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List of mass spectrometry software#MassBank

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

Proteomics software

{{further|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. In contrast, the latter infers peptide sequences without knowledge of genomic data.

=Database search algorithms=

class="sortable wikitable" style="text-align: left"
Name

! Type|| Description

Andromeda

| Freeware

Andromeda is a peptide search engine based on probabilistic scoring, developed by Jürgen Cox and others at the Max Planck Institute of Biochemistry. It can handle data with arbitrarily high fragment mass accuracy and is able to assign and score complex patterns of post-translational modifications, such as highly phosphorylated peptides. It can function independently or integrated into other software, enabling analysis of large datasets on a desktop computer.{{cite journal|last1=Cox|first1=Jürgen|last2=Neuhauser|first2=Nadin|last3=Michalski|first3=Annette|last4=Scheltema|first4=Richard A.|last5=Olsen|first5=Jesper V.|last6=Mann|first6=Matthias|title=Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment|journal=Journal of Proteome Research|volume=10|issue=4|year=2011|pages=1794–1805|issn=1535-3893|doi=10.1021/pr101065j|pmid=21254760|doi-access=free}}
Byonic

| Proprietary

Byonic is a database search algorithm released in 2011 by Protein Metrics Inc. with original developments at PARC.{{cite journal|last1=Bern|first1=Marshall|last2=Cai|first2=Yuhan|last3=Goldberg|first3=David|title=Lookup Peaks: A Hybrid of de Novo Sequencing and Database Search for Protein Identification by Tandem Mass Spectrometry|journal=Analytical Chemistry|volume=79|issue=4|pages=1393–1400|year=2007|pmid=17243770|doi=10.1021/ac0617013|s2cid=27769662}} It searches MS/MS data from all types of instruments and internally employs the program Combyne,{{cite journal|last1=Bern|first1=Marshall|last2=Goldberg|first2=David|title=Improved Ranking Functions for Protein and Modification-Site Identifications|journal=Journal of Computational Biology|volume=15|issue=7|pages=705–719|year=2008|pmid=18651800|doi=10.1089/cmb.2007.0119}} which combines peptide identifications to produce protein scores and identification probabilities.
CHIMERYS

|Proprietary

|CHIMERYS is a cloud-native database search algorithm that makes heavy use of artificial intelligence for the identification of peptides and the deconvolution of chimeric spectra. CHIMERYS is developed by MSAID GmbH, which was started at the Technical University of Munich.

Comet

| Open source

Comet is a command-line database search algorithm developed at the University of Washington. It takes in spectra in supported input formats and writes out .pep.xml, .pin.xml, .sqt and/or .out files.{{cite journal|last1=Eng|first1=Jimmy K.|last2=Jahan|first2=Tahmina A.|last3=Hoopmann|first3=Michael R.|title=Comet: An open-source MS/MS sequence database search tool|journal=Proteomics|volume=13|issue=1|year=2013|pages=22–24|issn=1615-9853|doi=10.1002/pmic.201200439|pmid=23148064|s2cid=13533125}}
Greylag

| Open source

Greylag is a database search algorithm developed at the Stowers Institute for Medical Research designed to perform large searches on computational clusters containing hundreds of nodes.
InsPecT

| Open source

InsPecT is an MS-alignment search algorithm developed by the Center for Computational Mass Spectrometry at the University of California, San Diego.{{cite news|title=Inspect and MS-Alignment}}
Mascot

| Proprietary

Mascot performs mass spectrometry data analysis through a statistical evaluation of matches between observed and projected peptide fragments.{{cite journal|last1=Perkins|first1=David N.|last2=Pappin|first2=Darryl J. C.|last3=Creasy|first3=David M.|last4=Cottrell|first4=John S.|title=Probability-based protein identification by searching sequence databases using mass spectrometry data|journal=Electrophoresis|volume=20|issue=18|pages=3551–67|year=1999|pmid=10612281|doi=10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2|s2cid=42423655}}
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

MassWiz is a search algorithm developed at the Institute of Genomics and Integrative Biology that can be used as a Windows command-line tool.{{Citation needed|date=April 2024}}
MetaMorpheus

| Open source

MetaMorpheus is a proteomics search software developed at the University of Wisconsin-Madison with integrated calibration, post-translational modification discovery, bottom-up and top-down proteomics search, cross-linking mass spectrometry (XL-MS) search, proteogenomic search, and label-free quantification (LFQ) capabilities.{{cite journal|last1=Solntsev|first1=Stefan K.|last2=Shortreed|first2=Michael R.|last3=Frey|first3=Brian L.|last4=Smith|first4=Lloyd M.|title=Enhanced Global Post-translational Modification Discovery with MetaMorpheus|url=|journal=Journal of Proteome Research|year=2018|volume=17|issue=5| pages=1844–1851|doi=10.1021/acs.jproteome.7b00873|pmid= 29578715}}
MSFragger

| Freeware

MSFragger is a database searching tool based on efficient fragment ion indexing developed at the University of Michigan. It is capable of open (mass-tolerant) searches for post-translational modification discovery, O- and N-linked glycoproteomics searches, semi- and non-enzymatic searches, and traditional database searches.{{cite journal|last1=Kong|first1=Andy T.|last2=Leprevost|first2=Felipe V.|last3=Avtonomov|first3=Dmitry M.|last4=Mellacheruvu|first4=Dattatreya|last5=Nesvizhskii|first5=Alexey I.|title=MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics|url=|journal=Nature Methods|year=2017|volume=14|issue=5| pages=513–520|doi=10.1038/nmeth.4256|pmid=28394336|pmc=5409104}}
MS-GF+

| Open source

MS-GF+ (also known as MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database. MS-GF+ was developed at the Center for Computational Mass Spectrometry at the University of California, San Diego, with later work at Pacific Northwest National Laboratory (PNNL).
MS-LAMP

|Open Source

|MS-LAMP is 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.{{Cite journal|last1=Sabareesh|first1=Varatharajan|last2=Singh|first2=Gurpreet|date=2013|title=Mass spectrometry-based lipid(ome) analyzer and molecular platform: a new software to interpret and analyze electrospray and/or matrix-assisted laser desorption/ionization mass spectrometric data of lipids: a case study from Mycobacterium tuberculosis|journal=Journal of Mass Spectrometry|volume=48|issue=4|pages=465–477|doi=10.1002/jms.3163|pmid=23584940|issn=1096-9888|bibcode=2013JMSp...48..465S}}

MyriMatch

| Open source

MyriMatch is a 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.{{cite journal|last1=Tabb|first1=David L.|last2=Fernando|first2=Christopher G.|last3=Chambers|first3=Matthew C.|title=MyriMatch:  Highly Accurate Tandem Mass Spectral Peptide Identification by Multivariate Hypergeometric Analysis|journal=Journal of Proteome Research|volume=6|issue=2|pages=654–61|year=2007|pmid=17269722|pmc=2525619|doi=10.1021/pr0604054}}
NIST Mass Spectral Search v.3.0

| Commercial Program

This software contains the NIST/EPA/NIH Mass Spectral Library of electron ionization (EI) and the NIST Tandem Library of product-ion mass spectra in a searchable database. Additional features include the NIST MS Interpreter Program and AMDIS. It was developed by the National Institute of Standards and Technology.[https://chemdata.nist.gov/dokuwiki/lib/exe/fetch.php?media=chemdata:asms2023:asms2023_nist23_features.pdf NIST23 Features.] Retrieved February 6, 2024.
OMSSA

| Freeware

The Open Mass Spectrometry Search Algorithm (OMSSA) is a search engine for identifying MS/MS peptide spectra by searching libraries of known protein sequences. OMSSA identifies 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.{{cite web|url=https://pubchem.ncbi.nlm.nih.gov/omssa/|title=OMSSA ms/ms search engine|publisher=Pubchem.ncbi.nlm.nih.gov|access-date=2011-09-27}}{{cite journal|last1=Geer|first1=Lewis Y.|last2=Markey|first2=Sanford P.|last3=Kowalak|first3=Jeffrey A.|last4=Wagner|first4=Lukas|last5=Xu|first5=Ming|last6=Maynard|first6=Dawn M.|last7=Yang|first7=Xiaoyu|last8=Shi|first8=Wenyao|last9=Bryant|first9=Stephen H.|title=Open Mass Spectrometry Search Algorithm|journal=Journal of Proteome Research|volume=3|issue=5|pages=958–64|year=2004|pmid=15473683|doi=10.1021/pr0499491|arxiv=q-bio/0406002|bibcode=2004q.bio.....6002G|s2cid=12218715}}
PEAKS DB

|Proprietary

Peaks DB is a database search engine, run in parallel with de novo sequencing to automatically validate search results, allowing for more 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.{{cite conference|last1=Liang|first1=C|last2=Smith|first2=JC|last3=Hendrie|first3=Christopher|title=A Comparative Study of Peptide Sequencing Software Tools for MS/MS|conference=American Society for Mass Spectrometry|year=2003}} 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 was developed in 2002 in the Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.
Phenyx

| Proprietary

Phenyx is a sequence database search engine developed 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.{{cite journal|last1=Colinge|first1=Jacques|last2=Masselot|first2=Alexandre|last3=Giron|first3=Marc|last4=Dessingy|first4=Thierry|last5=Magnin|first5=Jérôme|title=OLAV: Towards high-throughput tandem mass spectrometry data identification|journal=Proteomics|volume=3|issue=8|pages=1454–63|year=2003|pmid=12923771|doi=10.1002/pmic.200300485|s2cid=36666495}}
ProbID

| Open source

ProbID is a software tool designed to identify peptides from tandem mass spectra using a protein sequence database. It was developed at the Bioinformatics Group, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.{{cite journal|last1=Zhang|first1=Zhuo|title=A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data|last2=Sun|first2=Shiwei|last3=Zhu|first3=Xiaopeng|last4=Chang|first4=Suhua|last5=Liu|first5=Xiaofei|last6=Yu|first6=Chungong|last7=Bu|first7=Dongbo|last8=Chen|first8=Runsheng|journal=BMC Bioinformatics|volume=7|issue=1|year=2006|pages=222|issn=1471-2105|doi=10.1186/1471-2105-7-222|pmid=16638152|pmc=1463009|doi-access=free}}
ProLuCID

| Freeware

ProLuCID is an algorithm for peptide identification using tandem mass spectrometry and protein sequence databases recently developed by Tao Xu and others in the Yates laboratory at The Scripps Research Institute.{{cite journal|last1=Xu|first1=T.|last2=Park|first2=S.K.|last3=Venable|first3=J.D.|last4=Wohlschlegel|first4=J.A.|last5=Diedrich|first5=J.K.|last6=Cociorva|first6=D.|last7=Lu|first7=B.|last8=Liao|first8=L.|last9=Hewel|first9=J.|last10=Han|first10=X.|last11=Wong|first11=C.C.L.|last12=Fonslow|first12=B.|last13=Delahunty|first13=C.|last14=Gao|first14=Y.|last15=Shah|first15=H.|last16=Yates|first16=J.R.|title=ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity|journal=Journal of Proteomics|volume=129|year=2015|pages=16–24|issn=1874-3919|doi=10.1016/j.jprot.2015.07.001|pmid=26171723|pmc=4630125}}
ProSightPC and ProSightPD

|Proprietary

|ProSightPC/PD are software tools for searching peptide and protein tandem mass spectrometry data against UniProt-derived databases to identify and characterize proteoforms.

ProteinPilot Software

| Proprietary

ProteinPilot uses 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 peptide identification. It considers hundreds of modifications, non-tryptic cleavages, and amino acid substitutions. It uses the Pro Group Algorithm for protein inference analysis to report a minimal set of proteins justified based on the peptide evidence. ProteinPilot supports quantification for label-based workflows (iTRAQ reagents, mTRAQ reagents and SILAC labeling). A translation layer converts user interface controls in the language of a proteomics scientist to underlying complex informatics parameters.{{cite journal|last1=Shilov|first1=Ignat V.|last2=Seymour|first2=Sean L.|last3=Patel|first3=Alpesh A.|last4=Loboda|first4=Alex|last5=Tang|first5=Wilfred H.|last6=Keating|first6=Sean P.|last7=Hunter|first7=Christie L.|last8=Nuwaysir|first8=Lydia M.|last9=Schaeffer|first9=Daniel A.|title=The Paragon Algorithm, a Next Generation Search Engine That Uses Sequence Temperature Values and Feature Probabilities to Identify Peptides from Tandem Mass Spectra|journal=Molecular & Cellular Proteomics|volume=6|issue=9|year=2007|pages=1638–1655|issn=1535-9476|doi=10.1074/mcp.T600050-MCP200|pmid=17533153|s2cid=7097773|doi-access=free}}
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 and Batch-Tag Web, with the results processed and displayed using Search Compare.
RAId

| Lost

RAId was developed at the National Center for Biotechnology Information, Robust Accurate Identification (RAId){{cite web|url=https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/raid/index.html|title=RAId MS/MS search engine|publisher=QMBP NCBI NLM NIH|access-date=2008-01-01}} is a suite of proteomics tools for statistical analysis of tandem mass spectrometry data.{{cite journal|last1=Alves|first1=Gelio|last2=Ogurtsov|first2=Aleksey Y.|last3=Yu|first3=Yi-Kuo|title=RAId_DbS: peptide identification using database searches with realistic statistics|journal=Biol Direct|volume=2|page=25|year=2007|pmid=17961253|doi=10.1186/1745-6150-2-25|pmc=2211744|doi-access=free}}
SEQUEST

|Proprietary

SEQUEST is a MS data analysis program used for protein identification. It correlates collections of tandem mass spectra to peptide sequences that have been generated from databases of protein sequences.{{cite journal|author1=Jimmy K. Eng|author2=Ashley L. McCormack|author3=John R. Yates, III|title=An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database|journal=Journal of the American Society for Mass Spectrometry|volume=5|pages=976–989|year=1994|doi=10.1016/1044-0305(94)80016-2|issue=11|pmid=24226387|bibcode=1994JASMS...5..976E |s2cid=18413192}}
SIMS

| Open source

SIMS was designed to perform unrestricted PTM searches over tandem mass spectra.{{cite journal|last1=Hricovíni|first1=Miloš|last2=Tvaroška|first2=Igor|last3=Hirsch|first3=Ján|last4=Duben|first4=Anthony J.|title=Nuclear overhauser effects and the flexibility of saccharides: methyl β-xylobioside|journal=Carbohydrate Research|volume=210|year=1991|pages=13–20|issn=0008-6215|doi=10.1016/0008-6215(91)80109-Z|pmid=1878875}}
SimTandem

| Freeware

SimTandem is 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.{{cite journal|first1=Jiri|last1=Novak|first2=Timo|last2=Sachsenberg|first3=David|last3=Hoksza|first4=Tomas|last4=Skopal|first5=Oliver|last5=Kohlbacher|title=On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications|journal=Journal of Integrative Bioinformatics|volume=10|issue=3|pages=1–15|year=2013|doi=10.1515/jib-2013-228|pmid=24231142|s2cid=22469656|doi-access=free}}
SQID

| Open source

SeQuence IDentification (SQID) is an intensity-incorporated protein identification algorithm for tandem mass spectrometry.
Tide (rewrite of Crux)

| Open source

Tide is a tool to identify peptides from tandem mass spectra. It is an independent re-implementation 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 was re-engineered to achieve speed improvement while replicating SEQUEST XCorr scores. It was developed at the University of Washington.{{cite journal|last1=Diament|first1=Benjamin J.|last2=Noble|first2=William Stafford|title=Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra|journal=Journal of Proteome Research|volume=10|issue=9|year=2011|pages=3871–3879|issn=1535-3893|doi=10.1021/pr101196n|pmid=21761931|pmc=3166376}}
TopMG

| Open source

TopMG (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 and phosphorylated proteoforms, using mass graphs. 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.{{cite journal|last1=kou|first1=Qiang|last2=Wu|first2=Si|last3=Tolić|first3=Nikola|last4=Paša-Tolić|first4=Ljiljana|last5=Liu|first5=Yunlong|last6=Liu|first6=Xiaowen|title=A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra.|journal=Bioinformatics|volume=33|issue=9|year=2017|pages=1309–1316|issn=1460-2059|doi=10.1093/bioinformatics/btw806|pmid=28453668|pmc=5860502}}
TopPIC

| Open source

TopPIC (Top-down mass spectrometr/y-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 identifies proteoforms with unexpected alterations, such as mutations and post-translational modifications (PTMs), estimates the statistical significance of identifications, and characterizes reported proteoforms with unknown mass shifts. Techniques used such as indexes, spectral alignment, generation function methods and the modification identification score (MIScore) seek to increase speed, sensitivity, and accuracy.{{cite journal|last1=kou|first1=Qiang|last2=Xun|first2=Likun|last3=Liu|first3=Xiaowen|title=TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization.|journal=Bioinformatics|volume=32|issue=22|year=2016|pages=3495–3497|issn=1460-2059|doi=10.1093/bioinformatics/btw398|pmid=27423895|pmc=5181555}}
X!Tandem

| Open source

X!Tandem matches tandem mass spectra with peptide sequences.
WsearchVS2020

|Freeware

|WsearchVS2020 is a data analysis software that can display spectra acquired on commercial MS instruments and can also search/match the NIST commercial database.

=De novo sequencing algorithms=

De novo peptide sequencing algorithms are, in general, based on the approach proposed in Bartels et al. (1990).{{cite journal|last=Bartels|first=Christian|title=Fast algorithm for peptide sequencing by mass spectroscopy|journal=Biological Mass Spectrometry|date=31 May 1990|volume=19|issue=6|pages=363–368|doi=10.1002/bms.1200190607|pmid=24730078}}

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Name

! Type|| Description

CycloBranch

| Open source

CycloBranch is a 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.{{cite journal|first1=Jiri|last1=Novak|first2=Karel|last2=Lemr|first3=Kevin A.|last3=Schug|first4=Vladimir|last4=Havlicek|title=CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra|journal=Journal of the American Society for Mass Spectrometry|volume=26|issue=10|pages=1780–1786|pmid=26195308|year=2015|doi=10.1007/s13361-015-1211-1|bibcode=2015JASMS..26.1780N|s2cid=207470364}}
DeNoS| Sequencing of peptides uses all information from CAD and ECD spectra; it is part of the software tool Proteinmatching Analysis Software (PAS) which in turn is part of the software package Medicwave Bioinformatics Suite (MBS).{{cite journal|last1=Savitski|first1=Mikhail M.|last2=Nielsen|first2=Michael L.|last3=Kjeldsen|first3=Frank|last4=Zubarev|first4=Roman A.|title=Proteomics-Grade de Novo Sequencing Approach|journal=Journal of Proteome Research|volume=4|issue=6|year=2005|pmid=16335984|doi=10.1021/pr050288x|pages=2348–54}}
DeNovoX

| Proprietary

De novo sequencing on CID spectra acquired with ion trap mass spectrometers delivers complete and/or partial peptide sequences (sequence tags).[http://goliath.ecnext.com/coms2/gi_0199-1579589/Thermo-Finnigan-Introduces-DeNovoX-TM.html thermo finnigan introduces denovox – Search results ]{{Dead link|date=February 2015}}
Lutefisk

| Open source

This is software for the de novo interpretation of peptide CID spectra.
Novor

| Proprietary, free for academic research

This real-time de novo peptide sequencing engine is claimed to be fast, accurate and easily integrated into research pipelines.
PEAKS

| Proprietary

PEAKS provides de novo sequencing for each peptide, confidence scores on individual amino acid assignments with manually assisted mode and automated de novo sequencing on an entire LC run, with data processed faster than 1 spectrum per second.{{cite journal|last1=Ma|first1=Bin|last2=Zhang|first2=Kaizhong|last3=Hendrie|first3=Christopher|last4=Liang|first4=Chengzhi|last5=Li|first5=Ming|last6=Doherty-Kirby|first6=Amanda|last7=Lajoie|first7=Gilles|title=PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry|journal=Rapid Communications in Mass Spectrometry|volume=17|issue=20|pages=2337–42|year=2003|pmid=14558135|doi=10.1002/rcm.1196|bibcode=2003RCMS...17.2337M}}{{cite journal|last1=Tannu|first1=Nilesh S|last2=Hemby|first2=Scott E|title=De novo protein sequence analysis of Macaca mulatta|journal=BMC Genomics|volume=8|page=270|year=2007|pmid=17686166|pmc=1965481|doi=10.1186/1471-2164-8-270|doi-access=free}}
Supernovo

| Proprietary

This software automates de novo sequencing of monoclonal antibodies.{{Cite journal|last1=Sen|first1=K. Ilker|last2=Tang|first2=Wilfred H|last3=Nayak|first3=Shruti|last4=Kil|first4=Yong J|last5=Bern|first5=Marshall|last6=Ozoglu|first6=Berk|last7=Ueberheide|first7=Beatrix|last8=Davis|first8=Darryl|last9=Becker|first9=Christopher|date=2017-05-01|title=Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery|journal=Journal of the American Society for Mass Spectrometry|language=en|volume=28|issue=5|pages=803–810|doi=10.1007/s13361-016-1580-0|pmid=28105549|pmc=5392168|bibcode=2017JASMS..28..803S |issn=1044-0305}}
Casanovo

| Open source

Casanovo is a machine learning model that uses a transformer neural network architecture to translate the sequence of peaks in a tandem mass spectrum into the sequence of amino acids that comprise the generating peptide, enabling de novo peptide sequencing without prior information.{{cite journal

| last1 = Yilmaz

| first1 = Melih

| last2 = Fondrie

| first2 = William

| date = 2024-07-30

| title = Sequence-to-sequence translation from mass spectra to peptides with a transformer model

| url = https://www.nature.com/articles/s41467-024-49731-x

| journal = Nature Communications

| doi = 10.1038/s41467-024-49731-x

| access-date = 2025-04-25

| hdl = 10067/2075800151162165141

| hdl-access = free

}}

InstaNovo

|Open source

InstaNovo is a transformer neural network that can translate fragment ion peaks into the sequence of amino acids that make up the studied peptide(s), enabling de novo peptide sequencing without prior information. Trained on 28 million labeled spectra, it outperforms current state-of-the-art methods on benchmark datasets. InstaNovo+, a multinomial diffusion model built upon human intuition, further improves performance through iterative refinement of predicted sequences.{{cite journal

| last1 = Eloff

| first1 = Kevin

| last2 = Kalogeropoulos

| first2 = Konstantinos

| date = 2024-03-04

| title = InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments

| url = https://www.nature.com/articles/s42256-025-01019-5

| journal = Nature Machine Intelligence

| doi = 10.1038/s42256-025-01019-5

| access-date = 2022-04-25

| doi-access = free

}}

=Homology searching algorithms=

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Name

! Type|| Description

MS-Homology

| Open source

MS-Homology is a database search program within the Protein Prospector package that permits searching with strings that combine masses and amino acid stretches and where one can specify the number of amino acid mismatches allowed.
SPIDER

| Proprietary

The 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|Quantitative proteomics}}

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Name

! Type|| Description

BACIQ

| Open source

BACIQ is a mathematically rigorous approach that integrates peptide intensities and peptide-measurement agreement into confidence intervals for protein ratios.
Byos

| Proprietary

Byos commercial software allows XIC of peptide level mass spec data from any MS vendor and relative quantity of PTM vs unmodified. It is specialized for biopharmaceutical applications.
DIA-NN

|Freeware

|This automated quantitative Data-independent acquisition-proteomics software, developed by the Demichev and Ralser labs at the Charité in Berlin, Germany, implements a machine-learning algorithm based on an ensemble of deep neural networks, to boost proteomic depth and reliability of peptide and protein identification. DIA-NN is optimized for processing of large-scale experiments. It supports DIA-based profiling of PTMs, such as phosphorylation and ubiquitination, new technologies such as Scanning SWATH{{Cite journal|last1=Messner|first1=Christoph B.|last2=Demichev|first2=Vadim|last3=Bloomfield|first3=Nic|last4=Yu|first4=Jason S. L.|last5=White|first5=Matthew|last6=Kreidl|first6=Marco|last7=Egger|first7=Anna-Sophia|last8=Freiwald|first8=Anja|last9=Ivosev|first9=Gordana|last10=Wasim|first10=Fras|last11=Zelezniak|first11=Aleksej|date=July 2021|title=Ultra-fast proteomics with Scanning SWATH|journal=Nature Biotechnology|language=en|volume=39|issue=7|pages=846–854|doi=10.1038/s41587-021-00860-4|pmid=33767396|pmc=7611254|issn=1546-1696}} and dia-PASEF,{{Cite journal|last1=Demichev|first1=Vadim|last2=Yu|first2=Fengchao|last3=Teo|first3=Guo Ci|last4=Szyrwiel|first4=Lukasz|last5=Rosenberger|first5=George A.|last6=Decker|first6=Jens|last7=Kaspar-Schoenefeld|first7=Stephanie|last8=Lilley|first8=Kathryn S.|last9=Mülleder|first9=Michael|last10=Nesvizhskii|first10=Alexey I.|last11=Ralser|first11=Markus|date=2021-03-09|title=High sensitivity dia-PASEF proteomics with DIA-NN and FragPipe|url=https://www.biorxiv.org/content/10.1101/2021.03.08.434385v1|journal=bioRxiv|language=en|pages=2021.03.08.434385|doi=10.1101/2021.03.08.434385|s2cid=232223730}} and can perform library-free analyses (acts as a database search engine).{{Cite journal|last1=Demichev|first1=Vadim|last2=Messner|first2=Christoph B.|last3=Vernardis|first3=Spyros I.|last4=Lilley|first4=Kathryn S.|last5=Ralser|first5=Markus|date=January 2020|title=DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput|journal=Nature Methods|language=en|volume=17|issue=1|pages=41–44|doi=10.1038/s41592-019-0638-x|pmid=31768060|pmc=6949130|issn=1548-7105}}

FlashLFQ

| Open source

FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.{{cite journal|last1=Millikin|first1=Robert J.|last2=Solntsev|first2=Stefan K.|last3=Shortreed|first3=Michael R.|last4=Smith|first4=Lloyd M.|title=Ultrafast Peptide Label-Free Quantification with FlashLFQ|journal=Journal of Proteome Research|date=2018|volume=17|issue=1|pages=386–391|doi=10.1021/acs.jproteome.7b00608|pmid= 29083185|pmc=5814109}} FlashLFQ is also bundled into MetaMorpheus search software, which is described above.
MarkerView Software

| Proprietary

This commercial software is for statistical analysis of quantitative mass spec data sets from metabolomics and proteomic profiling applications.
Mascot Distiller

| Proprietary

This software for peak picking and raw data preprocessing has an optional toolbox for label-free quantification, as well as isobaric labeling and isotopic labeling. It supports raw file formats from all major instrument vendors.
Mascot Server

| Proprietary

The search engine supports quantification based on isobaric labeling as long as all the required information is part of the MS/MS spectrum.
MassChroQ

| Open source

Peptide quantification analysis of label-free or various isotopic labeling methods (SILAC, ICAT, N-15, C-13 ...) works with high and low resolution spectrometer systems and supports complex data treatments, such as peptide or protein fractionation, prior to LC-MS analysis (SCX, SDS-PAGE, etc.).
[https://www.maxquant.org MaxQuant]

| Freeware

Quantitative proteomics software developed by Jürgen Cox and others at the Max Planck Institute of Biochemistry in Martinsried, Germany was written in C#, which allows the analysis of label free and SILAC-based proteomics experiments. MaxQuant uses the andromeda search engine for the interpretation of the MS/MS spectra.{{Cite journal |last=Cox |first=Jürgen |last2=Mann |first2=Matthias |date=December 2008 |title=MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification |url=https://www.nature.com/articles/nbt.1511 |journal=Nature Biotechnology |language=en |volume=26 |issue=12 |pages=1367–1372 |doi=10.1038/nbt.1511 |issn=1546-1696|url-access=subscription }}
MultiQuant Software

| Proprietary

This software can process quantitative data sets from TripleTOF or QTRAP systems, including MRM and SWATH Acquisition.
OpenMS / TOPP

| Open source

The software C++ library for LC-MS/MS data management and analysis offers an infrastructure for the development of mass spectrometry-related software. It allows peptide and metabolite quantification and supports label-free and isotopic-label-based quantification (such as iTRAQ and TMT and SILAC) as well as targeted SWATH-MS quantification.{{cite journal|vauthors=Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O|title=OpenMS: a flexible open-source software platform for mass spectrometry data analysis|journal=Nat. Methods|volume=13|issue=9|pages=741–8|year=2016|pmid=27575624|doi=10.1038/nmeth.3959|s2cid=873670|url=http://edoc.mdc-berlin.de/15966/13/15966oa.pdf}}
OpenPIP

|Website, open access

|OpenPIP is a tool developed by InterVenn Biosciences to integrate peaks acquired in multiple reaction monitoring (MRM) experiments. The software is powered by recurrent neural networks and guided by a large collection of manually-annotated chromatographic peaks.

ProtMax

| Freeware

ProtMAX{{cite journal|vauthors=Egelhofer V, Hoehenwarter W, Lyon D, Weckwerth W, Wienkoop S|title=Using ProtMAX to create high-mass-accuracy precursor alignments from label-free quantitative mass spectrometry data generated in shotgun proteomics experiments|journal=Nat Protoc|volume=8|issue=3|pages=595–601|year=2013|pmid=23449253|doi=10.1038/nprot.2013.013|s2cid=29653992}} is a software tool for analyzing shotgun proteomics mass spectrometry data sets, developed by Volker Egelhofer at the University of Vienna.
Skyline

| Open source

Skyline is open source (Apache 2.0) Windows client software developed in the MacCoss lab at University of Washington.{{cite journal|last=Maclean|first=B|title=Skyline: An Open Source Document Editor for Creating and Analyzing Targeted Proteomics Experiments|journal=Bioinformatics|date=2010|volume=26|issue=7|pages=966–968|doi=10.1093/bioinformatics/btq054|pmid=20147306|pmc=2844992}} It 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 analysis of the resulting mass spectrometer data.
Spectronaut

| Proprietary

Biognosys AG (Schlieren, Switzerland) developed this commercial software for quantitative proteomics based on the mProphet algorithm{{cite journal|last=Reiter|first=L|title=mProphet: automated data processing and statistical validation for large-scale SRM experiments|journal=Nat Methods|date=2011|volume=8|issue=5|pages=430–435|doi=10.1038/nmeth.1584|pmid=21423193|s2cid=205419625|display-authors=etal}} that allows the targeted analysis of data independent acquisition (DIA) data sets for label-free peptide quantitation, also called SWATH acquisition.{{cite journal|last=Law|first=KP|author2=Lim YP|title=Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring|journal=Expert Rev Proteomics|date=2013|volume=10|issue=6|pages=551–566|doi=10.1586/14789450.2013.858022|pmid=24206228|s2cid=29969570}}
SWATH Software 2.0

| Proprietary

This commercial software processing tool within PeakView 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.

Other software

class="sortable wikitable" style="text-align: left"
Name

! Type|| Description

Advanced Chemistry Development

| Proprietary

ACD offers commercial solutions for the interpretation of MS and xC/MS data with spectrum/structure matching, identification of known and unknown metabolites, as well as identification of compounds through spectral comparison.
AMDIS

| Freeware

NIST created this software for GC/MS data in various formats. It deconvolutes coeluting mass spectra, displays mass chromatograms, calculates retention indexes, allows for target compound libraries, and will export spectra to the NISMS Mass Spectral Search Program.
Analyst

| Proprietary

Analyst was created by AB Sciex, a division of The Danaher Corporation, for control of LC-MS/MS systems.
AnalyzerPro

| Proprietary

AnalyzerPro is a 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 with MatrixAnalyzer for the comparison of multiple data sets. It was recently extended to include statistical analysis and visualization tools (PCA). AnalyzerPro XD is a 64-bit version that includes support for 2 dimensional data processing such as GCxGC-MS.
ArtIST by Clover Biosoft

| Proprietary

Artificial Intelligence Strain Typing is an online service offering MALDI-TOF MS data analysis and biomarker discovery tools, based on artificial intelligence and machine learning algorithms.
ASCENT

| Proprietary

ASCENT is an LC and GC-MS data analysis automation tool, provided as SaaS over a cloud platform. It uses machine learning algorithms to analyze MS plots and reduce the amount of manual review required.
CFM-ID

| Open source

This software is for in-silico ESI-MS/MS spectra prediction, MS/MS spectra annotation, and compound identification based on an MS/MS spectrum. It was developed in Wishartlab{{Cite journal|url=|doi=10.1093/nar/gku436|title=CFM-ID: A web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra|year=2014|last1=Allen|first1=Felicity|last2=Pon|first2=Allison|last3=Wilson|first3=Michael|last4=Greiner|first4=Russ|author5-link=David S. Wishart|last5=Wishart|first5=David|journal=Nucleic Acids Research|volume=42|issue=Web Server issue|pages=W94–W99|pmid=24895432|pmc=4086103}}{{Cite journal|url=https://doi.org/10.1007/s11306-014-0676-4|doi=10.1007/s11306-014-0676-4|title=Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification|year=2015|last1=Allen|first1=Felicity|last2=Greiner|first2=Russ|last3=Wishart|first3=David|journal=Metabolomics|volume=11|pages=98–110|arxiv=1312.0264|s2cid=256589}}{{Cite journal|url=https://doi.org/10.1021/acs.analchem.6b01622|doi=10.1021/acs.analchem.6b01622|title=Computational Prediction of Electron Ionization Mass Spectra to Assist in GC/MS Compound Identification|year=2016|last1=Allen|first1=Felicity|last2=Pon|first2=Allison|last3=Greiner|first3=Russ|last4=Wishart|first4=David|journal=Analytical Chemistry|volume=88|issue=15|pages=7689–7697|pmid=27381172|url-access=subscription}}{{Cite journal|url=|doi=10.3390/metabo9040072|title=CFM-ID 3.0: Significantly Improved ESI-MS/MS Prediction and Compound Identification|year=2019|last1=Djoumbou-Feunang|first1=Yannick|last2=Pon|first2=Allison|last3=Karu|first3=Naama|last4=Zheng|first4=Jiamin|last5=Li|first5=Carin|last6=Arndt|first6=David|last7=Gautam|first7=Maheswor|last8=Allen|first8=Felicity|last9=Wishart|first9=David S.|journal=Metabolites|volume=9|issue=4|page=72|pmid=31013937|pmc=6523630|s2cid=129941603|doi-access=free}}
Chromeleon

| Proprietary

Chromeleon is Thermo Fisher Scientific software used with mass spectrometry instruments, as well as chromatography instruments.
Clover MSDAS

| Proprietary

Cloud-based platform for data analysis with FTIR and MALDI TOF MS data. Subtyping and AMR detection in FTIR and MALDI spectra. Biomarker analysis, Quality control, reproducibility studies and training of machine learning models.
Crosslinx

| Open source

Identify cross-linked peptides from mzML files and use Python script or standalone executables for Linux and Windows. It is feasible to use with bigger databases with a two-step approach.{{cite journal|last1=Ozawa|first1=SI|last2=Bald|first2=T|last3=Onishi|first3=T|last4=Xue|first4=H|last5=Matsumura|first5=T|last6=Kubo|first6=R|last7=Takahashi|first7=H|last8=Hippler|first8=M|last9=Takahashi|first9=Y|title=Configuration of Ten Light-Harvesting Chlorophyll a/b Complex I Subunits in Chlamydomonas reinhardtii Photosystem I.|journal=Plant Physiology|date=October 2018|volume=178|issue=2|pages=583–595|doi=10.1104/pp.18.00749|pmid=30126869|pmc=6181050}}
DataAnalysis

| Proprietary

Software by Bruker used with mass spectrometry instruments.
DeNovoGUI

| Open source

The software has a graphical user interface for running parallelized versions of the freely available de novo sequencing software tools Novor and PepNovo+.{{cite journal|last1=Muth|first1=Thilo|last2=Weilnböck|first2=Lisa|last3=Rapp|first3=Erdmann|last4=Huber|first4=Christian G.|last5=Martens|first5=Lennart|last6=Vaudel|first6=Marc|last7=Barsnes|first7=Harald|title=DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra|journal=Journal of Proteome Research|volume=13|issue=2|year=2014|pages=1143–1146|issn=1535-3893|doi=10.1021/pr4008078|pmid=24295440|pmc=3923451}}
Easotope

| Open source

Easotope software archives, organizes, and analyzes mass spectrometer data. It is currently oriented toward clumped CO2 analysis but is also useful for bulk CO2 work and expandable to other isotopic systems.
El-MAVEN

|Open-source

|Desktop software by Elucidata processes 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.{{Citation|last1=Sahil|title=ElucidataInc/ElMaven: v0.6.1|date=2019-01-11|doi=10.5281/zenodo.2537593|last2=Shubhra Agrawal|last3=GeorgeSabu|last4=Rishabh Gupta|last5=Pankaj Kumar|last6=Saiful B. Khan|last7=kailash yadav|last8=Naman Gupta|last9=Raghav Sehgal}}

ESIprot| ESIprot can determine charge state and calculate molecular weight for low resolution electrospray ionization (ESI) mass spectrometry (MS) data of proteins.{{cite journal|last1=Winkler|first1=Robert|title=ESIprot: a universal tool for charge state determination and molecular weight calculation of proteins from electrospray ionization mass spectrometry data|journal=Rapid Communications in Mass Spectrometry|volume=24|issue=3|year=2010|pmid=20049890|doi=10.1002/rcm.4384|pages=285–94|bibcode=2010RCMS...24..285W|doi-access=free}}
Expressionist

| Proprietary

Expressionist is software for processing, analyzing, and reporting mass spectrometry data in application areas such as biotherapeutics characterization, quality monitoring, and related proteomics and metabolomics applications. It was developed by Genedata.
HIquant

|Open source

|This first-principles model and algorithm quantifies proteoform stoichiometries from bottom-up data.{{Cite journal|last1=Malioutov|first1=Dmitry|last2=Chen|first2=Tianchi|last3=Airoldi|first3=Edoardo|last4=Jaffe|first4=Jacob|last5=Budnik|first5=Bogdan|last6=Slavov|first6=Nikolai|date=2019-01-01|title=Quantifying Homologous Proteins and Proteoforms|url=https://www.mcponline.org/content/18/1/162|journal=Molecular & Cellular Proteomics|language=en|volume=18|issue=1|pages=162–168|doi=10.1074/mcp.TIR118.000947|doi-access=free |issn=1535-9476|pmid=30282776|pmc=6317479}}

KnowItAll Spectroscopy Software & Mass Spectral Library

| Proprietary

Software from Wiley with applications for mass spectrometry including: spectral analysis, database searching (spectrum, structure, peak, property, MS Adaptive Search, etc.), processing, database building (MS or multiple techniques including IR, Raman, NMR, UV, Chromatograms), spectral subtraction, plus tools for reporting and ChemWindow structure drawing, and MASSTransit file conversion software (updated with more formats).
LabSolutions LCMS

| Proprietary

Software by Shimadzu Corporation is used with mass spectrometry and HPLC instruments.
LipidXplorer

| Open source

| A high-throughput lipid identification software from shotgun mass spectra written in Python.{{Cite web|url=https://lifs-tools.org/wiki/index.php/Main_Page|title=LIFS LipidXplorer Wiki}}

Mass++

| Open source

Analysis software for mass spectrometry 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

|Open source

|MassBank and RMassBank development website is provided by the MassBank consortium. MassBank data are shared under a Creative Commons license.

MassBank.eu

|Website

|European MassBank server. The website is maintained and hosted by the Helmholtz Centre for Environmental Research (Leipzig, Germany). MassBank.eu is a core of the NFDI4Chem consortium.

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.
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 for analytical instrument control.
MassMap

| Proprietary

General-purpose software suite for automated evaluation of MS data by MassMap GmbH & Co. KG. It is 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 methods for the identification of unexpected/unknown components in very complex mixtures.
Mass Mountaineer

|Proprietary

|Qualitative analysis and reporting software includes chemometric functions for working with one or more text-format mass spectra.

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. It 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 pre-processed data for biomarker discovery, unsupervised clustering and supervised sample classification.{{cite journal|doi=10.1186/s12859-015-0752-4|volume=16|title=Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery|journal=BMC Bioinformatics|pmid=26437641|pmc=4595311|page=318|last1=López-Fernández|first1=H|last2=Santos|first2=HM|last3=Capelo|first3=JL|last4=Fdez-Riverola|first4=F|last5=Glez-Peña|first5=D|last6=Reboiro-Jato|first6=M| year=2015|doi-access=free}}
massXpert

| Open source GPL

Graphical user interface-based (GUI) software for simulating and analyzing mass spectrometric data obtained on known bio-polymer sequences.{{cite journal|last1=Rusconi|first1=F.|title=massXpert 2: a cross-platform software environment for polymer chemistry modeling and simulation/analysis of mass spectrometric data|journal=Bioinformatics|volume=25|issue=20|year=2009|pmid=19740912|doi=10.1093/bioinformatics/btp504|pages=2741–2|doi-access=free}} It is a successor to polyxmass and a program of the msXpertSuite software suite.
Mestrenova

|Proprietary

|A vendor-independent software for processing chromatography (LC, GC, SFC) data with any combination of detectors, e.g. LC-MS-UV-VIS, GC-MS, SFC-MS-UV in one environment. This multiplatform and web-based software was created by Mestrelab Research, S.L.

matchms

| Open source

Python library imports, cleans, processes and quantitatively compares MS/MS spectra and was developed at the Netherlands eScience Center.{{cite journal|last1=Huber|first1=Florian|last2=Verhoeven|first2=Stefan|last3=Meijer|first3=Christiaan|last4=Spreeuw|first4=Hanno|last5=Villanueva|first5=Efrain|last6=Geng|first6=Cunliang|last7=van der Hooft|first7=Justin J.J.|last8=Rogers|first8=Simon|last9=Belloum|first9=Adam|last10=Diblen|first10=Faruk|last11=Spaaks|first11=Jurriaan H.|title=matchms - processing and similarity evaluation of mass spectrometry data|journal=Journal of Open Source Software|year=2020|volume=5|issue=52|page=2411|doi=10.21105/joss.02411|bibcode=2020JOSS....5.2411H|s2cid=225186415|doi-access=free}}
METASPACE

| Free and open-source

Cloud platform for metabolite and lipid identification and a community-populated knowledge base of spatial metabolomes, with thousands of public datasets shared by the users: [https://metaspace2020.eu metaspace2020.eu]. It also provides capacities for online data visualization, sharing, and publishing.
METLIN Database and Technology Platform

| Proprietary

Tandem mass spectrometry (MS/MS) database of over 930,000 (as of December 2023){{Cite web |date=2023-12-12 |title=The Analytical Scientist Innovation Awards 2023 |url=https://theanalyticalscientist.com/techniques-tools/the-analytical-scientist-innovation-awards-2023 |access-date=2023-12-16 |website=The Analytical Scientist |language=en}} metabolites and other molecular entities, generated from high resolution quadrupole time-of-flight tandem mass spectrometry.{{Cite journal |last1=Xue |first1=Jingchuan |last2=Guijas |first2=Carlos |last3=Benton |first3=H. Paul |last4=Warth |first4=Benedikt |last5=Siuzdak |first5=Gary |date=October 2020 |title=METLIN MS2 molecular standards database: a broad chemical and biological resource |journal=Nature Methods |language=en |volume=17 |issue=10 |pages=953–954 |doi=10.1038/s41592-020-0942-5 |issn=1548-7105 |pmc=8802982 |pmid=32839599}} It also includes, ion mobility,{{Cite journal |last1=Baker |first1=Erin S. |last2=Hoang |first2=Corey |last3=Uritboonthai |first3=Winnie |last4=Heyman |first4=Heino M. |last5=Pratt |first5=Brian |last6=MacCoss |first6=Michael |last7=MacLean |first7=Brendan |last8=Plumb |first8=Robert |last9=Aisporna |first9=Aries |last10=Siuzdak |first10=Gary |date=December 2023 |title=METLIN-CCS: an ion mobility spectrometry collision cross section database |journal=Nature Methods |language=en |volume=20 |issue=12 |pages=1836–1837 |doi=10.1038/s41592-023-02078-5 |pmid=37932399 |issn=1548-7105|pmc=10843661 }} neutral loss,{{Cite journal |last1=Aisporna |first1=Aries |last2=Benton |first2=H. Paul |last3=Chen |first3=Andy |last4=Derks |first4=Rico J. E. |last5=Galano |first5=Jean Marie |last6=Giera |first6=Martin |last7=Siuzdak |first7=Gary |date=2022-03-02 |title=Neutral Loss Mass Spectral Data Enhances Molecular Similarity Analysis in METLIN |journal=Journal of the American Society for Mass Spectrometry |language=en |volume=33 |issue=3 |pages=530–534 |doi=10.1021/jasms.1c00343 |issn=1044-0305 |pmc=10131246 |pmid=35174708}} and LC/MS data.{{Cite web|title=METLIN - Database Commons|url=https://ngdc.cncb.ac.cn/databasecommons/database/id/5907|access-date=2023-11-28|website=ngdc.cncb.ac.cn}}{{Cite journal |last1=Domingo-Almenara |first1=Xavier |last2=Guijas |first2=Carlos |last3=Billings |first3=Elizabeth |last4=Montenegro-Burke |first4=J. Rafael |last5=Uritboonthai |first5=Winnie |last6=Aisporna |first6=Aries E. |last7=Chen |first7=Emily |last8=Benton |first8=H. Paul |last9=Siuzdak |first9=Gary |date=2019-12-20 |title=The METLIN small molecule dataset for machine learning-based retention time prediction |journal=Nature Communications |language=en |volume=10 |issue=1 |pages=5811 |doi=10.1038/s41467-019-13680-7 |issn=2041-1723 |pmc=6925099 |pmid=31862874|bibcode=2019NatCo..10.5811D }}
mineXpert

| Open source GPL

This graphical user interface-based (GUI) software for mass spectral data visualization/mining supports ion mobility mass spectrometry{{cite journal|last1=Rusconi|first1=F.|title=mineXpert: Biological Mass Spectrometry Data Visualization and Mining with Full JavaScript Ability|journal=J. Proteome Res.|volume=18|issue=5|year=2019|pmid=30950277|doi=10.1021/acs.jproteome.9b00099|pages=2254–2259|s2cid=96435891|url=https://hal-cnrs.archives-ouvertes.fr/hal-02379614/file/minexpert-filippo-rusconi-jproteomeres-2019.pdf}}{{cite journal|last1=Rusconi|first1=F.|title=mineXpert2: Full-Depth Visualization and Exploration of MSn Mass Spectrometry Data|journal=Journal of the American Society for Mass Spectrometry|volume=32|issue=4|year=2021|pmid= 33683899|doi=10.1021/jasms.0c00402|pages=1138–1141}} and is a program of the msXpertSuite software suite.
mMass

| Open source

Multi-platform package of tools for mass spectrometric data analysis and interpretation written in Python (no longer 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.
msAxel

|Proprietary

|Software used by JEOL time-of-flight mass spectrometers

msFineAnalysis

|Proprietary

|Qualitative analysis software for JEOL GC-MS systems. The msFineAnalysis AI version for JEOL's GC-time-of-flight mass spectrometers contains a searchable in-silico database of mass spectra calculated for the 100 million structures in the PubChem database.

MSGraph

| Open source

This tool does qualitative analysis of mass spectrometric (MS) data and is hosted by Sourceforge.
MSight

| Freeware

Software for mass spectrometry imaging developed by the Swiss Institute of Bioinformatics.{{cite journal|last1=Palagi|first1=Patricia M.|last2=Walther|first2=Daniel|last3=Quadroni|first3=Manfredo|last4=Catherinet|first4=SéBastien|last5=Burgess|first5=Jennifer|last6=Zimmermann-Ivol|first6=Catherine G.|last7=Sanchez|first7=Jean-Charles|last8=Binz|first8=Pierre-Alain|last9=Hochstrasser|first9=Denis F.|title=MSight: An image analysis software for liquid chromatography-mass spectrometry|journal=Proteomics|volume=5|issue=9|pages=2381–4|year=2005|pmid=15880814|doi=10.1002/pmic.200401244|last10=Appel|first10=Ron D.|s2cid=33296427|doi-access=free}}
MSiReader

| Freeware

Vendor-neutral interface built on the Matlab platform designed to view and perform data analysis of mass spectrometry imaging (MSI) data.{{cite journal|last1=Robichaud|first1=Guillaume|last2=Garrard|first2=Kenneth P.|last3=Barry|first3=Jeremy A.|last4=Muddiman|first4=David C.|date=March 2013|journal=Journal of the American Society for Mass Spectrometry|volume=24|issue=5|pages=718–721|title=MSiReader: An Open-Source Interface to View and Analyze High Resolving Power MS Imaging Files on Matlab Platform|doi=10.1007/s13361-013-0607-z|pmid=23536269|pmc=3693088|bibcode=2013JASMS..24..718R}} Matlab is not required to use MSiReader.
MS Interpreter

| Freeware

Software by NIST for compression of structure with mass spectra. The program seeks to find mechanisms and their rates for all fragmentation types (EI, Tandem positive and negative mode) and correlates mass spectral peaks to a probable origin structure. It contains an isotope calculator and other features and on-line help. This program is a companion to the NIST Spectra Search Program, v.3.0. It is usable as a standalone with the import of a structure and spectrum.
mspire

| Open-source

Mspire is an MS informatics developer's 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.{{Cite journal| last1=Prince|first1=J. T.| last2=Marcotte|first2=E. M.| doi=10.1093/bioinformatics/btn513| title=Mspire: Mass spectrometry proteomics in Ruby| journal=Bioinformatics| volume=24| issue=23| pages=2796–2797| year=2008| pmid=18930952| pmc=2639276}}
MSqRob

| Open-source

This is an "R" package with graphical user interface for differential abundance analysis of label-free quantitative proteomics data.{{Cite journal

| last1=Goeminne|first1=L. J. E.

| last2=Gevaert|first2=K.

| last3=Clement|first3=L.

| doi=10.1074/mcp.M115.055897

| title=Peptide-level Robust Ridge Regression Improves Estimation, Sensitivity, and Specificity in Data-dependent Quantitative Label-free Shotgun Proteomics.

| journal=Molecular & Cellular Proteomics

| volume=15

| issue=2

| pages=657–668

| year=2016

|doi-access=free

| pmid=26566788

| pmc=4739679

}}{{Cite journal

| last1=Goeminne|first1=L. J. E.

| last2=Gevaert|first2=K.

| last3=Clement|first3=L.

| doi=10.1016/j.jprot.2017.04.004

| title=Experimental design and data analysis in label-free quantitative LC/MS proteomics: A tutorial with MSqRob.

| journal=Journal of Proteomics

| volume=171

| pages=23–26

| year=2018

| pmid=28391044

|url=https://zenodo.org/record/7541882

}}{{Cite journal

| last1=Goeminne|first1=L. J. E.

| last2=Sticker|first2=A.

| last3=Martens|first3=M.

| last4=Gevaert|first4=K.

| last5=Clement|first5=L.

| doi=10.1021/acs.analchem.9b04375

| title=MSqRob takes the missing hurdle: uniting intensity- and count-based proteomics

| journal=Analytical Chemistry

| volume=XXXX

| issue=XX

| pages=6278–6287

| year=2020

| pmid=32227882

|hdl=1854/LU-8671265

| s2cid=214751205

| url=https://biblio.ugent.be/publication/8671265

| hdl-access=free

}}

ms2mz

| Freeware

Utility converts between mass spectrometer file formats, e.g. to convert proprietary binary files to MGF peak list files, to prepare for upload to Proteome Cluster.
Multimaging

|Proprietary

|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

| Open source

An open-source software for mass spectrometry data processing, with the main focus on LC-MS data.
OmicsHub Proteomics| Laboratory information management software for mass spectrometry information management and data analysis.
OpenChrom

| Open source

Chromatography and mass spectrometry software that can be extended using plug-ins and can run on several operating systems (Microsoft Windows, Linux, Unix, Mac OS X) and processor architectures (x86, x86_64, ppc). It has converters for the native access of various data files, e.g. converters for mzXML, netCDF, Agilent, Finnigan and Varian file formats.
ORIGAMI

|Open source

|The ORIGAMI software suite is for analysis of mass spectrometry and ion mobility mass spectrometry datasets. It was originally developed to improve the analysis workflows of activated IM-MS/collision-induced unfolding (CIU) datasets and allow seamless visualization of results. Recently, ORIGAMI was modified to be more accepting of non-MS centric and enables visualization of results from other sources as well as the exporting of results in an interactive format, where the user can share any dataset and visualize results in a web browser.{{Cite journal|last1=Migas|first1=Lukasz G.|last2=France|first2=Aidan P.|last3=Bellina|first3=Bruno|last4=Barran|first4=Perdita E.|date=April 2018|title=ORIGAMI : A software suite for activated ion mobility mass spectrometry (aIM-MS) applied to multimeric protein assemblies|journal=International Journal of Mass Spectrometry|volume=427|pages=20–28|doi=10.1016/j.ijms.2017.08.014|issn=1387-3806|bibcode=2018IJMSp.427...20M|url=https://www.research.manchester.ac.uk/portal/en/publications/origami-a-software-suite-for-activated-ion-mobility-mass-spectrometry-aimms-applied-to-multimeric-protein-assemblies(36cd403d-e95c-4294-beb8-b03ef318f98a).html}}

PatternLab

| Freeware

Software for post-analysis of SEQUEST, ProLuCID or Comet database search results filtered by DTASelect or Census.{{cite journal|last1=Carvalho|first1=Paulo C|last2=Fischer|first2=Juliana SG|last3=Chen|first3=Emily I|last4=Yates|first4=John R|last5=Barbosa|first5=Valmir C|title=PatternLab for proteomics: a tool for differential shotgun proteomics|journal=BMC Bioinformatics|volume=9|page=316|year=2008|pmid=18644148|pmc=2488363|doi=10.1186/1471-2105-9-316|doi-access=free}}
pyOpenMS

| Open source

pyOpenMS is an open-source Python library for mass spectrometry, specifically for the analysis of proteomics and metabolomics data in Python.
Peaksel

| Proprietary

This web-based (available both in cloud as SaaS and as on-prem installation) software for LC/MS data processing supports batch processing and high-throughput experiments. It is "vendor agnostic."
PeakStrainer

| Open source

| Intensity-Independent Noise Filtering in FT MS and FT MS/MS spectra for Shotgun Lipidomics (Python){{cite journal|doi=10.17617/1.47|year=2017|last1=Ackerman|first1=Miranda|last2=Jacobo|first2=Eduardo|title=Peak Strainer}}

Peacock

| Open source

Mac OS X application developed by Johan Kool that can be used to interpret gas-chromatography/mass-spectrometry (GC/MS) data files.
PeakInvestigator

| Proprietary

A program designed to detect and deconvolve overlapping MS data, which can increase the effective resolution of spectra by 3-4 times.
PetroOrg

|Proprietary

|Software was developed specifically for analyzing petroleum, but it is also used to analyze "other complex mixtures, including anthropogenic environmental contaminants and natural organic matter."{{Cite web |last=Laboratory |first=National High Magnetic Field |title=ICR Software - MagLab |url=https://nationalmaglab.org/user-facilities/icr/software/#:~:text=PetroOrg%20was%20developed%20specifically%20for,contaminants%20and%20natural%20organic%20matter. |access-date=2024-01-12 |website=nationalmaglab.org |language=en}}

Pinnacle

|Proprietary

|A proteomics analysis software with modules for translational proteomics, glycoproteomics, and biopharma analysis. It includes comprehensive quantitation of thousands of proteins across hundreds of samples using DDA, DIA, PRM or SRM with fully integrated statistics and biological interpretation. There is a complete N-linked glycoprotein identification routine and an in-depth analysis in protein characterization, including peptide mapping, error tolerant search and disulfide analysis.

PIQMIe

| Web

Proteomics Identifications/quantitations data management and integration service is a web-based tool that aids scalable data management, analysis and visualization of semi-quantitative (SILAC) proteomics experiments.{{cite journal|title=PIQMIe: a web server for semi-quantitative proteomics data management and analysis.|journal=Nucleic Acids Res|year=2014|volume=42|issue=W1|pages=W100–W106|doi=10.1093/nar/gku478|last1=Kuzniar|first1=A.|last2=Kanaar|first2=R.|pmid=24861615|pmc=4086067}}
POTAMOS

| Open source

This web application calculates mass spectrometry data independently of instrumentation and is focused on a well known protein family of histones whose PTMs are believed to play a crucial role in gene regulation. It calculates the kind, number and combinations of the possible PTMs corresponding to a given peptide sequence and mass.
ProMass

| Proprietary

ProMass is an automated biomolecule deconvolution and reporting software package used to process ESI/LC/MS data or single ESI mass spectra. It uses the deconvolution algorithm, ZNova, to produce artifact-free deconvoluted mass spectra. There is also a "lite" browser-based format called ProMass for the Web that does not require any installation or software download.
ProteoIQ

| Proprietary

Software for the post-analysis of Mascot, SEQUEST, or X!Tandem database search results.{{cite journal|last1=Weatherly|first1=D. B.|title=A Heuristic Method for Assigning a False-discovery Rate for Protein Identifications from Mascot Database Search Results|journal=Molecular & Cellular Proteomics|volume=4|pages=762–72|year=2005|doi=10.1074/mcp.M400215-MCP200|pmid=15703444|issue=6|last2=Atwood Ja|first2=3rd|last3=Minning|first3=TA|last4=Cavola|first4=C|last5=Tarleton|first5=RL|last6=Orlando|first6=R|s2cid=18408543|doi-access=free}}{{cite journal|last1=Keller|first1=Andrew|last2=Nesvizhskii|first2=Alexey I.|last3=Kolker|first3=Eugene|last4=Aebersold|first4=Ruedi|title=Empirical Statistical Model To Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search|journal=Analytical Chemistry|volume=74|issue=20|pages=5383–92|year=2002|pmid=12403597|doi=10.1021/ac025747h}}{{cite journal|doi=10.1021/ac0341261|last1=Nesvizhskii|first1=AI|last2=Keller|first2=A|last3=Kolker|first3=E|last4=Aebersold|first4=R|title=A statistical model for identifying proteins by tandem mass spectrometry|journal=Analytical Chemistry|volume=75|issue=17|pages=4646–58|year=2003|pmid=14632076}}
PROTRAWLER| LC/MS data reduction application that reads raw mass spectrometry vendor data (from several well-known instrument companies) and creates triplet lists {mass, retention time, integrated signal intensity} summarizing the LC/MS chromatogram.
Proteomatic

| Freeware

Data processing pipeline created for the purpose of evaluating mass spectrometric proteomics experiments.{{cite journal|last1=Specht|first1=Michael|last2=Kuhlgert|first2=Sebastian|last3=Fufezan|first3=Christian|last4=Hippler|first4=Michael|title=Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows|journal=Bioinformatics|volume=27|issue=8|pages=1183–1184|year=2011|doi=10.1093/bioinformatics/btr081|pmid=21325302|doi-access=free}}
ProteomicsTools

| Open source

Software for the post-analysis of MASCOT, SEQUEST, Comet, XTandem, PFind, PeptidePhophet, MyriMatch, MSGF, OMSSA, MSAmanda or Percolator database search results.{{cite journal|last1=Sheng|first1=Quanhu|last2=Dai|first2=Jie|last3=Wu|first3=Yibo|last4=Tang|first4=Haixu|last5=Zeng|first5=Rong|title=BuildSummary: using a group-based approach to improve the sensitivity of peptide/protein identification in shotgun proteomics|journal=J Proteome Res|volume=11|issue=3|pages=1494–1502|year=2012|doi=10.1021/pr200194p|pmid=22217156}}
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 analyzes differential quantification data and is assisted by tools and visualization options. It is possible to process label-free and tandem mass-tagged data.{{cite journal|last1=Gallant|first1=James|last2=Heunis|first2=Tiaan|last3=Sampson|first3=Samantha|last4=Bitter|first4=Wilbert|title=ProVision: A web based platform for rapid analysis of proteomics data processed by MaxQuant| journal=Bioinformatics|volume=36|year=2020|issue=19|pages=4965–4967|doi=10.1093/bioinformatics/btaa620|pmid=32638008|pmc=7723325}}
pymzML

| Open source

Python module to interface mzML data in Python, based on cElementTree with additional tools for MS-informatics.{{cite journal|last1=Bald|first1=Till|last2=Barth|first2=Johannes|last3=Niehues|first3=Anna|last4=Specht|first4=Michael|last5=Hippler|first5=Michael|last6=Fufezan|first6=Christian|title=pymzML – Python module for high throughput bioinformatics on mass spectrometry data|journal=Bioinformatics|year=2012|doi=10.1093/bioinformatics/bts066|volume=28|issue=7|pages=1052–3|pmid=22302572}}
Pyteomics

| Open source

A Python framework for proteomics data analysis.{{cite journal|last1=Goloborodko|first1=Anton|last2=Levitsky|first2=Lev|last3=Ivanov|first3=Mark|last4=Gorshkov|first4=Mikhail|title=Pyteomics — a Python framework for exploratory data analysis and rapid software prototyping in proteomics|journal=Journal of the American Society for Mass Spectrometry|year=2013|doi=10.1007/s13361-012-0516-6|pmid=23292976|volume=24|issue=2|pages=301–4|bibcode=2013JASMS..24..301G|s2cid=22009929}}
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. It is compatible with a variety of MSI instruments, including Bruker, Sciex, Thermo and with the iMZML data format.

Rational Numbers Excel Add-In

| Proprietary

De novo identification tool for small molecules that works with Microsoft Excel (2010, 2013, 2016 and 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

| Proprietary

This seeks to identify small molecules by comparing accurate-mass fragmentation data to a database of 250,000 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| An 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}.
RemoteAnalyzer

| Proprietary

Software 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. NMR instrumentation and data processing are also supported.
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, with support for data analysis acquired using the Analyst software suite.

SCiLS Lab

|Proprietary

| Multi-vendor software for statistical analysis of mass spectrometry imaging data.

SFINX

|Open source and web

|The straightforward filtering index (SFINX) allows separation of true positive from false positive protein interactions in affinity purification - mass spectrometry and related datasets.{{Cite journal|last1=Titeca|first1=Kevin|last2=Meysman|first2=Pieter|last3=Gevaert|first3=Kris|last4=Tavernier|first4=Jan|last5=Laukens|first5=Kris|last6=Martens|first6=Lennart|last7=Eyckerman|first7=Sven|date=2016-01-04|title=SFINX: Straightforward Filtering Index for Affinity Purification-Mass Spectrometry Data Analysis|url=https://pubmed.ncbi.nlm.nih.gov/26616242|journal=Journal of Proteome Research|volume=15|issue=1|pages=332–338|doi=10.1021/acs.jproteome.5b00666|issn=1535-3907|pmid=26616242}}{{Cite journal|last1=Titeca|first1=Kevin|last2=Van Quickelberghe|first2=Emmy|last3=Samyn|first3=Noortje|last4=De Sutter|first4=Delphine|last5=Verhee|first5=Annick|last6=Gevaert|first6=Kris|last7=Tavernier|first7=Jan|last8=Eyckerman|first8=Sven|date=May 2017|title=Analyzing trapped protein complexes by Virotrap and SFINX|url=https://pubmed.ncbi.nlm.nih.gov/28358392|journal=Nature Protocols|volume=12|issue=5|pages=881–898|doi=10.1038/nprot.2017.014|issn=1750-2799|pmid=28358392|s2cid=4391127}} It is accessible via its web-interface and as an R package.{{Cite journal|last1=Titeca|first1=Kevin|last2=Meysman|first2=Pieter|last3=Laukens|first3=Kris|last4=Martens|first4=Lennart|last5=Tavernier|first5=Jan|last6=Eyckerman|first6=Sven|date=2017-06-15|title=sfinx: an R package for the elimination of false positives from affinity purification-mass spectrometry datasets|journal=Bioinformatics|volume=33|issue=12|pages=1902–1904|doi=10.1093/bioinformatics/btx076|issn=1367-4811|pmid=28186257|doi-access=free}}

SIM-XL

| Freeware

Spectrum Identification Machine for Cross-linked Peptides (SIM-XL) is an XL search engine that is part of the PatternLab for proteomics environment, to analyze tandem mass spectrometry data derived from cross-linked peptides.{{Cite journal

|pmid=25638023

| year=2015

| last1=Lima

| first1=D. B.

| title=SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis

| journal=Journal of Proteomics

| last2=De Lima

| first2=T. B.

| last3=Balbuena

| first3=T. S.

| last4=Neves-Ferreira

| first4=A. G.

| last5=Barbosa

| first5=V. C.

| last6=Gozzo

| first6=F. C.

| last7=Carvalho

| first7=P. C.

| doi=10.1016/j.jprot.2015.01.013

|volume=129

|pages=51–5

| hdl=11449/158584

| hdl-access=free

}}

SimGlycan

| Proprietary

Predicts the structure of glycans and glycopeptides using mass spectrometry MS/MS data.
SIMION

| Proprietary

SIMION is an ion optics simulation program.
SIRIUS

|Open source and web service

|An umbrella application for the annotation of small molecules from LC-MS/MS data.

Spectrolyzer

| Proprietary

Spectrolyzer is a Microsoft Windows-based software package developed by Binary Detect (previously named Medicwave) that provides bioinformatics data analysis tools for different mass spectrometers. It focuses on finding protein biomarkers and detecting protein deviations.
Spectromania

| Proprietary

Software for analysis and visualization of mass spectrometric data.{{cite journal|last1=Zucht|first1=Hans-Dieter|last2=Lamerz|first2=Jens|last3=Khamenia|first3=Valery|last4=Schiller|first4=Carsten|last5=Appel|first5=Annette|last6=Tammen|first6=Harald|last7=Crameri|first7=Reto|last8=Selle|first8=Hartmut|title=Datamining Methodology for LC-MALDI-MS Based Peptide Profiling|journal=Combinatorial Chemistry & High Throughput Screening|volume=8|pages=717–23|year=2005|doi=10.2174/138620705774962481|pmid=16464158|issue=8}}
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.{{cite journal|last=Götze|first=Michael|author2=Pettelkau J|author3=Schaks S|author4=Bosse K|author5=Ihling CH|author6=Krauth F|author7=Fritzsche R|author8=Kühn U|author9=Sinz A.|title=StavroX--a software for analyzing crosslinked products in protein interaction studies|journal=Journal of the American Society for Mass Spectrometry|date=January 2012|volume=23|issue=1|pages=76–87|doi=10.1007/s13361-011-0261-2|pmid=22038510|bibcode=2012JASMS..23...76G|s2cid=38037472|doi-access=free}}
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.
TopFD

| Open source

TopFD (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 them to monoisotopic neutral masses. In addition, it extracts proteoform features from LC-MS or CE-MS data.
Trans-Proteomic Pipeline (TPP)

| Open source

The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics. It includes: PeptideProphet for the Statistical validation of PSMs using search engine results; iProphet for distinct peptide sequence validation, using PeptideProphet results (can combine results of multiple search engines); and ProteinProphet for Protein identification and validation, using PeptideProphet or iProphet results. TPP also does: Protein Quantification with XPRESS (calculates relative peptide/protein abundances 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. It was developed at the Seattle Proteomic Centre (SPC).{{cite book|last1=Pedrioli|first1=Patrick G. A.|title=Proteome Bioinformatics|journal=|volume=604|year=2010|pages=213–238|doi=10.1007/978-1-60761-444-9_15|pmid=20013374|chapter=Trans-Proteomic Pipeline: A Pipeline for Proteomic Analysis|series=Methods in Molecular Biology|isbn=978-1-60761-443-2}}{{cite journal|last1=Deutsch|first1=Eric W.|last2=Mendoza|first2=Luis|last3=Shteynberg|first3=David|last4=Farrah|first4=Terry|last5=Lam|first5=Henry|last6=Tasman|first6=Natalie|last7=Sun|first7=Zhi|last8=Nilsson|first8=Erik|last9=Pratt|first9=Brian|last10=Prazen|first10=Bryan|last11=Eng|first11=Jimmy K.|last12=Martin|first12=Daniel B.|last13=Nesvizhskii|first13=Alexey I.|last14=Aebersold|first14=Ruedi|title=A guided tour of the Trans-Proteomic Pipeline|journal=Proteomics|volume=10|issue=6|year=2010|pages=1150–1159|issn=1615-9853|doi=10.1002/pmic.200900375|pmid=20101611|pmc=3017125}}
TurboMass

| Proprietary

TurboMass is GC/MS software created by PerkinElmer.
Universal Mass Calculator

| Freeware

UMC is programmed as a mass spectrometry tool to assist interpreting measurement results, mainly derived from molecular or quasi-molecular ions.

It can be used for the calculation of:

  • Mass deviation (mmu or ppm) of measured mass from given empirical formula
  • Mass differences of two empirical formulas
  • Elemental compositions (also considering measured intensity pattern, "most abundant" algorithm{{Cite journal |last1=Cody |first1=Robert B. |last2=Fouquet |first2=Thierry |date=2019-07-01 |title=Elemental Composition Determinations Using the Abundant Isotope |url=https://pubs.acs.org/doi/10.1007/s13361-019-02203-9 |journal=Journal of the American Society for Mass Spectrometry |language=en |volume=30 |issue=7 |pages=1321–1324 |doi=10.1007/s13361-019-02203-9 |pmid=31062289 |bibcode=2019JASMS..30.1321C |issn=1044-0305|url-access=subscription }} included)
  • Isotope pattern simulation from empirical formulas
  • Analysis of the degree of isotope labelling with D, 13C, 15N or 18O.
VIPER| VIPER analyzes accurate mass and chromatography retention times of LC-MS features (accurate mass and time tag approach).{{cite journal|last1=Monroe|first1=M. E.|last2=Tolić|first2=N.|last3=Jaitly|first3=N.|last4=Shaw|first4=J. L.|last5=Adkins|first5=J. N.|last6=Smith|first6=R. D.|title=VIPER: an advanced software package to support high-throughput LC-MS peptide identification|journal=Bioinformatics|volume=23|issue=15|year=2007|pmid=17545182|doi=10.1093/bioinformatics/btm281|pages=2021–3|doi-access=free}}
Xcalibur

| Proprietary

Software by Thermo Fisher Scientific used with mass spectrometry instruments.
XCMS Online (Cloud-Based)

| Proprietary

Freely available and a widely used metabolomic and lipidomic data-processing platform.

See also

References

{{Reflist|2}}

External links

{{Mass spectrometry}}

{{DEFAULTSORT:Mass Spectrometry Software}}

List

Category:Proteomics

Category:Lists of bioinformatics software