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    Standards in proteomics research

    Analysis of proteomes

    Proteome Analyst

    online tool to rapidly analyze proteins. Using machine learning technologies, PA can accurately predict the subcellular localization and high level function of user submitted proteins.


    Comprehensive subcellular location analysis for all E. coli proteins, created using the publicly available prediction algorithms together with experimental data and in-house manual curation.


    Predicted subcellular localization for entire proteomes (Human, Arabidopsis, Fruit Fly, Worm, & Yeast)

    Interactomics tools


    Literature navigation tool for protein interactions

    Software/Search engines


    Bioinformatics solution for storage, integration and analysis of quantitative proteomics data. It is based on a core data model describing fundamentals such as experiment description and identified proteins. The extended data models are built on top of the core data model to capture more specific aspects of the data. A number of public databases and bioinformatical tools have been integrated giving the user access to large amounts of relevant data. A statistical and graphical package, R, is used for statistical and graphical analysis. The current implementation handles quantitative data from 2D gel electrophoresis and multidimensional liquid chromatography/mass spectrometry experiments. Available for download at SourceForge.[pubmed]


    The Computational Proteomics Analysis System (CPAS) integrates many openly available software infrastructure for systematic proteomic data analyses and data management into a single Web-based platform for mining liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic experiments. CPAS incorporates several tools currently used in proteomic analysis, including the X! Tandem search engine and the PeptideProphet and ProteinProphet data mining tools. The application is built on the open-source LabKey platform, an extensible architecture for developing high-throughput biological applications. The CPAS analysis pipeline acts on data in standardized file formats, so that researchers may use CPAS with other search engines, including Mascot or SEQUEST, that follow a standardized procedure for reporting search engine results.[pubmed]


    Integrates complex datasets with 3D virtual world platforms. The platform supports some advanced scientific operations, especially relevant for the field of genetic analysis, such as overlay of mass spectrometry and/or microarray information onto images of specimens; integration with all the major proteomics and genomics databases; and import of molecular models into the virtual space

    LIMS for 2-DGE-based proteomics workflow (open source)

    Main features of its design are compactness, flexibility and connectivity to public databases. It supports the handling of data imported from mass spectrometry software and 2-D gel image analysis software. The LIMS is equipped with the same input interface for 2-D gel information as a clickable map on public 2DPAGE databases. The LIMS allows researchers to follow their own experimental procedures by reviewing the illustrations of 2-D gel maps and well layouts on the digestion plates and MS sample plates. [pubmed]


    The MAss SPECTRometry Analysis System is a platform for management and analysis of proteomics LC-MS/MS data. MASPECTRAS is based on the Proteome Experimental Data Repository (PEDRo) relational database schema and follows the guidelines of the Proteomics Standards Initiative (PSI). Analysis modules include: 1) import and parsing of the results from the search engines SEQUEST, Mascot, Spectrum Mill, X! Tandem, and OMSSA; 2) peptide validation, 3) clustering of proteins based on Markov Clustering and multiple alignments; and 4) quantification using the Automated Statistical Analysis of Protein Abundance Ratios algorithm (ASAPRatio).The system provides customizable data retrieval and visualization tools, as well as export to PRoteomics IDEntifications public repository (PRIDE). [pubmed]


    tool to visualize theoretical distributions of peptide pI on a given pH range, and proposes a fractionation scheme that generates fractions with similar peptide frequencie


    Web application integrating electrophoretic and mass spectral data from proteome analyses into a relational database. The graphical web-interface allows users to upload, analyse and share experimental proteome data. It offersthe possibility to query all previously analysed datasets and can visualize selected features, such as the presence of a certain set of ions in a peptide mass spectrum, on the level of the two-dimensional gel. Download: from Requires a web server that runs PHP 5 ( and MySQL. [pubmed]


    Using a web portal, ProSight PTM allows identification and characterization of intact proteins (and their post- translational modifications, PTMs) using the Top-Down Approach. This site has many tools and graphical features to facilitate analysis of single (recombinant) proteins, proteins in mixtures, and proteins fragmented in parallel. Our ProSight Warehouses are annotated with all known post-translational modifications (PTMs), alternative splicing events and single nucleotide polymorphisms (SNPs) using the technique of Shotgun Annotation developed in the Kelleher Research Group. ProSightPTM is the only proteomics software that allows the user to search their tandem MS data against proteome warehouses containing the known biological complexity present in UniProt.


    Label Free Quantitation -Support for replicate analyses View protein expression plots


    Workflow-optimized laboratory information management system for 2-D electrophoresis-centered proteomics

    Proteincenter (Proxeon)

    Compare multiple protein lists and get to biology of proteomics data

    Rosetta Biosoftware

    Informatics Solutions for Life Science Research

    Proteios SE

    Proteios SE (or ProSE) is meant to be installed on a local server in a proteomics laboratory. The server is accessed using any web browser using personal login accounts with administrated access levels. With his or her own account, a user can enter data into the database, group experiments together into projects, run protein identification engines and other analysis tools. Users can choose to share almost any database item (e.g. samples, data, experiments, files, etc) with other users to facilitate online collaboration.


    PRoteomics IDEntifications database


    Proteomics, Protein ID & Characterization, ESI-MS, 2DE


    A tool which takes advantage of the Gene Ontology (GO) to extract the proteinsΥ main attributes.


    A search engine for cross-linked peptides from complex samples. Presented at the ASMS07;published in Nature Methods. xQuest works with small and large protein databases and features flexible fragment ion assignment, advanced scoring, and interactive evaluation tools.

    ESI vs MALDI


    GE/Thermo poster

    General Mass Spectrometry Sites

    Vanderbilt Mass Spectrometry Center Site

    Comprehensive site covering most aspects of mass spectrometry.  It includes leading references to the literature

    Mass Spectrometry Web Address

    Mass Spectrometry data analysis tools


    Site includes useful programs for analyzing the mass spectra of proteins and peptides.

    Sheffield ChemPuter:  Isotope Patterns Calculator

    Site predicts isotope pattern based on molecular formula.

    Virtual Proteomics Data Analysis Cluster

    ViPDAC is a set of free tools to be used in combination with Amazon's inexpensive "cloud computing" service, which provides the option to rent processing time on its powerful servers; and free open-source software from the National Institutes of Health (NIH) and the University of Manitoba.


    Little Encyclopedia of Mass Spectrometry

    Site with numerous definitions of terms used in mass spectrometry


    Companies resources

    Register for free resources including: Literature, CD, Posters

    Proteomics 2.0

    A blog and discussion forum for tools, insights and approaches for the next generation of proteomics analysis.

    Industry links

    The Hellenic Biocluster

    Collaboration Tools

    Convert PDF to Word


    280 Slides-Presentations (read review)

    Micogo-online collaboration (read review)