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

Proteomics software

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 Name Type DescriptionAndromeda 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.Byonic Proprietary Byonic is a database search algorithm released in 2011 by Protein Metrics Inc. with original developments at PARC. It searches MS/MS data from all types of instruments and internally employs the program Combyne, which combines peptide identifications to produce protein scores and identification probabilities.CHIMERYSProprietaryCHIMERYS 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. 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. Mascot Proprietary Mascot performs mass spectrometry data analysis through a statistical evaluation of matches between observed and projected peptide fragments.MassMatrix Freeware MassMatrix is a database search algorithm for tandem mass spectrometric data. It uses a mass accuracy-sensitive, probabilistic scoring model to rank peptide and protein matches. MassWiz Open source MassWiz is a search algorithm developed at the Institute of Genomics and Integrative Biology that can be used as a Windows command-line tool. 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. 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. 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-LAMPOpen SourceMS-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.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. 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.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.PEAKS DBProprietary 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. 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. 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.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.ProSightPC and ProSightPDProprietaryProSightPC/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.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) is a suite of proteomics tools for statistical analysis of tandem mass spectrometry data. SEQUESTProprietary 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.SIMS Open source SIMS was designed to perform unrestricted PTM searches over tandem mass spectra.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. 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.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.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.X!Tandem Open source X!Tandem matches tandem mass spectra with peptide sequences.WsearchVS2020FreewareWsearchVS2020 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).