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| About On-line Tools This is a listing of freely available, on-line proteomics tools. It is designed for users who simply want to know what tools they can use to help solve their problems. The tools are broken down in to arbitrary categories based on what users have been asking for. Please let us know if you have any suggestions for this page. |
INTERACThttp://tools.proteomecenter.org/Interact.phpINTERACT was developed to address the need to curate large datasets (from tens to hundreds of LC-MS/MS runs covering multiple tens of thousands of MS/MS spectra). INTERACT allows a user to quickly interrogate such large datasets with total flexibility including filtering, sorting, grouping, and highlighting of the data.
Out2Summaryhttp://tools.proteomecenter.org/out2summary.phpConvert Sequest and TurboSequest *.out files into a single HTML-Summary file ready for use with INTERACT.
Trans-Proteomic Pipelinehttp://tools.proteomecenter.org/TPP.phpThe TPP includes all steps of the ISB MS/MS analysis pipeline after results of database search: Peptide validation, Peptide quantitation, Protein identification, and Protein quantitation. XML-based, the TPP is easily extensible to additional search engines and analysis modules.
Scaffold - Free Viewerhttp://www.proteomesoftware.com/Scaffold/Scaffold_viewer.htmView .sfd files created with the Scaffold MS/MS analysis platform from Proteome Software.
PrestOMIChttp://code.google.com/p/prestomic/wiki/PrestOMICAn open-source suite of tools for storing data in a PostgreSQL database and for presenting the data in a user-friendly format via a browser.
Human ProteinpediAhttp://www.humanproteinpedia.orgHuman ProteinpediA is a community portal for sharing and integration of human protein data. It allows research laboratories to contribute and maintain protein annotations. Human Protein Reference Database (HPRD) integrates data, that is deposited in Human ProteinpediA along with the existing literature curated information at the context of an individual protein. All the public data contributed to Human ProteinpediA can be queried, viewed and downloaded.
Microbial Protein-Protein Interaction Database - MiPPIhttp://mippi.ornl.govA Research Program for Identification and Characterization of Protein Complexes
Integrated Post-Genomic Data Resourcehttp://www.proteomicsresource.org/The Biodefense Proteomics Catalog is a searchable directory of data and reagent information generated by the Proteomics Research Centers and available to the research community. A search yields information about organism studies, experimental data, research protocols, research reagents, identified proteins, publications and proteomes. It includes visualization and analysis tools.
Mascot File Parsing and Quantificationhttp://mfpaq.sourceforge.net
MFPaQ (Mascot File Parsing and Quantification) is a new software developed at the IPBS (Institut de Pharmacologie et de Biologie Structurale, Toulouse, France) proteomics platform and dedicated to parse, validate, and quantify proteomics data. It allows fast and user-friendly verification of Mascot result files, as well as data quantification from an experiment performed by isotopic labeling using either ICAT or SILAC methods.
This new tool provides a convenient interface to retrieve Mascot protein lists, sort them according to Mascot scoring or to user-defined criteria based on the number, the score and the rank of identified peptides, and to validate the results. The software extracts quantitative data from raw files obtained by nanoLC-MS/MS, calculates peptide ratios, and generates a non-redundant list of proteins identified in a multi-search experiment with their calculated averaged and normalized ratio.
It is based on three modules, the Mascot File Parser (MFP) Module, the quantification module and a third module designed for differential analysis, in which validated protein lists are compared. The input of the MFP module is a list of mascot .dat files and the input of the quantification module is a list of .wiff files generated by Analyst QS on a Qstar instrument (coming soon: version of the quantification module compatible with other mass spectrometers).
The next section provides details about the downloading and installation processes.
Quanthttp://www.biomedcentral.com/1471-2105/8/214
Mass spectrometry based quantification of peptides can be performed using the iTRAQ reagent in conjunction with mass spectrometry. This technology yields information about the relative abundance of single peptides. A method for the calculation of reliable quantification information is required in order to obtain biologically relevant data at the protein expression level.
RAP, JRAP, RAMPhttp://tools.proteomecenter.org/rap.phpmzXML data parsers.
T2Extractor 2.0http://www.proteomecommons.org/archive/1114637208624/A JDBC-based tool that can access the ABI 4700's database and can extract T2D files as well as peak lists.
Peak List Conversion Utility (Java Web Start)http://www.proteomecommons.org/current/531/ConvertPeakList.jnlpThe ProteomeCommons.org IO Framework's tool for converting peak list and spectrum files between different formats. The tool can also merge multiple peak lists in to a single concatinated peak list. The tools uses Java Web Start and runs locally on your computer.
mzXML2Otherhttp://www.proteomecommons.org/current/522/Converter from mzXML to sequest dta, mascot generic and micromass pkl formats. This is based on Xerces-c parser
ReAdWhttp://tools.proteomecenter.org/ReAdW.phpThermoFinnigan Xcalibur format to mzXML converter.
MassWolfhttp://tools.proteomecenter.org/MassWolf.phpMicromass MassLynx format to mzXML converter.
mxStarhttp://tools.proteomecenter.org/mzStar.phpSCIEX/ABI Analyst format to mzXML converter.
Prototype C-Sharp Converterhttp://tools.proteomecenter.org/PrototypeCSharpConverter.phpDriven in large part by recent rapid advances in proteomics, the need for a vendor-independent means of accurate and robust representation and exchange for mass spectroscopy data has become apparent. Two major formats have emerged: mzXML, developed at the Institute for Systems Biology (ISB) and highly integrated into the Trans-proteomic Pipeline (TPP) software tool chain, and mzData, developed by the HUPO Proteomics Standards Initiative (PSI) MS working group. Both the proteomics research community and instrument vendors would clearly benefit from a single standard. Recently, the PSI-MS group, the ISB, and instrument vendors collaborated to produce a draft specification for a unified data format, tentatively titled dataXML, with the intention of combining the best features of the mzXML and msData formats. Here, we present work towards an open-source reference implementation for converters from raw data to both the mzXML and dataXML formats, which could be extended to other formats as well.
Mascot Peptide Mass Fingerprinthttp://www.matrixscience.com/cgi/search_form.pl%3fFORMVER=2%26SEARCH=PMFA free on-line version of Matrix Science's Mascot MS fingerprint search engine. You can select from a variety of different sets of known protein sequences to search against.
Aldentehttp://www.expasy.org/tools/aldente/Aldente is a tool to identify proteins from PMF data. This new, fast and powerful PMF tool uses the Hough transform to determine the mass spectrometer deviation, to realign the experimental masses and to exclude outliers. Some unique advantages and features: It extensively uses the Swiss-Prot annotations (PTM, alternative splicing, etc.) and it is completely interconnected with other ExPASy proteomics tools, offering the functionality of protein characterization as part of the identification procedure. The scores may be tailored by fully customizable parameters. Besides from the usual chemical amino acid modifications, it considers also any user-defined modifications, such as alkylation products on cysteine residues, with the possibility to define their contribution to the score. For more information about Aldente see the documentation: http://www.expasy.org/tools/aldente/help.html
PROCLAMEhttp://proclame.unc.edu/A Web-based application that uses whole-protein masses determined by mass spectrometry to identify putative co- and posttranslational proteolytic cleavages and chemical modifications. The protein cleavage and modification engine (PROCLAME) requires as input an intact mass measurement and a precursor identification based on peptide mass fingerprinting or tandem mass spectrometry.
Genome-based Peptide Fingerprint Scanning (GFS)http://gfs.unc.edu/Genome-based fingerprint scanning (GFS) is a recently reported method developed by the Giddings lab (Giddings et al., 2003) that maps peptide mass fingerprint data directly to raw genomic sequence, enabling rapid, low-cost identification of proteins in genomes for which annotation is lacking. The program takes as input an experimentally obtained peptide mass fingerprint, scans a genome sequence of interest, and outputs the most likely regions of the genome from which the mass fingerprint is derived. The software first generates a theoretical mass list by translating the genome of interest in 6 reading frames (3 each on the forward and reverse strands) and digesting the resulting proteins in silico according to cleavage rules associated with the specified protease (trypsin in this case). The algorithm then finds matches (within a given mass tolerance) between these theoretical masses and the input experimental masses.
Human ProteinpediAhttp://www.humanproteinpedia.orgHuman ProteinpediA is a community portal for sharing and integration of human protein data. It allows research laboratories to contribute and maintain protein annotations. Human Protein Reference Database (HPRD) integrates data, that is deposited in Human ProteinpediA along with the existing literature curated information at the context of an individual protein. All the public data contributed to Human ProteinpediA can be queried, viewed and downloaded.
TheGPM (Human)http://human.thegpm.orgA web interface to the XTandem search engine that will search your MSMS data against known human protein sequences.
TheGPM (Prokaryotes)http://bacteria.thegpm.orgA web interface to the XTandem search engine that will search your MSMS data against known prokaryotic protein sequences.
TheGPM (Plant UniGene)http://plant.thegpm.orgA web interface to the XTandem search engine that will search your MSMS data against known plant protein sequences.
TheGPMhttp://www.thegpm.orgA web interface to the XTandem search engine that will search your MSMS data against known protein sequences.
Suggested Citation: TANDEM: matching proteins with mass spectra, Robertson Craig and Ronald C. Beavis, Bioinformatics, 2004, 20, 1466-7.
TheGPM (Xenopus)http://xenopus.thegpm.orgA web interface to the XTandem search engine that will search your MSMS data against known Xenopus protein sequences.
TheGPM (T. brucei)http://tb.thegpm.orgA web interface to the XTandem search engine that will search your MSMS data against T. brucei protein sequences.
Mascot MS/MS Ion Searchhttp://www.matrixscience.com/cgi/search_form.pl%3fFORMVER=2%26SEARCH=MISA free on-line version of Matrix Science's Mascot search engine. You can choose to search against a number of different known protein data sets.
The Open Mass Spectrometry Search Algorithm (OMSSA)http://pubchem.ncbi.nlm.nih.gov/omssa/index.htmA free, public-domain MSMS search engine sponsored by the NCBI.
Phenyx Web Interface (PWI)http://phenyx.vital-it.ch/pwi/login/login.jspA free on-line version of GeneBio's software platform for the identification and characterization of proteins and peptides from MS data.
PeptideProphethttp://tools.proteomecenter.org/PeptideProphet.phpA tool for validating peptide identifications made by tandem mass spectrometry (MS/MS) and database searching; probabilities are assigned to the peptide identifications made by programs like SEQUEST or MASCOT.
ProteinProphethttp://tools.proteomecenter.org/ProteinProphet.phpA statistical model for validation of peptide identifications at the protein level.
InsPecT: high-throughput identification of peptide mass spectrahttp://peptide.ucsd.edu/inspect.htmlInsPecT performs high-throughput identification of peptide mass spectra with an emphasis on efficiently and confidently identifying modified peptides. Modifications include in vivo post-translational modifications such as phosphorylation, as well as in vitro chemical damage. We are able to search and score a broad range of modifications in a single search, or even identify unanticipated changes such as point mutations.
VEMS 3.0http://yass.sdu.dk/VEMS Virtual Expert Mass Spectrometrist is a program for integrated proteome analysis. VEMS offers processing of raw data, MSMS database searches with many variable modifications, correlation of spectra for finding more hits, validation functions, data mining functions, quantitative time studies both with and without stable isotope labelling, clustering of quantitative results and export of data in Proteios XML standard format. The functions are included in one user friendly executable file. The VEMS application also works as an interface to other programs such as blast, Lutefisk and a sequence analysis tool.
Sequit! 4.0 Onlinehttp://www.proteomefactory.com/sub/s505-Sequit.htmSequit! 4.0 is a De Novo Peptide Sequencing Tool using MSMS fragment spectra for peptide and protein identification. It is online available as well as a commercial local version which runs under Windows 2000/XP. The local version allows batch analyses of MSMS spectra and automatic submission to BLAST search.
Pep_Probehttp://bart.scripps.edu/public/search/pep_probe/search.jspAn MSMS search engine based from the Yates lab described in the following publications. Central Limit Theorem as an Approximation for Intensity-Based Scoring Function Sadygov, R.; Wohlschlegel, J.; Park, S. K.; Xu, T.; Yates, J. R., III Anal. Chem.; (Article); 2006; 78(1); 89-95. A Hypergeometric Probability Model for Protein Identification and Validation Using Tandem Mass Spectral Data and Protein Sequence Databases Sadygov, R. G.; Yates, J. R., III Anal. Chem.; (Article); 2003; 75(15); 3792-3798.
Popitamhttp://www.expasy.org/tools/popitam/Popitam, a new tool available from the ExPASy proteomics website, identifies and characterizes peptides with unexpected modifications (e.g. mutations or post-translational modifications) from peptide fragment fingerprinting (MS/MS) data.
Scaffold from Proteome Softwarehttp://www.proteomesoftware.com/Proteome_software_prod_Scaffold.htmlScaffold is a post MS/MS search tool, but has X! Tandem, an open MS/MS search tool imbedded in it. With Scaffold you can easily see your data from multiple points of view, compare samples easily, and with our free viewer, share and publish your results with ease.
PEAKS Onlinehttp://www.bioinformaticssolutions.com:8080/peaksonline/PEAKS confidently identifies proteins with the aid of a protein sequence database. The PEAKS approach to protein database searching is unique; it differs from conventional approaches in that it uses de novo sequences to help out in the protein identification process. This approach is shown to have equivalent result quality as compared to the leading traditional approach, but with fewer false positives. Most find it useful for dealing with non-standard samples.
Genome Annotating Proteomic Pipeline (GAPP)http://www.gapp.info/GAPP - a totally automated publicly available software pipeline for the identification of peptides and proteins from human proteomic tandem mass spectrometry data. Feel free to browse the results repository or register to automatically process your own data.
Insilicos Proteomics Pipeline (IPP)http://www.insilicos.com/IPP.htmlIPP is a proteomics data analysis platform that contains tools for protein identification and quantification developed form the Institute for System Biology's (ISB) Trans-Proteomic Pipeline (TPP). IPP includes PeptideProphet, ProteinProphet, ASAPRatio, XPRESS and Libra in a software package optimized for performance, ease of use and quick results.
Suggested Citation: Insilicos LLC, Seattle, WA
PANORAMICShttp://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2007/79/i10/abs/ac070202e.htmlA peptide identification tool that uses a probability model for determining the likelihood that peptides are correctly assigned to proteins. This model derives consistent probability estimates for assembled proteins. The probability scores make it easier to confidently identify proteins in complex samples and to accurately estimate false-positive rates.
GNU polyxmass projecthttp://www.polyxmass.org/This is a feature-rich software suite for predicting and analyzing mass spec data on any polymer sequence of any polymer type.
Wildcat Toolbox: Perl scripts for mass spectral data analysis and sortinghttp://proteomics.arl.arizona.edu/perl.htmlA collection of perl scripts for manipulating fasta files and mass spectral data, particularly DTA files.
GPMDB-UShttp://gpmdb-us.thegpm.orgThis is a US mirror of the GPMDB server. The GPMDB server is a data repository for the GPM servers. Protein identifications and MSMS to peptide matches can be compared to previously identified data.
GPMDB-based Include List Generator (Click to Run)http://www.proteomecommons.org/current/559/IncludeListGenerator.jnlpThis is a tool originally developed for aiding in MALDI TOF/TOF data post processing. For weakly identified proteins, e.g. one hit wonders, we wanted a way to generate an included list of all other peptides that should be identified for the weakly identified protein. The masses for those peptides would then be made in to an include list, and the MALDI plate would be reanalyzed looking for those specific peptides. The include list is nothing more than a plain text file with the masses of the expected peptides. The trick to this tool is having a good way to find other peptides that should be seen. To do this we mine information about what peptides others have observed directly from the GPMDB. Additionally, the tool allows you to restrict peptides based on give mass ranges or theoretical tryptic peptides. The tool also allows you to modify peptides using any potential modification or any arbitrary mass shift.
Make2D-DB IIhttp://www.expasy.org/ch2d/make2ddb/Make2D-DB II is a tool to create, convert, interconnect and keep up-to-date 2-DE databases. It has been designed to ensure high consistency of data. It allows dynamic interconnection between any numbers of similar remote databases and offers many other features, including automatic data updates related to external data, dynamic cross-references to similar databases, intuitive search engine and data visualization combined with exports in various formats.
Illinois Bio-Grid Mass Spec Toolkithttp://gridweb.cti.depaul.edu/twiki/bin/view/IBG/MassSpecToolkitThis project entails developing solutions for anaylsis of Mass Spectrometry data. This includes analysis tools such as SpectralMatch and HDXRates but also a set of C libraries which gives IO and data structure support to developers. Most of the current code is written in C but we do have some functionality written in Java which correlates to our IBG Desktop project.
MassSieve: A New Tool for Mass Spectrometry-Based Proteomicshttp://www.proteomecommons.org/dev/masssieve/
The success of peptide sequence assignment algorithms such as OMSSA and Mascot for mass spectrometry has led to the need for a tool to evaluate the results. DBParser is such a software tool, previously developed by the Laboratory of Neurotoxicology (LNT) lab for this purpose. Its value for parsimonious analysis of proteins associated with experiments has led to its use for analyzing larger datasets than initially anticipated (hundreds of data files with millions of spectra). MassSieve builds on this experience and is designed as open-source protein assignment software that can be scaled to apply parsimony principles to very large experiments without dataset size limitations. In addition it allows a more interactive view of the results.
Adipose Proteome Databasehttp://proteome.biochem.mpg.de/adipoIn our 3T3-L1 adipocyte proteome database, we provide protein and peptide list of the adipocyte with their subcellular localization information. Using the database, it is easy to search proteins or peptides by IPI accession number, protein name, description, subcellular location and peptide sequence, and also do batch search.
Organellar Map Databasehttp://proteome.biochem.mpg.de/ormd/In our Organellar Map Database, we provide protein and peptide list with organellar map information. Use the database, it is easy to search proteins or peptides by IPI accession number, Uniprot accession number, protein name, description, location and peptide sequence, and also do batch search.
Body Fluid Database - Seminalhttp://proteome.biochem.mpg.de/seminal/In our bodily fluid protein database, we provide protein and peptide list of cerebrospinal fluid (CSF), urine, tear and seminal plasma. All of our data were obtained by a state of the art mass spectrometer, a linear ion trap-Fourier transform instrument (LTQ-FT) or a linear ion trap-Orbitrap (LTQ-Orbitrap) with extremely high mass accuracy. You can search proteins or peptides by protein ID (IPI), protein name and peptide sequence across four bodily fluids.
Body Fluid Database - Tearhttp://proteome.biochem.mpg.de/tear/In our bodily fluid protein database, we provide protein and peptide list of cerebrospinal fluid (CSF), urine, tear and seminal plasma. All of our data were obtained by a state of the art mass spectrometer, a linear ion trap-Fourier transform instrument (LTQ-FT) or a linear ion trap-Orbitrap (LTQ-Orbitrap) with extremely high mass accuracy. You can search proteins or peptides by protein ID (IPI), protein name and peptide sequence across four bodily fluids.
Body Fluid Database - Urinaryhttp://proteome.biochem.mpg.de/urine/In our bodily fluid protein database, we provide protein and peptide list of cerebrospinal fluid (CSF), urine, tear and seminal plasma. All of our data were obtained by a state of the art mass spectrometer, a linear ion trap-Fourier transform instrument (LTQ-FT) or a linear ion trap-Orbitrap (LTQ-Orbitrap) with extremely high mass accuracy. You can search proteins or peptides by protein ID (IPI), protein name and peptide sequence across four bodily fluids.
Red Blood Cell Databasehttp://proteome.biochem.mpg.de/rbc/Our Human Red Blood Cell Database (hRBCD) is divided into membrane and soluble proteins, providing information ranging from identification of specific isoforms to the class and metabolic status of identified proteins. It also provides information on the biochemical characteristics of the membrane proteins and related statistical peptide information. hRBCD can be used in the process of confirming the presence of a protein in the red blood cell and to obtain further information on specific proteins and their biochemical behavior. A range of search possibilities are offered to get the most information out of the database: IPI accession number, protein name, description and class. Batch searches can also be undertaken
GlycoPro from BioPharmaSofthttp://www.biopharmasoft.com/
A software tool, GlycoPro, is available now for automatic, high throughput glycopeptide MS/MS spectra interpretation. It searches */_thousands_/* of MS/MS spectra from a glycoprotein digest against an N-glycan structure library with over 140,000 entries, scores each hit, and displays a graphical drawing of the N-glycan fragment for each of the matched MS/MS peak. All is done in an hour or two on a personal computer. Included in the N-glycan structure library/database are acetylated, phosphorylated and sulfated N-glycans (based on biosynthetic rules). Also available is an even larger library with over 500,000 entries. It may represent a breakthrough in glycomics. It is a practical tool for researchers interpreting MS/MS spectra manually (for N-glycan structure determination). For more info: www.BioPharmaSoft.com
GlycoPro takes an MS2 data folder name and the average MH+ of the peptide as its input and automatically finds any N-glycans attached to the peptide. The MS2 spectra data (in DTA format) can be ALL those that are obtained from an LC-MS/MS run of a tryptic digest of one or a mixture of a couple of glycoproteins, under the same experimental conditions as in a typtical proteomics experiment using mass spectrometry.
ProteoWizardhttp://proteowizard.sourceforge.net
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.
The software is available for download now, under the Apache open source license.
Features
Tools
MASPECTRAShttps://maspectras.genome.tugraz.at/maspectras/
The MAss SPECTRometry Analysis System (MASPECTRAS) is a web based platform for management and analysis of proteomics MS/MS data. 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 ASAPRatio algorithm. The system provides unique features that include the merging of results originating from different search engines, a chromatogram viewer and export to the public PRIDE repository via PRIDE-XML. MASPECTRAS has been developed on the basis of the PEDRo relational database schema and has been adapted to fulfill the MIAPE standard provided by the Proteomics Standards Initiative (PSI). The scalable platform is based on the Java 2 Enterprise Edition (J2EE) and enables the outsourcing of computationally intensive tasks to a computing cluster. MASPECTRAS is freely available at http://genome.tugraz.at/maspectras
XPRESShttp://tools.proteomecenter.org/XPRESS.phpThe XPRESS software calculates the relative abundance of proteins, such as those obtained from an ICAT-reagent labeled experiment, by reconstructing the light and heavy elution profiles of the precursor ions and determining the elution areas of each peak.
ASAPRatiohttp://tools.proteomecenter.org/ASAPRatio.phpAutomated Statistical Analysis on Protein Ratio (ASAPRatio) accurately calculates the relative abundances of proteins and the corresponding confidence intervals from ICAT-type ESI-LC/MS data.
ZoomQuanthttp://proteomics.mcw.edu/zoomquant/index.jspZoomQuant is a stand-alone program that allows for the rapid quantitation of stable isotope labeled quantitative proteomics experiments using data from the ubiquitous ThermoFinnigan LCQ and LTQ ion trap instruments. The zoom scan feature of these instruments allows users to collect short range, high resolution spectra that can be rapidly quantitated using ZoomQuant. Labeling peptides using 18O provides an inexpensive and convenient method to label almost all of the peptides in the sample, but due to incomplete exchange of oxygens and the 2 Da mass shift makes analysis with other tools difficult. ZoomQuant was specifically designed for this task and can accurately deconvolute the overlapping labeled and unlabeled isotopic envelopes and integrate the areas. Additionally, ZoomQuant can be used to quantitate any type of SILAC experiment using its flexible label shift profile method.
OpenMS - A Software Platform for Shotgun Proteomicshttp://www.openms.deOpenMS is an open source C++ library for LC/MS data management, visualisation, and processing. The library implements algorithms and data structures for peak picking (centroiding and smoothing), quantitation and visualisation of MS data. It is compatible to the common PSI-MS standards. OpenMS is a joint research project of several German research groups for Bioinformatics / Computer Science in T?bingen, Saarbr?cken und Berlin.
APEX Quantitative Proteomics Toolhttp://pfgrc.jcvi.org/index.php/bioinformatics/apex.html
The APEX Quantitative Proteomics Tool is a free and open source Java implementation of the APEX technique for the absolute quantitation of proteins based on standard LC- MS/MS proteomics data. The underlying methodology, described by Lu et al. in 2007 [Nature Biotech., 25(1):117-124, 2007], uses machine learning techniques to improve quantitation accuracy and is a label-free technique and requires no protein standards for quantitation. The APEX Tool provides an intuitive user interface, an integrated help system, and rich documentation. A tutorial and sample data set is included to help first time users become acquainted with the system.
Atomic Masseshttp://www.proteomecommons.org/archive/1129086318745/docs/atom-reference.htmlThe ProteomeCommons.org JAF reference for the common atoms, including isotopes. The masses are based on the published NIST standards.
Residue Combination Tool (Click to Run)http://www.proteomecommons.org/current/511/ResidueCombinationCalculator.jnlpA tool that will dynamically list amino acid residues or combinations of amino acid residues that match a particular mass given a mass tolerance.
Amino Acid Combo Listhttp://www.proteomecommons.org/current/511/docs/residue-combination-reference.htmlThe HTML version of the Residue Combination Calculator. This is a big HTML page that lists the masses of amino acid combinations (up to 5), including commonly observed modifications of amino acids.
Amino Acid Masseshttp://www.proteomecommons.org/current/511/docs/residue-reference.htmlThe ProteomeCommons.org JAF reference for amino acids, including common modifications of amino-acids. The masses are based on published NIST standards, and are very accurate.
Microbial Protein-Protein Interaction Database - MiPPIhttp://mippi.ornl.govA Research Program for Identification and Characterization of Protein Complexes
Integrated Post-Genomic Data Resourcehttp://www.proteomicsresource.org/The Biodefense Proteomics Catalog is a searchable directory of data and reagent information generated by the Proteomics Research Centers and available to the research community. A search yields information about organism studies, experimental data, research protocols, research reagents, identified proteins, publications and proteomes. It includes visualization and analysis tools.
NIST Library of Peptide Ion Fragmentation Spectrahttp://www.proteomecommons.org/data/National%20Institute%20of%20Standards%20and%20Technology%20(NIST)/SRD1A.jspThis is the ProteomeCommons.org mirror of the NIST Library of Peptide Ion Fragmentation Spectra, June 2006 Version. Links also include a search tool that uses the library. NIST allows free distribution of this library and related software with minor restrictions on use.
X! Hunterhttp://h201.thegpm.org/tandem/thegpm_hunter.htmlX! Hunter is a search engine that compares experimentally observed spectra directly with consensus mass spectra obtained from the GPMDB. It can identify proteins for human, budding yeast, mouse and thale cress samples. Because the sequence modifications and cleavage sites for the peptides in the sequence library are already known, it is not necessary to specify as many parameters for this type of search as in more conventional search engines.
SpectraSThttp://www.peptideatlas.org/spectrast/
Developed at ISB by H.Lam. Included as part of the Trans-Proteomic Pipeline (TPP) distribution. A free to use online version of the tool is also available.
It is designed for high-throughput identications with NIST-style libraries (Visit http://www.peptideatlas.org/speclib/ for library download), but can also be used to search X!Hunter libraries.
BiblioSpechttp://proteome.gs.washington.edu/bibliospec/documentation/Part of the BiblioSpec suite, developed at the MacCoss Lab at the University of Washington. BiblioSpec is a set of annotated mass spectra libraries and a software program for compiling and searching mass spectra libraries.
MSExpedite (click to run)http://www.proteomecommons.org/current/530/MSViewerApp.jnlpA Java-based viewer for visualizing MS and MSMS data in many different formats including MGF and mzXML. The tool uses Java Web Start and runs locally on your computer without any installation required.
Insilicos mzXML Viewerhttp://insilicos.com/viewer.htmlAn mzXML viewer application that can display MS and MSMS data from mzXML files, RAW files, and several other file formats.
mzXML Viewerhttp://tools.proteomecenter.org/mzXMLViewer.phpA Java-based viewer for displaying mzXML data.
Cytoscapehttp://tools.proteomecenter.org/Cytoscape.phpCytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.
MSighthttp://www.expasy.org/MSight/A standalone Windows application for visualising, comparing and analysing sets of LC/MS data. It supports RAW files, mzXML and other formats from the majority of mass spectrometers.
Insilicos mzXML Viewerhttp://www.insilicos.com/Insilicos_Viewer.htmlInsilicos Viewer is a program for viewing tandem mass spec proteomics data. It can also be used for viewing other mass spec data. Insilicos Viewer supports mzXML, mzData, ANDI, and TF (RAW) files. Insilicos Viewer runs on Windows 2000, Windows XP, and Windows XP Pro operating systems.
Suggested Citation: Insilicos LLC, Seattle, WA
PATIKA toolshttp://www.patika.orgThe PATIKA project provides software tools for acquisition, integration, analysis and visualization of biological pathways.
JVirGel 2.0http://www.jvirgel.deJVirGel is a software package for the visualization of whole proteomes under consideration of secreted and membrane proteomes.
SameSpotshttp://samespots.com/try_it.aspSameSpots is unique technology delivering a major advance for the analysis of single stain or 2D DIGE images. SameSpots redefines the 2D image analysis workflow, creating new possibilities for proteomics research with significant improvements in: Speed, Objectivity, and Statistical Power.
PepNovohttp://peptide.ucsd.edu/pepnovo.htmlPepNovo is a software for de novo sequencing of peptides from mass spectra. PepNovo uses a probabilistic network to model the peptide fragmentation events in a mass spectrometer. In addition, it uses a likelihood ratio hypothesis test to determine if the peaks observed in the mass spectrum are more likely to have been produced under the fragmentation model, than under a probabilistic model that treats the appearance of peaks as random events.
LutefiskXPhttp://www.hairyfatguy.com/lutefisk/De novo sequencing program optimized for CID performed within traps and quadrupole collision cells.
PEAKS Onlinehttp://www.bioinformaticssolutions.com:8080/peaksonline/PEAKS is renowned for its ability to provide the sequence of a peptide without the aid of a protein sequence database -- a process known as de novo sequencing. PEAKS is the only true de novo software that provides you with a complete sequence for each peptide, confidence scores on individual amino acid assignments, simple reporting for high-throughput analysis, and all the information you need for in depth investigation. CID, ECD and ETD enabled, and tuned to take advantage of high mass accuracy, and/or low resolution data.
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