List of mass spectrometry software

Mass spectrometry software is software used for data acquisition,[1] analysis, or representation in mass spectrometry.

Proteomics software
Further information: protein mass spectrometry

In protein mass spectrometry, tandem mass spectrometry (also known as MS/MS or MS2) experiments are used for protein/peptide identification. Peptide identification algorithms fall into two broad classes: database search and de novo search. The former search takes place against a database containing all amino acid sequences assumed to be present in the analyzed sample, whereas the latter infers peptide sequences without knowledge of genomic data.

Database search algorithms
Name TypeDescription
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 sourceTopPIC (Top-down mass spectrometry based Proteoform Identification and Characterization) 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 (PTMs), 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 (MIScore), to increase the speed, sensitivity, and accuracy.[2]
TopMG open sourceTopMG (Top-down mass spectrometry based proteoform identification using Mass Graphs) 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 (TopMCMC) is used for estimating the statistical significance of identifications.[3]
Andromeda (part of MaxQuant) freewareAndromeda 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.[4]
Byonic proprietaryDatabase search algorithm released in 2011 by Protein Metrics Inc. with original developments at PARC[5] that searches MS/MS data from all types of instruments and internally employs the program Combyne,[6] which combines peptide identifications to produce protein scores and identification probabilities.
Comet open sourceDatabase 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(s) to actually make use of Comet results (A GUI for Windows only is available).[7]
Tide (rewrite of Crux) open sourceTide 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.[8]
Greylag open sourceDatabase search algorithm developed at the Stowers Institute for Medical Research designed to perform large searches on computational clusters having hundreds of nodes.
InsPecT open sourceA MS-alignment search algorithm available at the Center for Computational Mass Spectrometry at the University of California, San Diego[9]
Mascot proprietaryPerforms mass spectrometry data analysis through a statistical evaluation of matches between observed and projected peptide fragments.[10]
MassMatrix freewareMassMatrix 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 sourceSearch algorithm developed at Institute of Genomics and Integrative Biology available as a windows commandline tool.
MS-GF + open sourceMS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database. It supports the HUPO PSI standard input file (mzML) 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 (PNNL)
MSFragger freewareFast database searching based on efficient fragment ion indexing. Capable of open (mass-tolerant) 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.[11]
MyriMatch open sourceDatabase 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.[12]
MS-LAMP Open Source A standalone software capable of aiding in interpreting electrospray ionization (ESI) and/or matrix-assisted laser desorption and ionization (MALDI) mass spectrometric data of lipids.[13]
OMSSA freewareThe 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. It is developed at the National Center for Biotechnology Information.[14][15]
PEAKS DB proprietaryDatabase 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 (Sequest, Mascot, X!Tandem, OMSSA, PEAKS DB) consensus reporting tool, inChorus.[16] The tool also provides a list of sequences identified exclusively by de novo sequencing.
pFind freewarepFind 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 proprietaryDeveloped by Geneva Bioinformatics (GeneBio) in collaboration with the Swiss Institute of Bioinformatics (SIB). 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.[17]
ProbID open sourcePI 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.[18]
ProLuCID freewareProLuCID 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.[19]
ProteinPilot Software proprietaryUses Paragon database search algorithm that combines the generation of short sequence tags (‘taglets’) 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 (iTRAQ reagents, mTRAQ reagents and SILAC labeling). A translation layer translates user interface controls in the language of the proteomics experimental scientist to underlying complex informatics parameters.[20]
Protein Prospector open sourceProtein 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 lostDeveloped at the National Center for Biotechnology Information, Robust Accurate Identification (RAId)[21] is a suite of proteomics tools for analyzing tandem mass spectrometry data with accurate statistics.[22]
SEQUEST proprietaryIdentifies collections of tandem mass spectra to peptide sequences that have been generated from databases of protein sequences.[23]
SIMS open sourceSIMS (Sequential Interval Motif Search) 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.[24]
SimTandem freewareA 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.[25]
SQID open sourceSeQuence IDentification (SQID) is an intensity-incorporated protein identification algorithm for tandem mass spectrometry.
X!Tandem open sourceMatches tandem mass spectra with peptide sequences.
WsearchVS2020 freeware Data analysis software that can display spectra acquired on commercial MS instruments. Can also search/match NIST commercial database

De novo sequencing algorithms

De novo peptide sequencing algorithms are based, in general, on the approach proposed in Bartels et al. (1990).[26]

Name TypeDescription
CycloBranch open sourceA stand-alone, cross-platform and open-source de novo engine for identification of nonribosomal peptides (linear, cyclic, branched and branch-cyclic) from accurate product ion spectra.[27]
DeNovoX proprietaryDe novo sequencing on CID spectra acquired with ion trap mass spectrometers delivering complete and/or partial peptide sequences (sequence tags).[28]
DeNoS Sequencing of peptides using all information from CAD and ECD spectra; part of the software tool Proteinmatching Analysis Software (PAS) which in turn is part of the software package Medicwave Bioinformatics Suite (MBS).[29]
Lutefisk open sourceSoftware for the de novo interpretation of peptide CID spectra.
Novor proprietary, free for academic researchReal-time de novo peptide sequencing engine that is fast, accurate and easy to be integrated into research pipelines. Novor can de novo sequence more than 300 MS/MS spectra per second on a Macbook Pro laptop computer.[30]
PEAKS proprietaryDe novo sequencing for each peptide, confidence scores on individual amino acid assignments with manually assisted modeand automated de novo sequencing on an entire LC run processed data faster than 1 spectrum per second.[31][32]
Supernovo proprietaryA unique, hands-free solution for end-to-end de novo sequencing of monoclonal antibodies

Homology searching algorithms
Name TypeDescription
MS-Homology open sourceMS-Homology is a database search program within the Protein Prospector package that permits searching with strings that combine masses and amino acid stretches, where one can specify the number of amino acid mismatches allowed.
SPIDER proprietaryThe SPIDER algorithm matches sequence tags with errors to database sequences for the purpose of protein and peptide identification and can be used in conjunction with PEAKS mass spectrometry data analysis software.

MS/MS peptide quantification
Further information: Quantitative proteomics
Name TypeDescription
MarkerView Software proprietaryCommercial software for statistical analysis for quantitative mass spec data sets from metabolomics and proteomic profiling applications.
Mascot Distiller proprietarySoftware for peak picking and raw data preprocessing. Has an optional toolbox for label-free quantification as well as isobaric labeling and isotopic labeling. Supports raw file formats from all major instrument vendors.
Mascot Server proprietaryThe search engine supports quantification based on isobaric labeling as long as all the required information is part of the MS/MS spectrum.
MassChroQ open sourcePeptide quantification analysis of label free or various isotopic labeling methods (SILAC, ICAT, N-15, C-13 …), works with high and low resolution spectrometer systems, supports complex data treatments as peptide or protein fractionation prior to LC-MS analysis (SCX, SDS-PAGE, etc.).
MaxQuant freewareQuantitative proteomics software developed by Jürgen Cox and others at the Max Planck Institute of Biochemistry in Martinsried, Germany written in C# that allows the analysis of label free and SILAC based proteomics experiments.
MultiQuant Software proprietaryCan process quantitative data sets from TripleTOF or QTRAP systems, including MRM and SWATH Acquisition.
OpenMS / TOPP open sourceSoftware C++ library for LC-MS/MS data management and analysis that offers an infrastructure for the development of mass spectrometry related software. Allows peptide and metabolite quantification, supporting label-free and isotopic-label based quantification (such as iTRAQ and TMT and SILAC) as well as targeted SWATH-MS quantification.[33]
OpenPIP website, open access OpenPIP is an open access, web based tool, developed by InterVenn Biosciences to integrate peaks acquired in multiple reaction monitoring (MRM) experiments. The software is powered by recurrent neural networks and was trained on a massive collection of manually-annotated chromatographic peaks.
ProtMax freewareProtMAX[34] is a software tool for analyzing shotgun proteomics mass spectrometry data sets, developed by Volker Egelhofer at the University of Vienna.
Spectronaut proprietaryCommercial software for quantitative proteomics developed by Biognosys AG (Schlieren, Switzerland) based on the mProphet algorithm[35] that allows the targeted analysis of data independent acquisition (DIA) data sets for label-free peptide quantitation, also called SWATH acquisition.[36]
Skyline open sourceOpen source (Apache 2.0) Windows client software developed in the MacCoss lab at University of Washington[37] that supports building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM - Targeted MS/MS), Data Independent Acquisition (DIA/SWATH) and targeted DDA with MS1 quantitative methods and analyzing the resulting mass spectrometer data.
SWATH Software 2.0 proprietaryCommercial software processing tool within PeakView that allows targeted data processing of SWATH acquisition data. Using a protein/peptide ion library, fragment ion extracted ion chromatograms (XICs) are generated, scored and quantified for peptides from the library. After false discovery rate analysis (FDR), results are filtered and quantitative peptide/protein data can be exported for statistical analysis.
BACIQ open sourceBACIQ is a mathematically rigorous approach that integrates peptide intensities and peptide-measurement agreement into confidence intervals for protein ratios (BACIQ). The main advantages of BACIQ are: 1) it removes the need to threshold reported peptide signal based on an arbitrary cut-off, thereby reporting more measurements from a given experiment; 2) confidence can be assigned without replicates; 3) for repeated experiments BACIQ provides confidence intervals for the union, not the intersection, of quantified proteins; 4) for repeated experiments, BACIQ confidence intervals are more predictive than confidence intervals based on protein measurement agreement.

Other software
Name TypeDescription
HIquant open source A first-principles model and algorithm for quantifying proteoform stoichiometries from bottom-up data.[38]
TopFD open sourceTopFD (Top-down mass spectral Feature Detection) 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(Artificial Intelligence Straing Typing) 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 proprietaryCommercial 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 proprietarySoftware by AB Sciex, a division of The Danaher Corporation.
AnalyzerPro proprietaryA vendor independent software application from SpectralWorks 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 (PCA). AnalyzerPro XD is a 64 bit version that includes support for 2 dimensional data processing such as GCxGC-MS.
CFM-ID open sourceSoftware for in-silico ESI-MS/MS spectra prediction, MS/MS spectra annotation, and compound identification based on MS/MS spectrum. Developed in Wishartlab[39][40][41][42]
Chromeleon proprietarySoftware by Thermo Fisher Scientific used with mass spectrometry instruments, as well as chromatography instruments.
Crosslinx open sourceIdentify cross-linked peptides from mzML files. Python script or standalone executables for Linux and Windows. Feasible for bigger databases with a two-step approach.[43]
DeNovoGUI open sourceSoftware with a graphical user interface for running parallelized versions of the freely available de novo sequencing software tools Novor and PepNovo+.[44]
Easotope open sourceSoftware 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.
[El-MAVEN] open-source Desktop software by Elucidata for processing labeled LC-MS, GC-MS and LC-MS/MS data in open-formats (mzXML, mzML, CDF). 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.[45]
ESIprot Enables the charge state determination and molecular weight calculation for low resolution electrospray ionization (ESI) mass spectrometry (MS) data of proteins.[46]
Expressionist proprietaryAn 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.
KnowItAll Spectroscopy Software & Mass Spectral Library proprietarySoftware from Wiley with solutions for mass spectrometry including: spectral analysis, database searching (spectrum, structure, peak, property, etc.), processing, database building (MS or multiple techniques including IR, Raman, NMR, UV, Chromatograms), spectral subtraction, plus tools for reporting and ChemWindow structure drawing.
LabSolutions LCMS proprietarySoftware by Shimadzu Corporation used with mass spectrometry and HPLC instruments.
Mass++ open sourceAnalysis software for mass spectrometry that can import and export files with open-formats (mzXML, mzML) and load some instrument vendor formats; users can develop and add original functions as Mass++ plug-ins.
MassBank.jp websitewebsite 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 (Leipzig, Germany)
MassBank open source MassBank and RMassBank development website provided by the MassBank consortium. MassBank data is shared under a Creative Commons license.
MassCenter proprietarySoftware by JEOL used with mass spectrometry instruments.
Mass Frontier proprietarySoftware by HighChem used for interpretation and management of mass spectra of small molecules.
MassLynx proprietarySoftware by Waters Corporation.
MassMap proprietaryGeneral-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-sourceUtility 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.[47]
massXpert open source GPLGraphical user interface-based (GUI) software for simulating and analyzing mass spectrometric data obtained on known bio-polymer sequences.[48] Successor to polyxmass. A program of the msxpertsuite.org software suite.
matchms open sourcePython library to import, clean, process and quantitatively compare MS/MS spectra. Developed at the Netherlands eScience Center.[49]
METLIN Database and Technology Platform proprietaryCreated 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 GPLGraphical user interface-based (GUI) software for mass spectral data visualization/mining. Supports ion mobility mass spectrometry.[50] A program of the msxpertsuite.org software suite.
mMass open sourceMulti-platform package of tools for mass spectrometric data analysis and interpretation written in Python (no more developed).
MolAna MolAna was developed by Phenomenome Discoveries Inc, (PDI) for use in IONICS Mass Spectrometry Group's 3Q Molecular Analyzer, Triple quadrupole mass spectrometer
ms2mz freewareUtility 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 freewareSoftware for mass spectrometry imaging developed by the Swiss Institute of Bioinformatics.[51]
MSiReader freewareVendor-neutral interface built on the Matlab platform designed to view and perform data analysis of mass spectrometry imaging (MSI) data.[52] Matlab is not required to use MSiReader.
mspire open-sourceMass 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.[53]
MSqRob open-sourceR package with graphical user interface for robust differential abundance analysis of label-free quantitative proteomics data.[54][55][56]
Multimaging proprietary Software for mass spectrometry imaging designed to normalize, validate and interpret MS images.
multiMS-toolbox open sourcems-alone and multiMS-toolbox is a tool chain for mass spectrometry data peak extraction and statistical analysis.
mzCloud websiteWeb-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 sourceAn 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 sourceChromatography and mass spectrometry software that can be extended using plug-ins and is available for several operating systems (Microsoft Windows, Linux, Unix, Mac OS X) and processor architectures (x86, x86_64, ppc). 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 (CIU) 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.[57]
PatternLab freewareSoftware for post-analysis of SEQUEST, ProLuCID or Comet database search results filtered by DTASelect or Census.[58]
pyOpenMS open sourcepyOpenMS is an open-source Python library for mass spectrometry, specifically for the analysis of proteomics and metabolomics data in Python.
SIM-XL freewareSpectrum Identification Machine for Cross-linked Peptides (SIM-XL) 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.[59]
Peacock open sourceMac OS X application developed by Johan Kool that can be used to interpret gas-chromatography/mass-spectrometry (GC/MS) data files.
PeakInvestigator proprietary3-4X 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 (no user-to-user variation). 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 webProteomics 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 (SILAC) proteomics experiments.[60]
POTAMOS open sourceWeb 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 proprietaryProMass 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 (from a variety of well-known instrument companies) and creates lists of {mass, retention time, integrated signal intensity} triplets summarizing the LC/MS chromatogram.
ProteoIQ proprietarySoftware for the post-analysis of Mascot, SEQUEST, or X!Tandem database search results.[61][62][63]
Proteomatic FreewareData processing pipeline created for the purpose of evaluating mass spectrometric proteomics experiments.[64]
ProteomicsTools open sourceSoftware for the post-analysis of MASCOT, SEQUEST, Comet, XTandem, PFind, PeptidePhophet, MyriMatch, MSGF, OMSSA, MSAmanda or Percolator database search result.[65]
ProteoWizard open sourceLink 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 proprietaryCloud-based software for proteomics data analysis including COMET, Peptide Prophet, ProteinProphet and extensive data sorting, filtering and annotation tools.
Provision open sourceCloud-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.[66]
pymzML open sourcePython module to interface mzML data in Python based on cElementTree with additional tools for MS-informatics.[67]
Pyteomics open sourceA Python framework for proteomics data analysis.[68]
Quantem Software for ESI-MS quantification without analytical standards. Developed in Kruvelab, distributed by Quantem Analytics
Quantinetix proprietary 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 proprietaryDe novo identification tool for small molecules that works with Microsoft Excel 2010, Excel 2013, Excel 2016, and Excel 2019. This software treats small molecules as mathematical partitions of the molecular mass and generates subfragment formulas with atoms that are sets of partitions comprising the molecular formula.
Rational Numbers SPS proprietaryIdentification of small molecules by comparison of accurate-mass fragmentation data to a database of 250000 molecules represented as mathematical partitions of the exact molecular masses. SPS (Similar Partition Searching) is designed to rapidly analyze and summarize multiple chromatographic MS/MS datasets acquired by DDA (data dependent acquisition).
REGATTA LC/MS list comparison application that works with ProTrawler (but accepts input in Excel/CSV form) to provide an environment for LC/MS results list filtering and normalization {mass, retention time, integrated intensity} lists.
RemoteAnalyzer proprietarySoftware by SpectralWorks 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 proprietarySuite 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 proprietary Multi-vendor software for statistical analysis of mass spectrometry imaging data.
SimGlycan proprietaryPredicts the structure of glycans and glycopeptides using mass spectrometry MS/MS data.
SIMION proprietaryIon 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 proprietarySoftware for analysis and visualization of mass spectrometric data.[69]
StavroX freewareSoftware 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.[70]
Swiss Mass Abacus open sourceSwiss 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 proprietarySoftware by Markes International used with BenchTOF time-of-flight mass spectrometers
TurboMass proprietaryGC/MS software by PerkinElmer.
Trans-Proteomic Pipeline (TPP) open sourceThe Trans-Proteomic Pipeline (TPP) 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 (can also combine the results of multiple search engines) and ProteinProphet for Protein identification and validation, using PeptideProphet OR iProphet results. TPP does also Protein Quantification with XPRESS (Calculation of relative abundances of peptides and proteins from isotopically labeled MS/MS samples), ASAPRatio (Automated Statistical Analysis on Protein Ratio; an alternative to XPRESS) and Libra (Quantification of isobarically-labeled samples (e.g. iTraq, TMT, etc.) for any number of channels). The TPP currently supports Sequest, Mascot, ProbID, X!Tandem, Comet, SpectraST, MSGF+, Inspect, MyriMatch, and Phenyx. Developed at the Seattle Proteomic Centre (SPC).[71]

[72]

Universal Mass Calculator Universal Mass Calculator (UMC) 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 (accurate mass and time tag approach).[73]
Xcalibur proprietarySoftware by Thermo Fisher Scientific used with mass spectrometry instruments.
XCMS Online (Cloud-Based) proprietaryFreely available and the most widely used metabolomic and lipidomic data processing platform with over 21,000 users as of 2017.

See also

References
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