List of mass spectrometry software

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

Proteomics software[edit]

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[edit]

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]
MassMatrix MassMatrix is a database search software package for tandem mass spectrometric data. It uses a mass accuracy sensitive probabilistic scoring model to rank peptide and protein matches. download
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]
ProteinPilot Software 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 the peptide identification considering hundreds of modifications, non-tryptic cleavages and amino acid substitutions. Uses the Pro Group Algorithm for protein inference analysis to report the minimal set of proteins justified based on the peptide evidence. Supports quantification for label-based workflows (iTRAQ reagents, mTRAQ reagents and SILAC labeling). A translation layer translates user interface controls in the language of the proteomics experimental scientist to underlying complex informatics parameters.[10] pate/content/6/9/1638.short

download

Protein Prospector open source Protein Prospector is a package of about twenty proteomic analysis tools developed at the University of California San Francisco. The tandem mass spectrometry searching software is Batch-Tag / Batch-Tag Web, with the results processed and displayed using Search Compare. It uses scoring systems tailored to instrument and fragmentation mode to optimize analysis of different types of fragmentation data. server
RAId Developed at the National Center for Biotechnology Information, Robust Accurate Identification (RAId)[11] is a suite of proteomics tools for analyzing tandem mass spectrometry data with accurate statistics.[12]
SEQUEST proprietary Identifies collections of tandem mass spectra to peptide sequences that have been generated from databases of protein sequences.[13]
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 freeware A database search engine for identification of peptide sequences from LC/MS/MS data; the engine can be used as an external tool in OpenMS/TOPP.[14] download
SQID open source SeQuence IDentification (SQID) is an intensity-incorporated protein identification algorithm for tandem mass spectrometry. download
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[edit]

De novo peptide sequencing algorithms are based, in general, on the approach proposed in Bartels et al. (1990).[15]

Name Type Description Link
CycloBranch open source 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.[16] download
DeNovoX De novo sequencing on CID spectra acquired with ion trap mass spectrometers delivering complete and/or partial peptide sequences (sequence tags).[17]
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).[18] server[dead link]
Lutefisk open source Software for the de novo interpretation of peptide CID spectra. server
Novor proprietary, free for academic research Real-time de novo peptide sequencing engine that is fast, accurate and easy to be integrated into research pipelines. Novor can de novo sequence more than 300 MS/MS spectra per second on a Macbook Pro laptop computer.[19] download 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.[20][21]
Supernovo proprietary A unique, hands-free solution for end-to-end de novo sequencing of monoclonal antibodies server

Homology searching algorithms[edit]

Name Type Description Link
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, where one can specify the number of amino acid mismatches allowed. server
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[edit]

For more details on this topic, see Quantitative proteomics.
Name Type Description Link
MarkerView Software Provides statistical analysis for quantitative mass spec data sets from metabolomics and proteomic profiling applications. Includes principal components analysis (PCA) or principal component analysis-discriminant analysis (PCA-DA) to reveal groupings within results as well as principal component variable Grouping to assign specific features (metabolites, proteins, etc.) to groups. Interactive visuals allow detailed data interrogation. download
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
MultiQuant Software Process quantitative data sets from TripleTOF or QTRAP systems, including MRM and SWATH Acquisition, using powerful peak integration algorithms. Review results with flexible user interface and exporting and reporting tools. The software allows for the generation of standard concentration curves and provides statistical analysis, outlier flagging and ion ratio computations to enable rapid data review 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[22] 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)[23] and can perform quantitation on both precursor (MS1) and product ions (MS2) level.[24] server
SWATH Software 2.0 Processing tool within PeakView Software (SCIEX) to enable the targeted data processing of SWATH acquisition data (data independent acquisition (DIA) 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 to MarkerView™ software or other tools for statistical analysis. website

Other software[edit]

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.
Easotope open source Software for archiving, organizing, and analyzing mass spectrometer data. Currently oriented toward clumped CO2 analysis but also useful for bulk CO2 work and expandable to other isotopic systems. website
ESIprot Enables the charge state determination and molecular weight calculation for low resolution electrospray ionization (ESI) mass spectrometry (MS) data of proteins.[25] server, online
LabSolutions LCMS proprietary Software by Shimadzu Corporation used with mass spectrometry and HPLC instruments.
Mass++ open source Analysis software for mass spectrometry that can import and export files with open-formats (mzXML, mzML) and load some instrument vendor formats; users can develop and add original functions as Mass++ plug-ins. website
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. website
MassBank.eu website European MassBank server with mirrored mass spectral data from MassBank.jp and special mass spectral data related to environmental organic compounds and pollutants. The website is provided by the NORMAN Network and hosted by the Helmholtz Centre for Environmental Research (Leipzig, Germany) website
MassBank open source MassBank and RMassBank development website provided by the MassBank consortium github
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.[26] download
massXpert Graphical user interface-based (GUI) software for simulating and analyzing mass spectrometric data obtained on known bio-polymer sequences.[27] 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.[28]
MSiReader freeware Vendor-neutral interface built on the Matlab platform designed to view and perform data analysis of mass spectrometry imaging (MSI) data.[29] 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.[30]
Multimaging Software for mass spectrometry imaging designed to normalize, validate and interpret MS images. website
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.[31] 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.[32] 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
PeakInvestigator proprietary 3-4X effective resolution improvement in post-processing of raw profile data output from mass specs. Veritomyx advanced signal processing software for peak detection, deconvolution, and centroiding of raw profile mass spec data reveals multiple peaks hidden in overlapped data. Notable features: order-of-magnitude improvements in mass and abundance precision for deconvolved peaks; local dynamic baselining; advanced thresholding algorithm increases sensitivity across wide dynamic range; statistically-driven and completely automated (no user-to-user variation). More complete and precise resulting mass lists facilitate faster and cost-efficient subsequent determination of correct biomolecular identifications. website
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.[33] websitedownload
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.[34][35][36]
Proteomatic Freeware Data processing pipeline created for the purpose of evaluating mass spectrometric proteomics experiments.[37]
ProteomicsTools open source Software for the post-analysis of MASCOT, SEQUEST, Comet, XTandem, PFind, PeptidePhophet, MyriMatch, MSGF, OMSSA, MSAmanda or Percolator database search result.[38] GitHub
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.[39] 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; website
Rational Numbers Excel Add-In proprietary De novo identification tool that works with Microsoft Excel 2010, Excel 2013, and Excel 2016.

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[dead link]
Spectromania proprietary Software for analysis and visualization of mass spectrometric data.[40]
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.[41]
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).[42]
Xcalibur proprietary Software by Thermo Fisher Scientific used with mass spectrometry instruments.

See also[edit]

References[edit]

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  17. ^ thermo finnigan introduces denovox – Search results from HighBeam Business[dead link]
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  41. ^ 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. 
  42. ^ 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[edit]