Software Link mzData http://www.psidev.info/mzdata-1_0_5-docs mzXML http://sashimi.sourceforge.net/schema_revision/ mzML (replacement of mzXML u. mzData) http://www.psidev.info/mzml_1_0_0%20 TraML http://www.psidev.info/traml mzIdentML http://www.psidev.info/mzidentml mzQuantML http://www.psidev.info/mzquantml mz5 http://software.steenlab.org/mz5/ netCDF http://www.unidata.ucar.edu/software/netcdf/ Analyst http://sciex.com/products/software/analyst-software SWATH Acquisition http://sciex.com/swath-acquisition MetabolitePilot http://sciex.com/products/software/metabolitepilot-software ProteinPilot http://sciex.com/products/software/proteinpilot-software MultiQuant http://sciex.com/products/software/multiquant-software PeakView http://sciex.com/products/software/peakview-software Masshunter http://www.chem.agilent.com/en-US/products-services/Software-Informatics/MassHunter-Workstation-Software/Pages/default.aspx LCMS ChemStation http://www.chem.agilent.com/en-US/products-services/Software-Informatics/LC-MS-Chemstation-Software/Pages/default.aspx OpenLAB http://www.chem.agilent.com/en-US/products-services/Software-Informatics/OpenLAB-Chromatography-Data-System-(CDS)/Pages/default.aspx Proteome Discoverer http://www.thermoscientific.com/content/tfs/en/product/proteome-discoverer-software.html Xcalibur http://www.thermoscientific.com/en/product/xcalibur-software.html ProMass http://www.thermoscientific.com/en/product/promass-deconvolution-2-8-software.html MassLynx http://www.waters.com/waters/en_GB/MassLynx-Mass-Spectrometry-Software-/nav.htm?cid=513164&lset=1&locale=en_GB OpenLynx http://www.waters.com/waters/en_GB/OpenLynx-Open-Access/nav.htm?cid=10008851&locale=en_GB QuanLynx http://www.waters.com/waters/library.htm?locale=en_US&lid=1545661 ProteinLynx Global SERVER http://www.waters.com/waters/en_US/ProteinLynx-Global-SERVER-(PLGS)/nav.htm?cid=513821&locale=en_US Phenyx http://www.genebio.com/products/phenyx/solutions.html Seaquest http://fields.scripps.edu/researchtools.php PEAKS http://www.bioinfor.com Achroma http://openmasp.hswt.de/pages/project/achroma.php OpenChrom (free Community Edition) https://www.openchrom.net/ Maltcms/Maui [17] http://maltcms.sourceforge.net/ polyXmass / massXpert polyXmass: http://www.gnu.org/software/polyxmass/   massXpert: http://www.massxpert.org/wiki/ DeconLS http://omics.pnl.gov/software/decontools-decon2ls BioClipse http://www.bioclipse.net/ BioSunMS http://biosunms.sourceforge.net/ openMS http://open-ms.sourceforge.net/ MetaQuant http://bioinformatics.org/metaquant/ intelliMS http://intellims.proteomix.org/ mMass http://www.mmass.org/ MZMine2 http://mzmine.sourceforge.net/ pymzML http://pymzml.github.io/ MS-Spectre http://ms-spectre.sourceforge.net/ ProteoWizard http://proteowizard.sourceforge.net/ X!Tandem / X!!Tandem X!Tandem: http://www.thegpm.org/tandem/   X!!Tandem: http://wiki.thegpm.org/wiki/X!!Tandem Mascot (Server) (free search for 1200 spectra and limited functions) http://www.matrixscience.com/search_form_select.html PRIDE http://www.ebi.ac.uk/pride/archive/ TOPP http://open-ms.sourceforge.net/ MapQuant http://arep.med.harvard.edu/MapQuant/ SpecArray http://tools.proteomecenter.org/wiki/index.php?title=Software:SpecArray ATAQS http://tools.proteomecenter.org/ATAQS/ATAQS.html Skyline https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/begin.view msInspect http://proteomics.fhcrc.org/CPL/msinspect/ SuperHirn http://tools.proteomecenter.org/wiki/index.php?title=Software:SuperHirn MassSorter http://services.cbu.uib.no/software/massSorter PASSEL http://www.peptideatlas.org/passel/ jTraML https://github.com/compomics/jtraml HDX-analyzer http://people.tamu.edu/~syuan/hdxanalyzer/ PeptidePicker http://mrmpeptidepicker.proteincentre.com/peptidepicker9/ TPP (Trans-Proteomic Pipeline) http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP SpectraST http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST OMSSA (Open Mass Spectrometry Search Algorithm) No longer available, but some artifacts can be found here: http://www.ncbi.nlm.nih.gov/Web/Newsltr/V14N2/ Andromeda (Part of MaxQuant) http://www.andromeda-search.org/ MaxQuant http://www.maxquant.org/downloads.htm Proteios SE http://www.proteios.org/ MyriMatch No longer available, but a description how to obtain the source code can be found here: http://www.mc.vanderbilt.edu/root/vumc.php?site=msrc/bioinformatics&doc=27122 PAGIT http://www.sanger.ac.uk/resources/software/pagit/ MUMmer http://mummer.sourceforge.net/ VeSPA https://scion.duhs.duke.edu/vespa/project/wiki MINT http://mint.bio.uniroma2.it/mint/Welcome.do Mass Bank http://www.massbank.jp/ MSEA http://www.msea.ca/MSEA/ XANNpred http://www.compbio.dundee.ac.uk/xtal/cgi-bin/xannpred_in.pl

Table 2: List of web-links (last accessed on 2015.07.09) to the softwares presented in table 1.