List of mass spectrometry software

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

Proteomics software

For more details on this topic, see 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 Type Description Link
Byonic Database search program released in 2011 by Protein Metrics Inc. with original developments at PARC[1] that searches MS/MS data from all types of instruments and internally employs the program Combyne,[2] which combines peptide identifications to produce protein scores and identification probabilities. server
Greylag open source Database search program developed at the Stowers Institute for Medical Research designed to perform large searches on computational clusters having hundreds of nodes. server
InsPecT A MS-alignment search engine available at the Center for Computational Mass Spectrometry at the University of California, San Diego[3] download
Mascot proprietary Performs mass spectrometry data analysis through a statistical evaluation of matches between observed and projected peptide fragments.[4]
MassWiz open source Search algorithm developed at Institute of Genomics and Integrative Biology available as a windows commandline tool. download, server
MyriMatch open source Database search program developed at the Vanderbilt University Medical Center designed to run in a single-computer environment or across an entire cluster of processing nodes.[5] download
OMSSA open source database search program developed at the National Center for Biotechnology Information.[6][7]
PEAKS DB proprietary Database search engine, run in parallel with de novo sequencing to automatically validate search results, allowing for a higher number of found sequences for a given false discovery rate. In addition to providing an independent database search, results can be incorporated as part of the software’s multi-engine (Sequest, Mascot, X!Tandem, OMSSA, PEAKS DB) consensus reporting tool, inChorus.[8] The tool also provides a list of sequences identified exclusively by de novo sequencing.
Phenyx 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.[9]
RAId Developed at the National Center for Biotechnology Information, Robust Accurate Identification (RAId)[10] is a suite of proteomics tools for analyzing tandem mass spectrometry data with accurate statistics.[11]
SEQUEST proprietary Identifies collections of tandem mass spectra to peptide sequences that have been generated from databases of protein sequences.[12]
SIMS SIMS (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. server
SimTandem Tool for identification of peptide sequences from LC/MS/MS data; the engine can be used as an external tool in OpenMS/TOPP.[13] server
X!Tandem open source Matches tandem mass spectra with peptide sequences. server
pFind pFind Studio is a computational solution for mass spectrometry-based proteomics, it germinated in 2002 in Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China. download

De novo sequencing algorithms

De novo peptide sequencing algorithms are based, in general, on the approach proposed in Bartels et al. (1990).[14]

Name Type Description Link
DeNovoX De novo sequencing on CID spectra acquired with ion trap mass spectrometers delivering complete and/or partial peptide sequences (sequence tags).[15]
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).[16] server
Lutefisk open source Software for the de novo interpretation of peptide CID spectra. server
PEAKS De 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.[17][18]

Homology Searching Algorithms

Name Type Description Link
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. server

MS/MS peptide quantification

For more details on this topic, see Quantitative proteomics.
Name Type Description Link
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, supports complex data treatments as peptide or protein fractionation prior to LC-MS analysis (SCX, SDS-PAGE, etc.). server, download
MaxQuant freeware quantitative proteomics 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. download
OpenMS open source Software C++ library for LC-MS/MS data management and analysis that offers an infrastructure for the development of mass spectrometry related software. server, download
Spectronaut proprietary Software for quantitative proteomics developed by Biognosys AG (Schlieren, Switzerland) based on the mProphet algorithm[19] that allows the targeted analysis of data independent acquisition (DIA) data sets for label-free peptide quantitation, also called SWATH acquisition or hyper reaction monitoring (HRM)[20] and can perform quantitation on both precursor (MS1) and product ions (MS2) level.[21] server

Other software

Name Type Description Link
Advanced Chemistry Development proprietary Commercial solutions for the interpretation of MS and xC/MS data with spectrum/structure matching, identification of known and unknown metabolites, as well as for the identification of compounds through spectral comparison.
Analyst proprietary Software by AB Sciex, a division of The Danaher Corporation.
AnalyzerPro proprietary A vendor independent software application for processing mass spectrometry data that can analyze both GC-MS and LC-MS data using both qualitative and quantitative data processing and is used for metabolomics data processing using MatrixAnalyzer for the comparison of multiple data sets.
Chromeleon proprietary Software by Thermo Fisher Scientific used with mass spectrometry instruments, as well as chromatography instruments.
ESIprot Enables the charge state determination and molecular weight calculation for low resolution electrospray ionization (ESI) mass spectrometry (MS) data of proteins.[22] server, online
LabSolutions LCMS proprietary Software by Shimadzu Corporation used with mass spectrometry and HPLC instruments.
Mass++ freeware Analysis software for mass spectrometry that can load files with open-formats (mzXML, mzML, AIA(netCDF)) and some instrument vendor formats; users can develop and add original functions as Mass++ plug-ins. download
MassBank website website hosted by the Institute for Advanced Biosciences, in Keio University, Tsuruoka City, Yamagata, Japan with mass spectrometric data for organic compounds. website
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. website
MassLynx proprietary Software by Waters Corporation.
Mass-Up open-source Utility for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data that loads data from mzML, mzXML and CSV files and allows users to apply baseline correction, normalization, smoothing, peak detection and peak matching. download
massXpert Graphical user interface-based (GUI) software for simulating and analyzing mass spectrometric data obtained on known bio-polymer sequences.[23] manual
mMass open source Multi-platform package of tools for mass spectrometric data analysis and interpretation written in Python. website
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 freeware Utility for converting between mass spectrometer file formats, e.g. to convert proprietary binary files to MGF peak list files to prepare files for upload to Proteome Cluster. download
MSGraph open source sourceforge
MSight freeware Software for mass spectrometry imaging developed by the Swiss Institute of Bioinformatics.[24]
MSiReader freeware Vendor-neutral interface built on the Matlab platform designed to view and perform data analysis of mass spectrometry imaging (MSI) data.[25] Matlab is not required to use MSiReader. download
mspire open-source Mass spectrometry informatics developers toolbox written in ruby that includes an mzML reader/writer, in-silico digestion and isotopic pattern calculation etc.; submodules such as mspire-lipidomics, mspire-sequest, and mspire-simulator extend the functionality.[26]
multiMS-toolbox open source ms-alone and multiMS-toolbox is a tool chain for mass spectrometry data peak extraction and statistical analysis. website
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. website
OmicsHub Proteomics OmicsHub Proteomics combines a LIMS for mass spec information management with data analysis functionalities on one platform.
OpenChrom open source Chromatography and mass spectrometry software that can be extended using plug-ins and is available for several operating systems (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. website, sourceforge
PatternLab freeware Software for post-analysis of SEQUEST, ProLuCID or Comet database search results filtered by DTASelect or Census.[27] website
SIM-XL freeware Spectrum 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. A video demonstrating SIM-XL v1.0 in action is available at http://patternlabforproteomics.org/sim-xl/video. [28]website
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. Google Code
PIQMIe web Proteomics identifications and 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.[29] website
POTAMOS open source Web application that provides calculated mass spectrometry data independently of instrumentation focused on a well known protein family of histones whose PTMs are believed to play a crucial role in gene regulation; calculates the kind, the number and the combinations of the possible PTMs corresponding to a given peptide sequence and a given mass. 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 proprietary Software for the post-analysis of Mascot, SEQUEST, or X!Tandem database search results.[30][31][32]
Proteomatic Freeware Data processing pipeline created for the purpose of evaluating mass spectrometric proteomics experiments.[33]
ProteoWizard open source Link library and tools athat re a set of modular and extensible open-source, cross-platform tools and software libraries that facilitate proteomics data analysis. sourceforge
pymzML open source Python module to interface mzML data in Python based on cElementTree with additional tools for MS-informatics. [34] download
Quantinetix Software for mass spectrometry imaging designed to quantify and normalize MS images in various study types that is compatible with a variety of MSI instruments, including Bruker, Sciex, Thermo and with iMZML. server
Rational Numbers Excel Add-In proprietary De novo identification tool that works with both Microsoft Excel 2010 and Excel 2013

website

Rational Numbers Search proprietary Identification of small molecules by comparison of accurate-mass fragmentation data to a database of 250000 molecules represented as mathematical partitions

website

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 proprietary Software by SpectralWorks Limited 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 is provided.
Scaffold proprietary Suite of proteomics tools for analyzing spectra, peptides and proteins across multiple samples. server
SCiLS Lab Statistical analysis of MALDI imaging mass spectrometry data that integrates with Bruker MALDI imaging. server
SimGlycan proprietary Predicts the structure of glycans and glycopeptides using mass spectrometry MS/MS data. server
SIMION proprietary Ion optics simulation program server
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. server
Spectromania proprietary Software for analysis and visualization of mass spectrometric data.[35]
StavroX proprietary 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.[36]
TOF-DS proprietary Software by Markes International used with BenchTOF time-of-flight mass spectrometers
TurboMass proprietary GC/MS software by PerkinElmer.
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. server
VIPER Analysis of accurate mass and chromatography retention time analysis of LC-MS features (accurate mass and time tag approach).[37]
Xcalibur proprietary Software by Thermo Fisher Scientific used with mass spectrometry instruments.

See also

References

  1. ↑ Bern, Marshall; Cai, Yuhan; Goldberg, David (2007). "Lookup Peaks: A Hybrid of de Novo Sequencing and Database Search for Protein Identification by Tandem Mass Spectrometry". Analytical Chemistry 79 (4): 1393–1400. doi:10.1021/ac0617013. PMID 17243770.
  2. ↑ Bern, Marshall; Goldberg, David (2008). "Improved Ranking Functions for Protein and Modification-Site Identifications". Journal of Computational Biology 15 (7): 705–719. doi:10.1089/cmb.2007.0119. PMID 18651800.
  3. ↑ "Inspect and MS-Alignment".
  4. ↑ Perkins, David N.; Pappin, Darryl J. C.; Creasy, David M.; Cottrell, John S. (1999). "Probability-based protein identification by searching sequence databases using mass spectrometry data". Electrophoresis 20 (18): 3551–67. doi:10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2. PMID 10612281.
  5. ↑ Tabb, David L.; Fernando, Christopher G.; Chambers, Matthew C. (2007). "MyriMatch:  Highly Accurate Tandem Mass Spectral Peptide Identification by Multivariate Hypergeometric Analysis". Journal of Proteome Research 6 (2): 654–61. doi:10.1021/pr0604054. PMC 2525619. PMID 17269722.
  6. ↑ "OMSSA ms/ms search engine". Pubchem.ncbi.nlm.nih.gov. Retrieved 2011-09-27.
  7. ↑ Geer, Lewis Y.; Markey, Sanford P.; Kowalak, Jeffrey A.; Wagner, Lukas; Xu, Ming; Maynard, Dawn M.; Yang, Xiaoyu; Shi, Wenyao; Bryant, Stephen H. (2004). "Open Mass Spectrometry Search Algorithm". Journal of Proteome Research 3 (5): 958–64. doi:10.1021/pr0499491. PMID 15473683.
  8. ↑ Liang, C; Smith, JC; Hendrie, Christopher (2003). "A Comparative Study of Peptide Sequencing Software Tools for MS/MS".
  9. ↑ Colinge, Jacques; Masselot, Alexandre; Giron, Marc; Dessingy, Thierry; Magnin, Jérôme (2003). "OLAV: Towards high-throughput tandem mass spectrometry data identification". Proteomics 3 (8): 1454–63. doi:10.1002/pmic.200300485. PMID 12923771.
  10. ↑ "RAId MS/MS search engine". QMBP NCBI NLM NIH. Retrieved 2008-01-01.
  11. ↑ Alves, Gelio; Ogurtsov, Aleksey Y.; Yu, Yi-Kuo (2007). "RAId_DbS: peptide identification using database searches with realistic statistics". Biol Direct 2: 25. doi:10.1186/1745-6150-2-25. PMC 2211744. PMID 17961253.
  12. ↑ Jimmy K. Eng, Ashley L. McCormack, and John R. Yates, III (1994). "An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database". J Am Soc Mass Spectrom 5 (11): 976–989. doi:10.1016/1044-0305(94)80016-2. PMID 24226387.
  13. ↑ Novak, Jiri; Sachsenberg, Timo; Hoksza, David; Skopal, Tomas; Kohlbacher, Oliver (2013). "On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications". Journal of Integrative Bioinformatics 10 (3).
  14. ↑ Bartels, Christian (31 May 1990). "Fast algorithm for peptide sequencing by mass spectroscopy". Biological Mass Spectrometry 19 (6): 363–368. doi:10.1002/bms.1200190607.
  15. ↑ thermo finnigan introduces denovox - Search results from HighBeam Business
  16. ↑ Savitski, Mikhail M.; Nielsen, Michael L.; Kjeldsen, Frank; Zubarev, Roman A. (2005). "Proteomics-Grade de Novo Sequencing Approach". Journal of Proteome Research 4 (6): 2348–54. doi:10.1021/pr050288x. PMID 16335984.
  17. ↑ Ma, Bin; Zhang, Kaizhong; Hendrie, Christopher; Liang, Chengzhi; Li, Ming; Doherty-Kirby, Amanda; Lajoie, Gilles (2003). "PEAKS: powerful software for peptidede novo sequencing by tandem mass spectrometry". Rapid Communications in Mass Spectrometry 17 (20): 2337–42. doi:10.1002/rcm.1196. PMID 14558135.
  18. ↑ Tannu, Nilesh S; Hemby, Scott E (2007). "De novo protein sequence analysis of Macaca mulatta". BMC Genomics 8: 270. doi:10.1186/1471-2164-8-270. PMC 1965481. PMID 17686166.
  19. ↑ Reiter, L et al. (2011). "mProphet: automated data processing and statistical validation for large-scale SRM experiments". Nat Methods 8 (5): 430–435. doi:10.1038/nmeth.1584.
  20. ↑ Law, KP; Lim YP (2013). "Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring". Expert Rev Proteomics 10 (6): 551–566. doi:10.1586/14789450.2013.858022.
  21. ↑ Vowinckel, J et al. (2013). "The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics". F1000Research 2: 272. doi:10.12688/f1000research.2-272.v1.
  22. ↑ Winkler, Robert (2010). "ESIprot: a universal tool for charge state determination and molecular weight calculation of proteins from electrospray ionization mass spectrometry data". Rapid Communications in Mass Spectrometry 24 (3): 285–94. doi:10.1002/rcm.4384. PMID 20049890.
  23. ↑ Rusconi, F. (2009). "massXpert 2: a cross-platform software environment for polymer chemistry modelling and simulation/analysis of mass spectrometric data". Bioinformatics 25 (20): 2741–2. doi:10.1093/bioinformatics/btp504. PMID 19740912.
  24. ↑ Palagi, Patricia M.; Walther, Daniel; Quadroni, Manfredo; Catherinet, SéBastien; Burgess, Jennifer; Zimmermann-Ivol, Catherine G.; Sanchez, Jean-Charles; Binz, Pierre-Alain; Hochstrasser, Denis F.; Appel, Ron D. (2005). "MSight: An image analysis software for liquid chromatography-mass spectrometry". Proteomics 5 (9): 2381–4. doi:10.1002/pmic.200401244. PMID 15880814.
  25. ↑ Robichaud, Guillaume; Garrard, Kenneth P.; Barry, Jeremy A.; Muddiman, David C. (March 2013). "MSiReader: An Open-Source Interface to View and Analyze High Resolving Power MS Imaging Files on Matlab Platform". Journal of The American Society for Mass Spectrometry (Springer) 24 (5): 718–721. doi:10.1007/s13361-013-0607-z. PMID 23536269.
  26. ↑ Prince, J. T.; Marcotte, E. M. (2008). "Mspire: Mass spectrometry proteomics in Ruby". Bioinformatics 24 (23): 2796–2797. doi:10.1093/bioinformatics/btn513. PMC 2639276. PMID 18930952.
  27. ↑ Carvalho, Paulo C; Fischer, Juliana SG; Chen, Emily I; Yates, John R; Barbosa, Valmir C (2008). "PatternLab for proteomics: a tool for differential shotgun proteomics". BMC Bioinformatics 9: 316. doi:10.1186/1471-2105-9-316. PMC 2488363. PMID 18644148.
  28. ↑ Lima, D. B.; De Lima, T. B.; Balbuena, T. S.; Neves-Ferreira, A. G.; Barbosa, V. C.; Gozzo, F. C.; Carvalho, P. C. (2015). "SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis". Journal of Proteomics. doi:10.1016/j.jprot.2015.01.013. PMID 25638023.
  29. ↑ Kuzniar, A.; Kanaar, R. (2014). "PIQMIe: a web server for semi-quantitative proteomics data management and analysis.". Nucleic Acids Res 42 (W1): W100–W106. doi:10.1093/nar/gku478. PMID 24861615.
  30. ↑ Weatherly, D. B.; Atwood Ja, 3rd; Minning, TA; Cavola, C; Tarleton, RL; Orlando, R (2005). "A Heuristic Method for Assigning a False-discovery Rate for Protein Identifications from Mascot Database Search Results". Molecular & Cellular Proteomics 4 (6): 762–72. doi:10.1074/mcp.M400215-MCP200. PMID 15703444.
  31. ↑ Keller, Andrew; Nesvizhskii, Alexey I.; Kolker, Eugene; Aebersold, Ruedi (2002). "Empirical Statistical Model To Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search". Analytical Chemistry 74 (20): 5383–92. doi:10.1021/ac025747h. PMID 12403597.
  32. ↑ Nesvizhskii, AI; Keller, A; Kolker, E; Aebersold, R (2003). "A statistical model for identifying proteins by tandem mass spectrometry". Analytical chemistry 75 (17): 4646–58. doi:10.1021/ac0341261. PMID 14632076.
  33. ↑ Specht, Michael; Kuhlgert, Sebastian; Fufezan, Christian; Hippler, Michael (2011). "Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows". Bioinformatics 27 (8): 1183–1184. doi:10.1093/bioinformatics/btr081. PMID 21325302.
  34. ↑ Bald, Till; Barth, Johannes; Niehues, Anna; Specht, Michael; Hippler, Michael; Fufezan, Christian (2012). "pymzML - Python module for high throughput bioinformatics on mass spectrometry data". Bioinformatics 28 (7): 1052–3. doi:10.1093/bioinformatics/bts066. PMID 22302572.
  35. ↑ Zucht, Hans-Dieter; Lamerz, Jens; Khamenia, Valery; Schiller, Carsten; Appel, Annette; Tammen, Harald; Crameri, Reto; Selle, Hartmut (2005). "Datamining Methodology for LC-MALDI-MS Based Peptide Profiling". Combinatorial Chemistry & High Throughput Screening 8 (8): 717–23. doi:10.2174/138620705774962481.
  36. ↑ Götze, Michael; Pettelkau J; Schaks S; Bosse K; Ihling CH; Krauth F; Fritzsche R; Kühn U; Sinz A. (January 2012). "StavroX--a software for analyzing crosslinked products in protein interaction studies". J Am Soc Mass Spectrom. 23 (1): 76–87. doi:10.1007/s13361-011-0261-2. PMID 22038510. Retrieved 6 November 2013.
  37. ↑ Monroe, M. E.; Tolić, N.; Jaitly, N.; Shaw, J. L.; Adkins, J. N.; Smith, R. D. (2007). "VIPER: an advanced software package to support high-throughput LC-MS peptide identification". Bioinformatics 23 (15): 2021–3. doi:10.1093/bioinformatics/btm281. PMID 17545182.


External links