSSA parser MSSA Parser is a Java based parser for OMSSA (Open Mass Spectrometry Search Algorithm) omx files. Initially created by Steffen Huber for Prof. Dr. Albert Sickmann under the guidance of Dr. Lennart Martens, and further developed by Harald Barsnes, including the addition of a simple, lightweight and platform independent OMSSA Viewer. None
Results processing Mascot datfile Parses Mascot output None
Results processing MassSieve MassSieve is a free tool for parsing MS/MS search engine results. It allows you to combine the results of several searches into a single experiment and parsimoniously separate the results. Many different experiments can be loaded and the results can be compared and contrasted. None
Quantitation MsQuant MSQuant is a tool for quantitative proteomics/mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change. MSQuant’s main purpose is to make quantitation of proteins and peptides possible in the area of mass spectrometry/proteomics (science/analytical chemistry/molecular biology). E.g. an experiment where one heavy isotope-labelled sample from treated cells is compared to unlabelled, untreated cells to give quantitative answers about cellular processees. None
Quantitation MaxQuant MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high resolution MS data None
Quantitation Census A quantitative analysis software tool for mass spectrometry-based proteomics. Sung Kyu Park, John D Venable, Tao Xu, John R Yates III, Nature Methods, 2008, 5, 319-322. None
Protein Inference ProteinProphet roteinProphet(TM) automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST. Importantly, it addresses two critical issues: (1) Peptides corresponding to 'single-hit' proteins (those to which no other peptides correspond) are less likely to be correct that those corresponding to 'multi-hit' proteins. (2) Many peptides are present in more than a single database protein entry. None
Protein Inference IDPicker Accurate, transparent, and parsimonious protein assembly for MS/MS search results None
Protein Inference Combyne Byne integrates ByOnic's peptide identifications into a list of proteins, ranked by confidence (p-value). The combination of ByOnic and ComByne greatly outperforms current standards, such as Mascot and ProteinProphet. ByOnic typically identifies 50 to 100 percent more spectra. On complex samples with many low-abundance proteins, ComByne then identifies 30 to 50 percent more proteins. None
Protein Inference EBP Empirical Bayes Protein identification algorithm. EBP is the first generally applicable protein identification method that can combine the results of multiple search algorithms and replicated LC MS/MS experiments. EBP is compatible with the Trans-Proteomic Pipeline (TPP) from and can be used as an alternative to the ProteinProphet algorithm. None

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