 | This article contains content that is written like an advertisement .(September 2019) |
Mass spectrometry software is used for data acquisition, analysis, or representation in mass spectrometry.
| This article contains content that is written like an advertisement .(September 2019) |
Mass spectrometry software is used for data acquisition, analysis, or representation in 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.
| 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. [1] |
| Byonic | Proprietary | Byonic is a database search algorithm released in 2011 by Protein Metrics Inc. with original developments at PARC. [2] It searches MS/MS data from all types of instruments and internally employs the program Combyne, [3] 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. [4] |
| 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. [5] |
| Mascot | Proprietary | Mascot performs mass spectrometry data analysis through a statistical evaluation of matches between observed and projected peptide fragments. [6] |
| 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 ] |
| 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. [7] |
| 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. [8] |
| 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. [9] |
| 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. [10] |
| 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. [11] |
| 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. [12] [13] |
| 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. [14] 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. [15] |
| 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. [16] |
| 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. [17] |
| 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. [18] |
| 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) [19] is a suite of proteomics tools for statistical analysis of tandem mass spectrometry data. [20] |
| 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. [21] |
| SIMS | Open source | SIMS was designed to perform unrestricted PTM searches over tandem mass spectra. [22] |
| 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. [23] |
| 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. [24] |
| 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. [25] |
| 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. [26] |
| 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 peptide sequencing algorithms are, in general, based on the approach proposed in Bartels et al. (1990). [27]
| 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. [28] |
| 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). [29] | |
| DeNovoX | Proprietary | De novo sequencing on CID spectra acquired with ion trap mass spectrometers delivers complete and/or partial peptide sequences (sequence tags). [30] |
| 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. [31] [32] |
| Supernovo | Proprietary | This software automates de novo sequencing of monoclonal antibodies. [33] |
| 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. [34] |
| 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. [35] |
| 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. |
| 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 [36] and dia-PASEF, [37] and can perform library-free analyses (acts as a database search engine). [38] |
| FlashLFQ | Open source | FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. [39] 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.). |
| 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. |
| 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. [40] |
| 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 [41] 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. [42] 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 [43] that allows the targeted analysis of data independent acquisition (DIA) data sets for label-free peptide quantitation, also called SWATH acquisition. [44] |
| 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. |
| 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 [45] [46] [47] [48] |
| 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 analyisis, 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. [49] |
| 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+. [50] |
| 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. [51] |
| ESIprot | ESIprot can determine charge state and calculate molecular weight for low resolution electrospray ionization (ESI) mass spectrometry (MS) data of proteins. [52] | |
| 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. [53] |
| 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. [54] |
| 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. [55] |
| massXpert | Open source GPL | Graphical user interface-based (GUI) software for simulating and analyzing mass spectrometric data obtained on known bio-polymer sequences. [56] 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. [57] |
| 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: 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) [58] metabolites and other molecular entities, generated from high resolution quadrupole time-of-flight tandem mass spectrometry. [59] It also includes, ion mobility, [60] neutral loss, [61] and LC/MS data. [62] [63] |
| mineXpert | Open source GPL | This graphical user interface-based (GUI) software for mass spectral data visualization/mining supports ion mobility mass spectrometry [64] [65] 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. [66] |
| MSiReader | Freeware | Vendor-neutral interface built on the Matlab platform designed to view and perform data analysis of mass spectrometry imaging (MSI) data. [67] 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. [68] |
| MSqRob | Open-source | This is an "R" package with graphical user interface for differential abundance analysis of label-free quantitative proteomics data. [69] [70] [71] |
| 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 an internet browser. [72] |
| PatternLab | Freeware | Software for post-analysis of SEQUEST, ProLuCID or Comet database search results filtered by DTASelect or Census. [73] |
| 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 software for LC/MS data processing supports batch editing 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) [74] |
| 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." [75] |
| 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. [76] |
| 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. [77] [78] [79] |
| 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. [80] |
| ProteomicsTools | Open source | Software for the post-analysis of MASCOT, SEQUEST, Comet, XTandem, PFind, PeptidePhophet, MyriMatch, MSGF, OMSSA, MSAmanda or Percolator database search results. [81] |
| 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. [82] |
| pymzML | Open source | Python module to interface mzML data in Python, based on cElementTree with additional tools for MS-informatics. [83] |
| Pyteomics | Open source | A Python framework for proteomics data analysis. [84] |
| 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. [85] [86] It is accessible via its web-interface [85] and as an R package. [87] |
| 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. [88] |
| 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. [89] |
| 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. [90] |
| 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). [91] [92] |
| 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:
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| VIPER | VIPER analyzes accurate mass and chromatography retention times of LC-MS features (accurate mass and time tag approach). [94] | |
| 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. |
Proteomics is the large-scale study of proteins. Proteins are vital macromolecules of all living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In addition, other kinds of proteins include antibodies that protect an organism from infection, and hormones that send important signals throughout the body.
Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more stages of analysis using one or more mass analyzer are performed with an additional reaction step in between these analyses to increase their abilities to analyse chemical samples. A common use of tandem MS is the analysis of biomolecules, such as proteins and peptides.
The Trans-Proteomic Pipeline (TPP) is an open-source data analysis software for proteomics developed at the Institute for Systems Biology (ISB) by the Ruedi Aebersold group under the Seattle Proteome Center. The TPP includes PeptideProphet, ProteinProphet, ASAPRatio, XPRESS and Libra.
PEAKS is a proteomics software program for tandem mass spectrometry designed for peptide sequencing, protein identification and quantification.
A tandem mass tag (TMT) is a chemical label that facilitates sample multiplexing in mass spectrometry (MS)-based quantification and identification of biological macromolecules such as proteins, peptides and nucleic acids. TMT belongs to a family of reagents referred to as isobaric mass tags which are a set of molecules with the same mass, but yield reporter ions of differing mass after fragmentation. The relative ratio of the measured reporter ions represents the relative abundance of the tagged molecule, although ion suppression has a detrimental effect on accuracy. Despite these complications, TMT-based proteomics has been shown to afford higher precision than Label-free quantification. In addition to aiding in protein quantification, TMT tags can also increase the detection sensitivity of certain highly hydrophilic analytes, such as phosphopeptides, in RPLC-MS analyses.
Protein mass spectrometry refers to the application of mass spectrometry to the study of proteins. Mass spectrometry is an important method for the accurate mass determination and characterization of proteins, and a variety of methods and instrumentations have been developed for its many uses. Its applications include the identification of proteins and their post-translational modifications, the elucidation of protein complexes, their subunits and functional interactions, as well as the global measurement of proteins in proteomics. It can also be used to localize proteins to the various organelles, and determine the interactions between different proteins as well as with membrane lipids.
Shotgun proteomics refers to the use of bottom-up proteomics techniques in identifying proteins in complex mixtures using a combination of high performance liquid chromatography combined with mass spectrometry. The name is derived from shotgun sequencing of DNA which is itself named after the rapidly expanding, quasi-random firing pattern of a shotgun. The most common method of shotgun proteomics starts with the proteins in the mixture being digested and the resulting peptides are separated by liquid chromatography. Tandem mass spectrometry is then used to identify the peptides.
Top-down proteomics is a method of protein identification that either uses an ion trapping mass spectrometer to store an isolated protein ion for mass measurement and tandem mass spectrometry (MS/MS) analysis or other protein purification methods such as two-dimensional gel electrophoresis in conjunction with MS/MS. Top-down proteomics is capable of identifying and quantitating unique proteoforms through the analysis of intact proteins. The name is derived from the similar approach to DNA sequencing. During mass spectrometry intact proteins are typically ionized by electrospray ionization and trapped in a Fourier transform ion cyclotron resonance, quadrupole ion trap or Orbitrap mass spectrometer. Fragmentation for tandem mass spectrometry is accomplished by electron-capture dissociation or electron-transfer dissociation. Effective fractionation is critical for sample handling before mass-spectrometry-based proteomics. Proteome analysis routinely involves digesting intact proteins followed by inferred protein identification using mass spectrometry (MS). Top-down MS (non-gel) proteomics interrogates protein structure through measurement of an intact mass followed by direct ion dissociation in the gas phase.
Isobaric tags for relative and absolute quantitation (iTRAQ) is an isobaric labeling method used in quantitative proteomics by tandem mass spectrometry to determine the amount of proteins from different sources in a single experiment. It uses stable isotope labeled molecules that can be covalent bonded to the N-terminus and side chain amines of proteins.
John R. Yates III is an American chemist and Ernest W. Hahn Professor in the Departments of Molecular Medicine and Neurobiology at The Scripps Research Institute in La Jolla, California.
Label-free quantification is a method in mass spectrometry that aims to determine the relative amount of proteins in two or more biological samples. Unlike other methods for protein quantification, label-free quantification does not use a stable isotope containing compound to chemically bind to and thus label the protein.
OpenMS is an open-source project for data analysis and processing in mass spectrometry and is released under the 3-clause BSD licence. It supports most common operating systems including Microsoft Windows, MacOS and Linux.
Kevin Downard is a British - Australian academic scientist whose research specialises in the improving responses to infectious disease through the application and development of mass spectrometry and other molecular approaches in the life and medical sciences. Downard has over 35 years of experience in the field and has written over 145 lead-author scientific peer-reviewed journal publications, and two books including a textbook for the Royal Society of Chemistry and the first book to be published on the role of mass spectrometry in the study of protein interactions.
Proteogenomics is a field of biological research that utilizes a combination of proteomics, genomics, and transcriptomics to aid in the discovery and identification of peptides. Proteogenomics is used to identify new peptides by comparing MS/MS spectra against a protein database that has been derived from genomic and transcriptomic information. Proteogenomics often refers to studies that use proteomic information, often derived from mass spectrometry, to improve gene annotations. The utilization of both proteomics and genomics data alongside advances in the availability and power of spectrographic and chromatographic technology led to the emergence of proteogenomics as its own field in 2004.
In bio-informatics, a peptide-mass fingerprint or peptide-mass map is a mass spectrum of a mixture of peptides that comes from a digested protein being analyzed. The mass spectrum serves as a fingerprint in the sense that it is a pattern that can serve to identify the protein. The method for forming a peptide-mass fingerprint, developed in 1993, consists of isolating a protein, breaking it down into individual peptides, and determining the masses of the peptides through some form of mass spectrometry. Once formed, a peptide-mass fingerprint can be used to search in databases for related protein or even genomic sequences, making it a powerful tool for annotation of protein-coding genes.
MassMatrix is a mass spectrometry data analysis software that uses a statistical model to achieve increased mass accuracy over other database search algorithms. This search engine is set apart from others dues to its ability to provide extremely efficient judgement between true and false positives for high mass accuracy data that has been obtained from present day mass spectrometer instruments. It is useful for identifying disulphide bonds in tandem mass spectrometry data. This search engine is set apart from others due to its ability to provide extremely efficient judgement between true and false positives for high mass accuracy data that has been obtained from present day mass spectrometer instruments.
In mass spectrometry, de novo peptide sequencing is the method in which a peptide amino acid sequence is determined from tandem mass spectrometry.
Ronald Charles Beavis is a Canadian protein biochemist, who has been involved in the application of mass spectrometry to protein primary structure, with applications in the fields of proteomics and analytical biochemistry. He has developed methods for measuring the identity and post-translational modification state of proteins obtained from biological samples using mass spectrometry. He is currently best known for developing new methods for analyzing proteomics data and applying the results of these methods to problems in computational biology.
In mass spectrometry, data-independent acquisition (DIA) is a method of molecular structure determination in which all ions within a selected m/z range are fragmented and analyzed in a second stage of tandem mass spectrometry. Tandem mass spectra are acquired either by fragmenting all ions that enter the mass spectrometer at a given time or by sequentially isolating and fragmenting ranges of m/z. DIA is an alternative to data-dependent acquisition (DDA) where a fixed number of precursor ions are selected and analyzed by tandem mass spectrometry.
Ancient proteins are complex mixtures and the term palaeoproteomics is used to characterise the study of proteomes in the past. Ancients proteins have been recovered from a wide range of archaeological materials, including bones, teeth, eggshells, leathers, parchments, ceramics, painting binders and well-preserved soft tissues like gut intestines. These preserved proteins have provided valuable information about taxonomic identification, evolution history (phylogeny), diet, health, disease, technology and social dynamics in the past.
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