| Name | Type | Description |
| ProSightPC and ProSightPD | proprietary | ProSightPC/PD are software tools for searching peptide and protein tandem mass spectrometry data against UniProt-derived databases. By using the set of know proteoforms, the software can efficiently search the known proteoform space, identifying and characterizing proteoforms. |
| TopPIC | open source | TopPIC identifies and characterizes proteoforms at the proteome level by searching top-down tandem mass spectra against a protein sequence database. TopPIC is a successor to MS-Align+. It efficiently identifies proteoforms with unexpected alterations, such as mutations and post-translational modifications, accurately estimates the statistical significance of identifications, and characterizes reported proteoforms with unknown mass shifts. It uses several techniques, such as indexes, spectral alignment, generation function methods, and the modification identification score, to increase the speed, sensitivity, and accuracy. |
| TopMG | open source | TopMG is a software tool for identifying ultra-modified proteoforms by searching top-down tandem mass spectra against a protein sequence database. It is capable of identifying proteoforms with multiple variable PTMs and unexpected alterations, such as histone proteoforms and phosphorylated ones. It uses mass graphs, which efficiently represent candidate proteoforms with multiple variable PTMs, to increase the speed and sensitivity in proteoform identification. In addition, approximate spectrum-based filtering methods are employed for protein sequence filtering, and a Markov chain Monte Carlo method is used for estimating the statistical significance of identifications. |
| Andromeda | freeware | Andromeda is a peptide search engine based on probabilistic scoring. On proteome data, Andromeda performs as well as Mascot, a widely used commercial search engine, as judged by sensitivity and specificity analysis based on target decoy searches. It can handle data with arbitrarily high fragment mass accuracy, it is able to assign and score complex patterns of post-translational modifications, such as highly phosphorylated peptides, and accommodates extremely large databases. Andromeda can function independently or integrated into MaxQuant. This combination enables analysis of large datasets on a desktop computer. Identification of co-fragmented peptides improves the number of identified peptides. Developed by Jürgen Cox and others at the Max Planck Institute of Biochemistry. |
| Byonic | proprietary | Database search algorithm released in 2011 by Protein Metrics Inc. with original developments at PARC that searches MS/MS data from all types of instruments and internally employs the program Combyne, which combines peptide identifications to produce protein scores and identification probabilities. |
| Comet | open source | Database search algorithm developed at the University of Washington available for Windows and Linux. Note that Comet is just a single command line binary that does MS/MS database search. It takes in spectra in some supported input format and writes out.pep.xml,.pin.xml,.sqt and/or.out files. You will need some other support tool to actually make use of Comet results. |
| Tide | open source | Tide is a tool for identifying peptides from tandem mass spectra. It is an independent reimplementation of the SEQUEST algorithm, which identifies peptides by comparing the observed spectra to a catalog of theoretical spectra derived in silico from a database of known proteins. The immediate ancestor of Tide is Crux, but Tide has been completely re-engineered to achieve a thousandfold improvement in speed while exactly replicating SEQUEST XCorr scores. Developed at the University of Washington. |
| Greylag | open source | Database search algorithm developed at the Stowers Institute for Medical Research designed to perform large searches on computational clusters having hundreds of nodes. |
| InsPecT | open source | A MS-alignment search algorithm available at the Center for Computational Mass Spectrometry at the University of California, San Diego |
| Mascot | proprietary | Performs mass spectrometry data analysis through a statistical evaluation of matches between observed and projected peptide fragments. |
| MassMatrix | freeware | MassMatrix is a database search algorithm for tandem mass spectrometric data. It uses a mass accuracy sensitive probabilistic scoring model to rank peptide and protein matches. |
| MassWiz | open source | Search algorithm developed at Institute of Genomics and Integrative Biology available as a windows commandline tool. |
| MS-GF + | open source | MS-GF+ performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database. It supports the HUPO PSI standard input file and saves results in the mzIdentML format, though results can easily be transformed to TSV. ProteomeXchange supports Complete data submissions using MS-GF+ search results. Developed at Center for Computational Mass Spectrometry at the University of California, San Diego, with later work at Pacific Northwest National Laboratory |
| MSFragger | freeware | Fast database searching based on efficient fragment ion indexing. Capable of open searches for post-translational modification discovery, O- and N-linked glycoproteomics searches, semi- and non-enzymatic searches in addition to traditional database searches. Developed at the University of Michigan. |
| MyriMatch | open source | Database search program developed at the Vanderbilt University Medical Center designed to run in a single-computer environment or across an entire cluster of processing nodes. |
| MS-LAMP | Open Source | A standalone software capable of aiding in interpreting electrospray ionization and/or matrix-assisted laser desorption and ionization mass spectrometric data of lipids. |
| OMSSA | freeware | The Open Mass Spectrometry Search Algorithm 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. It is developed at the National Center for Biotechnology Information. |
| PEAKS DB | proprietary | Database search engine, run in parallel with de novo sequencing to automatically validate search results, allowing for a higher number of found sequences for a given false discovery rate. In addition to providing an independent database search, results can be incorporated as part of the software’s multi-engine consensus reporting tool, inChorus. The tool also provides a list of sequences identified exclusively by de novo sequencing. |
| pFind | freeware | pFind Studio is a computational solution for mass spectrometry-based proteomics, it germinated in 2002 in Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China. |
| Phenyx | proprietary | Developed by Geneva Bioinformatics in collaboration with the Swiss Institute of Bioinformatics. Phenyx incorporates OLAV, a family of statistical scoring models, to generate and optimize scoring schemes that can be tailored for all kinds of instruments, instrumental set-ups and general sample treatments. |
| ProbID | open source | PI is a powerful suite on analysis of tandem mass spectrum. ProbID seeks to fill the need for the deep analysis of tandem mass spectrum, including the fragmentation rules, preference of cleavage, neutral losses, etc. Developed at the Bioinformatics Group, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China. |
| ProLuCID | freeware | ProLuCID is a fast and sensitive tandem mass spectra-based protein identification program recently developed by Tao Xu and others in the Yates laboratory at The Scripps Research Institute. |
| ProteinPilot Software | proprietary | Uses Paragon database search algorithm that combines the generation of short sequence tags for computation of sequence temperature values and estimates of feature probabilities to enable the peptide identification considering hundreds of modifications, non-tryptic cleavages and amino acid substitutions. Uses the Pro Group Algorithm for protein inference analysis to report the minimal set of proteins justified based on the peptide evidence. Supports quantification for label-based workflows. A translation layer translates user interface controls in the language of the proteomics experimental scientist to underlying complex informatics parameters. |
| Protein Prospector | open source | Protein Prospector is a package of about twenty proteomic analysis tools developed at the University of California San Francisco. The tandem mass spectrometry searching software is Batch-Tag / Batch-Tag Web, with the results processed and displayed using Search Compare. It uses scoring systems tailored to instrument and fragmentation mode to optimize analysis of different types of fragmentation data. |
| RAId | lost | Developed at the National Center for Biotechnology Information, Robust Accurate Identification is a suite of proteomics tools for analyzing tandem mass spectrometry data with accurate statistics. |
| SEQUEST | proprietary | Identifies collections of tandem mass spectra to peptide sequences that have been generated from databases of protein sequences. |
| SIMS | open source | SIMS is a software tool design to perform unrestrictive PTM search over tandem mass spectra; users do not have to characterize the potential PTMs. Instead, users only need to specify the range of modification mass for each individual amino acid. |
| SimTandem | freeware | A database search engine for identification of peptide sequences from LC/MS/MS data; the engine can be used as an external tool in OpenMS/TOPP. |
| SQID | open source | SeQuence IDentification is an intensity-incorporated protein identification algorithm for tandem mass spectrometry. |
| X!Tandem | open source | Matches tandem mass spectra with peptide sequences. |
| Name | Type | Description | - |
| HIquant | open source | A first-principles model and algorithm for quantifying proteoform stoichiometries from bottom-up data. | - |
| TopFD | open source | TopFD is a software tool for top-down spectral deconvolution and a successor to MS-Deconv. It groups top-down spectral peaks into isotopomer envelopes and converts isotopomer envelopes to monoisotopic neutral masses. In addition, it extracts proteoform features from LC-MS or CE-MS data. | - |
| ArtIST by Clover Biosoft | proprietary | MALDI-TOF MS data analysis and biomarker discovery tools, based on artificial intelligence and machine learning algorithms. ArtIST is an online service. | - |
| Advanced Chemistry Development | proprietary | Commercial solutions for the interpretation of MS and xC/MS data with spectrum/structure matching, identification of known and unknown metabolites, as well as for the identification of compounds through spectral comparison. | - |
| Analyst | proprietary | Software by AB Sciex, a division of The Danaher Corporation. | - |
| proprietary | A vendor independent software application from for processing mass spectrometry data. It can process both GC-MS and LC-MS data using qualitative and quantitative data processing and is used in metabolomics using MatrixAnalyzer for the comparison of multiple data sets. Recently extended to include statistical analysis and visualisation tools. AnalyzerPro XD is a 64 bit version that includes support for 2 dimensional data processing such as GCxGC-MS. | - |
| Chromeleon | proprietary | Software by Thermo Fisher Scientific used with mass spectrometry instruments, as well as chromatography instruments. | - |
| Crosslinx | open source | Identify cross-linked peptides from mzML files. Python script or standalone executables for Linux and Windows. Feasible for bigger databases with a two-step approach. | - |
| DeNovoGUI | open source | Software with a graphical user interface for running parallelized versions of the freely available de novo sequencing software tools Novor and PepNovo+. | |
| Easotope | open source | Software for archiving, organizing, and analyzing mass spectrometer data. Currently oriented toward clumped CO2 analysis but also useful for bulk CO2 work and expandable to other isotopic systems. | - |
| open-source | Desktop software by for processing labeled LC-MS, GC-MS and LC-MS/MS data in open-formats. The software has a graphical and command line interface with integration to a cloud platform for storage and further analyses like relative flux and quantification. | - |
| ESIprot | | Enables the charge state determination and molecular weight calculation for low resolution electrospray ionization mass spectrometry data of proteins. | - |
| Expressionist | proprietary | An enterprise software solution by Genedata for processing, analyzing, and reporting of mass spectrometry data in application areas such as biotherapeutics characterization, quality monitoring, and related proteomics and metabolomics applications. | - |
| Spectroscopy Software & Mass Spectral Library | proprietary | Software from Wiley with solutions for mass spectrometry including: spectral analysis, database searching, processing, database building, spectral subtraction, plus tools for reporting and ChemWindow structure drawing. | - |
| LabSolutions LCMS | proprietary | Software by Shimadzu Corporation used with mass spectrometry and HPLC instruments. | - |
| Mass++ | open source | Analysis software for mass spectrometry that can import and export files with open-formats and load some instrument vendor formats; users can develop and add original functions as Mass++ plug-ins. | - |
| MassBank.jp | website | website hosted by the Institute for Advanced Biosciences, in Keio University, Tsuruoka City, Yamagata, Japan with mass spectrometric data for organic compounds. | - |
| MassBank.eu | website | European MassBank server. The website is maintained and hosted by the Helmholtz Centre for Environmental Research | - |
| MassBank | open source | MassBank and RMassBank development website provided by the MassBank consortium. MassBank data is shared under a Creative Commons license. | - |
| MassCenter | proprietary | Software by JEOL used with mass spectrometry instruments. | - |
| Mass Frontier | proprietary | Software by HighChem used for interpretation and management of mass spectra of small molecules. | - |
| MassLynx | proprietary | Software by Waters Corporation. | - |
| MassMap | proprietary | General-purpose software suite for automated evaluation of MS data by MassMap GmbH & Co. KG, suitable for LC/MS and GC/MS data of all kinds of molecules, the analysis of intact mass spectra of proteins, the analysis of general HDX experiments and the HDX fragment analysis of peptides, with particular method for the identification of unexpected/unknown components in even very complex mixtures. | - |
| Mass-Up | open-source | Utility for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data that loads data from mzML, mzXML and CSV files and allows users to apply baseline correction, normalization, smoothing, peak detection and peak matching. In addition, it allows the application of different machine learning and statistical methods to the preprocessed data for biomarker discovery, unsupervised clustering and supervised sample classification. | - |
| massXpert | open source GPL | Graphical user interface-based software for simulating and analyzing mass spectrometric data obtained on known bio-polymer sequences. Successor to polyxmass. A program of the software suite. | - |
| METLIN Database and Technology Platform | proprietary | Created in 2003, METLIN now includes over a million molecules ranging from lipids, steroids, plant & bacteria metabolites, small peptides, carbohydrates, exogenous drugs/metabolites, central carbon metabolites and toxicants. The metabolites and other small molecules have been individually analyzed to provide both empirical and in silico MS/MS data. | - |
| mineXpert | open source GPL | Graphical user interface-based software for mass spectral data visualization/mining. Supports ion mobility mass spectrometry.. A program of the software suite. | - |
| mMass | open source | Multi-platform package of tools for mass spectrometric data analysis and interpretation written in Python. | - |
| MolAna | | MolAna was developed by Phenomenome Discoveries Inc, for use in IONICS Mass Spectrometry Group's 3Q Molecular Analyzer, Triple quadrupole mass spectrometer | - |
| ms2mz | freeware | Utility for converting between mass spectrometer file formats, e.g. to convert proprietary binary files to MGF peak list files to prepare files for upload to Proteome Cluster. | - |
| MSGraph | open source | | - |
| MSight | freeware | Software for mass spectrometry imaging developed by the Swiss Institute of Bioinformatics. | - |
| MSiReader | freeware | Vendor-neutral interface built on the Matlab platform designed to view and perform data analysis of mass spectrometry imaging data. Matlab is not required to use MSiReader. | - |
| mspire | open-source | Mass spectrometry informatics developers toolbox written in ruby that includes an mzML reader/writer, in-silico digestion and isotopic pattern calculation etc.; submodules such as mspire-lipidomics, mspire-sequest, and mspire-simulator extend the functionality. | - |
| open-source | R package with graphical user interface for robust differential abundance analysis of label-free quantitative proteomics data. | - |
| Multimaging | | Software for mass spectrometry imaging designed to normalize, validate and interpret MS images. | - |
| multiMS-toolbox | open source | ms-alone and multiMS-toolbox is a tool chain for mass spectrometry data peak extraction and statistical analysis. | - |
| mzCloud | website | Web-based mass spectral database that comprises a collection of high and low resolution tandem mass spectrometry data acquired under a number of experimental conditions. | - |
| MZmine 2 | open source | An open-source software for mass-spectrometry data processing, with the main focus on LC-MS data. | - |
| OmicsHub Proteomics | | OmicsHub Proteomics combines a LIMS for mass spec information management with data analysis functionalities on one platform. | - |
| OpenChrom | open source | Chromatography and mass spectrometry software that can be extended using plug-ins and is available for several operating systems and processor architectures. with converters for the native access of various data files, e.g. converters for mzXML, netCDF, Agilent, Finnigan and Varian file formats. | - |
| ORIGAMI | open source | Software suite for analysis of mass spectrometry and ion mobility mass spectrometry datasets. ORIGAMI was originally developed to improve the analysis workflows of activated IM-MS/collision induced unfolding datasets and allow seamless visualisation of results. Recently, ORIGAMI was modified to be more accepting of non-MS centric and enables visualisation of results from other sources as well as enables exporting of all results in an interactive format where the user can share any dataset and visualise in an internet browser. | - |
| PatternLab | freeware | Software for post-analysis of SEQUEST, ProLuCID or Comet database search results filtered by DTASelect or Census. | - |
| pyOpenMS | open source | pyOpenMS is an open-source Python library for mass spectrometry, specifically for the analysis of proteomics and metabolomics data in Python. | - |
| SIM-XL | freeware | Spectrum Identification Machine for Cross-linked Peptides is a fast and sensitive XL search engine which is part of the PatternLab for proteomics environment, to analyze tandem mass spectrometry data derived from cross-linked peptides. | - |
| Peacock | open source | Mac OS X application developed by Johan Kool that can be used to interpret gas-chromatography/mass-spectrometry data files. | - |
| PeakInvestigator | proprietary | 3-4X effective resolution improvement in post-processing of raw profile data output from mass specs. Veritomyx advanced signal processing software for peak detection, deconvolution, and centroiding of raw profile mass spec data reveals multiple peaks hidden in overlapped data. Notable features: order-of-magnitude improvements in mass and abundance precision for deconvolved peaks; local dynamic baselining; advanced thresholding algorithm increases sensitivity across wide dynamic range; statistically-driven and completely automated. More complete and precise resulting mass lists facilitate faster and cost-efficient subsequent determination of correct biomolecular identifications. | - |
| Pinnacle | Proprietary | From comprehensive quantitation of many thousands of proteins across of hundreds of samples using DDA, DIA, PRM or SRM with fully integrated statistics and biological interpretation, to complete N-linked glycoprotein identification routine, to a very in-depth analysis in protein characterization, including peptide mapping, error tolerant search and disulfide analysis, all of this is available in a single software. Analyzing hundreds of samples brings big challenges of LC and MS variation when run over months of acquisition, and the software can automatically correct for this. The visualization, editing and annotation capabilities can be tailored to be at the high level of proteins or at a much lower level of transitions or isotopes. | - |
| PIQMIe | web | Proteomics Identifications/quantitations data management and integration service is a web-based tool that aids in reliable and scalable data management, analysis and visualization of semi-quantitative proteomics experiments. | - |
| POTAMOS | open source | Web application that provides calculated mass spectrometry data independently of instrumentation focused on a well known protein family of histones whose PTMs are believed to play a crucial role in gene regulation; calculates the kind, the number and the combinations of the possible PTMs corresponding to a given peptide sequence and a given mass. | - |
| ProMass | proprietary | ProMass is an automated biomolecule deconvolution and reporting software package that is used to process ESI/LC/MS data or single ESI mass spectra. It uses the novel deconvolution algorithm, ZNova, to produce artifact-free deconvoluted mass spectra. ProMass is currently available for Thermo, Waters, and Shimadzu platforms. It is also available in a "lite" browser-based format called ProMass for the Web that does not require any installation or software download. | - |
| PROTRAWLER | | LC/MS data reduction application that reads raw mass spectrometry vendor data and creates lists of triplets summarizing the LC/MS chromatogram. | - |
| ProteoIQ | proprietary | Software for the post-analysis of Mascot, SEQUEST, or X!Tandem database search results. | - |
| Proteomatic | Freeware | Data processing pipeline created for the purpose of evaluating mass spectrometric proteomics experiments. | - |
| ProteomicsTools | open source | Software for the post-analysis of MASCOT, SEQUEST, Comet, XTandem, PFind, PeptidePhophet, MyriMatch, MSGF, OMSSA, MSAmanda or Percolator database search result. | - |
| ProteoWizard | open source | Link library and tools that are a set of modular and extensible open-source, cross-platform tools and software libraries that facilitate proteomics data analysis. | - |
| ProteoWorker | proprietary | Cloud-based software for proteomics data analysis including COMET, Peptide Prophet, ProteinProphet and extensive data sorting, filtering and annotation tools. | - |
| Provision | open source | Cloud-based software written in R for analysing proteomics data generated by MaxQuant. This software is geared towards analysis of differential quantification data and provides tools as well as visualisation options to facilitate analysis. It is possible to process label-free and tandem mass tagged data. | - |
| pymzML | open source | Python module to interface mzML data in Python based on cElementTree with additional tools for MS-informatics. | - |
| Pyteomics | open source | A Python framework for proteomics data analysis. | - |
| Quantinetix | | Software for mass spectrometry imaging designed to quantify and normalize MS images in various study types that is compatible with a variety of MSI instruments, including Bruker, Sciex, Thermo and with iMZML. | - |
| Rational Numbers Excel Add-In | proprietary | De novo identification tool that works with Microsoft Excel 2010, Excel 2013, and Excel 2016. | - |
| Rational Numbers Search | proprietary | Identification of small molecules by comparison of accurate-mass fragmentation data to a database of 250000 molecules represented as mathematical partitions | - |
| REGATTA | | LC/MS list comparison application that works with ProTrawler to provide an environment for LC/MS results list filtering and normalization lists. | - |
| proprietary | Software by for vendor independent 'Open Access' client/server based solutions to provide a walk-up and use LC-MS and GC-MS data system; instrument control and data processing support for multiple vendors' hardware. Also support NMR instrumentation and data processing. | - |
| Scaffold | proprietary | Suite of proteomics tools for analyzing spectra, peptides and proteins across multiple samples. | - |
| SCIEX OS | proprietary | Next generation software by SCIEX controlling the X-series mass spectrometers and support for data analysis acquired using the Analyst software suite. | - |
| SCiLS Lab | | Statistical analysis of MALDI imaging mass spectrometry data that integrates with Bruker MALDI imaging. | - |
| SimGlycan | proprietary | Predicts the structure of glycans and glycopeptides using mass spectrometry MS/MS data. | - |
| SIMION | proprietary | Ion optics simulation program | - |
| Spectrolyzer | | Spectrolyzer is a Microsoft Windows-based software package that provides bioinformatics data analysis tools for different mass spectrometers that focuses on finding protein biomarkers and detecting protein deviations. | - |
| Spectromania | proprietary | Software for analysis and visualization of mass spectrometric data. | - |
| StavroX | freeware | Software to identify cross-linked peptides from mass spectrometric data written in Java that can be used for a wide variety of cross linkers and proteases used in the cross linking MS experiment; it compares theoretical peptide-peptide cross link combinations for the analyzed proteins to MS/MS data. | - |
| Swiss Mass Abacus | open source | Swiss Mass Abacus is a calculator of peptide and glycopeptide masses. It is purposefully kept as simple as a basic calculator executing arithmetic operations. | - |
| TOF-DS | proprietary | Software by Markes International used with BenchTOF time-of-flight mass spectrometers | - |
| TurboMass | proprietary | GC/MS software by PerkinElmer. | - |
| Trans-Proteomic Pipeline | open source | The Trans-Proteomic Pipeline is a collection of integrated tools for MS/MS proteomics that includes PeptideProphet for the Statistical validation of PSMs using search engine results, iProphet for distinct peptide sequence validation, using PeptideProphet results and ProteinProphet for Protein identification and validation, using PeptideProphet OR iProphet results. TPP does also Protein Quantification with XPRESS, ASAPRatio and Libra. The TPP currently supports Sequest, Mascot, ProbID, X!Tandem, Comet, SpectraST, MSGF+, Inspect, MyriMatch, and Phenyx. Developed at the Seattle Proteomic Centre. | - |
| Universal Mass Calculator | | Universal Mass Calculator for Windows written in C++ is a proprietary toolbox for calculating relevant information from sum formulae, e.g. isotope distribution, mass differences, mass deviations and mass/isotope information of the elements, degree of deuteration. | - |
| VIPER | | Analysis of accurate mass and chromatography retention time analysis of LC-MS features. | - |
| Xcalibur | proprietary | Software by Thermo Fisher Scientific used with mass spectrometry instruments. | - |
| XCMS Online | proprietary | Freely available and the most widely used metabolomic and lipidomic data processing platform with over 21,000 users as of 2017. | - |
