Biology:List of mass spectrometry software

From HandWiki
Short description: None


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

Proteomics software

Further information: Biology: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
Andromeda (part of MaxQuant) Freeware Andromeda is a peptide search engine based on probabilistic scoring. It can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, such as highly phosphorylated peptides, and accommodates extremely large databases. It can function independently or integrated into MaxQuant, enabling analysis of large datasets on a desktop computer. Developed by Jürgen Cox and others at the Max Planck Institute of Biochemistry.[1]
Byonic Proprietary Byonic is a database search algorithm released in 2011 by Protein Metrics Inc. with original developments at PARC[2] that 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 text-generation, cloud-native database search algorithm for data-dependent acquisition data which makes heavy use of artificial intelligence for the identification of peptides and the deconvolution of chimeric spectra. CHIMERYS is developed by MSAID GmbH, a spin-off from the Technical University of Munich, and is integrated as node in Proteome Discoverer 3.0 software.
Comet Open source Comet is a command-line database search algorithm developed at the University of Washington available for Windows and Linux. It takes in spectra in some supported input format 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 having hundreds of nodes.
InsPecT Open source InsPecT is an MS-alignment search algorithm available at 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 Institute of Genomics and Integrative Biology available as a windows commandline tool.
MSFragger Freeware MSFragger is a fast database searching based on efficient fragment ion indexing. Capable of open (mass-tolerant) searches for post-translational modification discovery, O- and N-linked glycoproteomics searches, semi- and non-enzymatic searches, in addition to traditional database searches. Developed at the University of Michigan.[7]
MS-GF + Open source MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database. It supports the HUPO PSI standard input file (mzML) and saves results in the mzIdentML format, though results can easily be transformed to TSV. ProteomeXchange supports Complete data submissions using MS-GF+ search results. Developed at 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.[8]
MyriMatch Open source MyriMatch is 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.[9]
NIST Mass Spectral Search v.3.0 Commercial Program This software is provided with the NIST\EPA\NIH electron ionization (EI) Library and the NIST Tandem Library of product-ion mass spectra. There is a downloadable DEMO of v.2.3 of the Program with a small Demo EI Library at the NIST Website. This comes with the NIST MS Interpreter Program and AMDIS.
OMSSA Freeware The Open Mass Spectrometry Search Algorithm (OMSSA) is an efficient search engine for identifying MS/MS peptide spectra by searching libraries of known protein sequences. OMSSA scores 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.[10][11]
PEAKS DB Proprietary Peaks DB is 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.[12] 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 germinated in 2002 in the Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.
Phenyx Proprietary Phenyx was 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.[13]
ProbID Open source ProbID is a powerful suite on analysis of tandem mass spectrum. It seeks to fill the need for the deep analysis of tandem mass spectrum, including the fragmentation rules, preference of cleavage, neutral losses, etc. Developed at the Bioinformatics Group, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.[14]
ProLuCID Freeware ProLuCID is a fast and sensitive tandem mass spectra-based protein identification program recently developed by Tao Xu and others in the Yates laboratory at The Scripps Research Institute.[15]
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 the peptide identification considering hundreds of modifications, non-tryptic cleavages, and amino acid substitutions. It uses the Pro Group Algorithm for protein inference analysis to report the 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 translates user interface controls in the language of the proteomics experimental scientist to underlying complex informatics parameters.[16]
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.
RAId Lost RAId was developed at the National Center for Biotechnology Information, Robust Accurate Identification (RAId)[17] is a suite of proteomics tools for analyzing tandem mass spectrometry data with accurate statistics.[18]
SEQUEST Proprietary SEQUEST identifies collections of tandem mass spectra to peptide sequences that have been generated from databases of protein sequences.[19]
SIMS Open source SIMS was designed to perform unrestrictive PTM searches 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.[20]
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.[21]
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 for identifying peptides from tandem mass spectra. It is an independent reimplementation 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 has been completely re-engineered to achieve a great improvement in speed while exactly replicating SEQUEST XCorr scores. Developed at the University of Washington.[22]
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.[23]
TopPIC Open source TopPIC (Top-down mass spectrometry-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 efficiently identifies proteoforms with unexpected alterations, such as mutations and post-translational modifications (PTMs), accurately estimates the statistical significance of identifications, and characterizes reported proteoforms with unknown mass shifts. It uses several techniques, such as indexes, spectral alignment, generation function methods, and the modification identification score (MIScore), to increase the speed, sensitivity, and accuracy.[24]
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. Can also search/match 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).[25]

Name Type Description
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.[26]
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).[27]
DeNovoX proprietary De novo sequencing on CID spectra acquired with ion trap mass spectrometers delivering complete and/or partial peptide sequences (sequence tags).[28]
Lutefisk open source Software for the de novo interpretation of peptide CID spectra.
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.[29]
PEAKS proprietary 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 processed data faster than 1 spectrum per second.[30][31]
Supernovo proprietary Software for the automated de novo sequencing of monoclonal antibodies.[32]

Homology searching algorithms

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, where one can specify the number of amino acid mismatches allowed.
SPIDER proprietary The SPIDER algorithm matches sequence tags with errors to database sequences for the purpose of protein and peptide identification and can be used in conjunction with PEAKS mass spectrometry data analysis software.

MS/MS peptide quantification

Further information: Physics:Quantitative proteomics
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 (BACIQ).
Byos proprietary Commercial software for XIC of peptide level mass spec data from any mass spec vendor and relative quan of PTM vs unmodified. Specialized for biopharmaceutical applications.
DIA-NN freeware Automated quantitative Data-independent acquisition-proteomics software developed by the Demichev and Ralser labs at the Charité in Berlin, Germany , which 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[33] and dia-PASEF,[34] can perform library-free analyses, that is act as a database search engine.[35]
MarkerView Software proprietary Commercial software for statistical analysis for quantitative mass spec data sets from metabolomics and proteomic profiling applications.
Mascot Distiller proprietary Software for peak picking and raw data preprocessing. Has an optional toolbox for label-free quantification as well as isobaric labeling and isotopic labeling. 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, supports complex data treatments 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 written in C# that allows the analysis of label free and SILAC based proteomics experiments.
MultiQuant Software proprietary Can process quantitative data sets from TripleTOF or QTRAP systems, including MRM and SWATH Acquisition.
OpenMS / TOPP 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. Allows peptide and metabolite quantification, supporting label-free and isotopic-label-based quantification (such as iTRAQ and TMT and SILAC) as well as targeted SWATH-MS quantification.[36]
OpenPIP website, open access OpenPIP is an open access, web based tool, developed by InterVenn Biosciences to integrate peaks acquired in multiple reaction monitoring (MRM) experiments. The software is powered by recurrent neural networks and was trained on a massive collection of manually-annotated chromatographic peaks.
ProtMax freeware ProtMAX[37] is a software tool for analyzing shotgun proteomics mass spectrometry data sets, developed by Volker Egelhofer at the University of Vienna.
Skyline open source Open source (Apache 2.0) Windows client software developed in the MacCoss lab at University of Washington[38] that 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 analyzing the resulting mass spectrometer data.
Spectronaut proprietary Commercial software for quantitative proteomics developed by Biognosys AG (Schlieren, Switzerland) based on the mProphet algorithm[39] that allows the targeted analysis of data independent acquisition (DIA) data sets for label-free peptide quantitation, also called SWATH acquisition.[40]
SWATH Software 2.0 proprietary Commercial software processing tool within PeakView that allows targeted data processing of SWATH acquisition data. Using a protein/peptide ion library, fragment ion extracted ion chromatograms (XICs) are generated, scored and quantified for peptides from the library. After false discovery rate analysis (FDR), results are filtered and quantitative peptide/protein data can be exported for statistical analysis.

Other software

Name Type Description
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.
AMDIS freeware Software by NIST for GC/MS Data in various formats. 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 Software by AB Sciex, a division of The Danaher Corporation.
AnalyzerPro proprietary 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 using MatrixAnalyzer for the comparison of multiple data sets. 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) MALDI-TOF MS data analysis and biomarker discovery tools, based on artificial intelligence and machine learning algorithms. ArtIST is an online service.
ASCENT proprietary LC and GC-MS data analysis automation tool, provided as SaaS over a cloud platform. Uses machine learning algorithms to analyze MS plots and reduce the amount of manual review required.
CFM-ID
Chromeleon proprietary Software by Thermo Fisher Scientific used with mass spectrometry instruments, as well as chromatography instruments.
Crosslinx open source Identify cross-linked peptides from mzML files. Python script or standalone executables for Linux and Windows. Feasible for bigger databases with a two-step approach.[41]
DeNovoGUI open source Software with a graphical user interface for running parallelized versions of the freely available de novo sequencing software tools Novor and PepNovo+.[42]
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.
El-MAVEN open-source Desktop software by Elucidata for processing 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 analyzes like relative flux and quantification.[43]
ESIprot Enables the charge state determination and molecular weight calculation for low resolution electrospray ionization (ESI) mass spectrometry (MS) data of proteins.[44]
Expressionist proprietary An enterprise software solution by Genedata for processing, analyzing, and reporting of mass spectrometry data in application areas such as biotherapeutics characterization, quality monitoring, and related proteomics and metabolomics applications.
HIquant open source A first-principles model and algorithm for quantifying proteoform stoichiometries from bottom-up data.[45]
KnowItAll Spectroscopy Software & Mass Spectral Library proprietary Software from Wiley with solutions 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 used with mass spectrometry and HPLC instruments.
LipidXplorer open source High-throughput lipid identification from shotgun mass spectra (Python)[46]
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.
MassBank open source MassBank and RMassBank development website provided by the MassBank consortium. MassBank data is 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, 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 even very complex mixtures.
Mass Mountaineer proprietary Qualitative analysis and reporting software including 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 and 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 preprocessed data for biomarker discovery, unsupervised clustering and supervised sample classification.[47]
massXpert open source GPL Graphical user interface-based (GUI) software for simulating and analyzing mass spectrometric data obtained on known bio-polymer sequences.[48] Successor to polyxmass. A program of the msxpertsuite.org software suite.
Mestrenova proprietary A vendor independent software for processing chromatography (LC, GC, SFC) data with any combination detectors, e.g. LC-MS-UV-VIS, GC-MS, SFC-MS-UV in one environment. Multiplatform and web based software by Mestrelab Research, S.L.
matchms open source Python library to import, clean, process and quantitatively compare MS/MS spectra. Developed at the Netherlands eScience Center.[49]
METASPACE free and open-source Cloud platform for metabolite and lipid identification, and 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)[50] metabolites and other molecular entities, generated from high resolution quadrupole time-of-flight tandem mass spectrometry,[51] it also includes, ion mobility,[52] neutral loss,[53] and LC/MS data.[54][55]
mineXpert open source GPL Graphical user interface-based (GUI) software for mass spectral data visualization/mining. Supports ion mobility mass spectrometry.[56] A program of the msxpertsuite.org 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
MSight freeware Software for mass spectrometry imaging developed by the Swiss Institute of Bioinformatics.[57]
MSiReader freeware Vendor-neutral interface built on the Matlab platform designed to view and perform data analysis of mass spectrometry imaging (MSI) data.[58] Matlab is not required to use MSiReader.
MS Interpreter freeware Software by NIST for compression of structure with mass spectra. Major enhancement of mechanisms and their rates for all fragmentation types (EI, Tandem positive and negative mode), with new display features, isotope calculator and updated on-line help. This program connects mass spectral peaks to their probable chemical structure origin and can be quickly invoked from the NISTMS program with the F9 key. 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 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.[59]
MSqRob open-source R package with graphical user interface for robust differential abundance analysis of label-free quantitative proteomics data.[60][61][62]
ms2mz freeware Utility for converting 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 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.
ORIGAMI open source Software suite for analysis of mass spectrometry and ion mobility mass spectrometry datasets. ORIGAMI 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 enables exporting of all results in an interactive format where the user can share any dataset and visualize in an internet browser.[63]
PatternLab freeware Software for post-analysis of SEQUEST, ProLuCID or Comet database search results filtered by DTASelect or Census.[64]
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 Web based software for LCMS data processing. Supports batch editing and high-throughput experiments. Vendor agnostic.
PeakStrainer open source Intensity-Independent Noise Filtering in FT MS and FT MS/MS Spectra for Shotgun Lipidomics (Python)[65]
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 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.
PetroOrg proprietary Software developed specifically for analyzing petroleum, but it is also used to analyze "other complex mixtures, including anthropogenic environmental contaminants and natural organic matter."[66]
Pinnacle Proprietary From comprehensive quantitation of many thousands of proteins across of hundreds of samples using DDA, DIA, PRM or SRM with fully integrated statistics and biological interpretation, to complete N-linked glycoprotein identification routine, to a very in-depth analysis in protein characterization, including peptide mapping, error tolerant search and disulfide analysis, all of this is available in a single software. Analyzing hundreds of samples brings big challenges of LC and MS variation when run over months of acquisition, and the software can automatically correct for this. The visualization, editing and annotation capabilities can be tailored to be at the high level of proteins or at a much lower level of transitions or isotopes.
PIQMIe web Proteomics Identifications/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.[67]
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.
ProMass proprietary ProMass is an automated biomolecule deconvolution and reporting software package that is used to process ESI/LC/MS data or single ESI mass spectra. It uses the novel deconvolution algorithm, ZNova, to produce artifact-free deconvoluted mass spectra. ProMass is currently available for Thermo, Waters, and Shimadzu platforms. It is also available in 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.[68][69][70]
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.
Proteomatic Freeware Data processing pipeline created for the purpose of evaluating mass spectrometric proteomics experiments.[71]
ProteomicsTools open source Software for the post-analysis of MASCOT, SEQUEST, Comet, XTandem, PFind, PeptidePhophet, MyriMatch, MSGF, OMSSA, MSAmanda or Percolator database search result.[72]
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 is geared towards analysis of differential quantification data and provides tools as well as visualization options to facilitate analysis. It is possible to process label-free and tandem mass tagged data.[73]
pymzML open source Python module to interface mzML data in Python based on cElementTree with additional tools for MS-informatics.[74]
Pyteomics open source A Python framework for proteomics data analysis.[75]
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 that is compatible with a variety of MSI instruments, including Bruker, Sciex, Thermo and with iMZML.
Rational Numbers Excel Add-In proprietary De novo identification tool for small molecules that works with Microsoft Excel 2010, Excel 2013, Excel 2016, and Excel 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 Identification of small molecules by comparison of accurate-mass fragmentation data to a database of 250000 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 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 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. Also support NMR instrumentation and data processing.
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 and 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.[76][77] It is accessible via its web-interface[76] and as an R package.[78]
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.[79]
SimGlycan proprietary Predicts the structure of glycans and glycopeptides using mass spectrometry MS/MS data.
SIMION proprietary Ion optics simulation program
SIRIUS open source and web service Annotation of small molecules from LC-MS/MS data, umbrella application for CSI:FingerID, CANOPUS etc
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 that focuses on finding protein biomarkers and detecting protein deviations.
Spectromania proprietary Software for analysis and visualization of mass spectrometric data.[80]
StavroX
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 isotopomer envelopes 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 that includes PeptideProphet for the Statistical validation of PSMs using search engine results, iProphet for distinct peptide sequence validation, using PeptideProphet results (can also combine the results of multiple search engines) and ProteinProphet for Protein identification and validation, using PeptideProphet OR iProphet results. TPP does also Protein Quantification with XPRESS (Calculation of relative abundances of peptides and proteins 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. Developed at the Seattle Proteomic Centre (SPC).[81]

[82]

TurboMass proprietary GC/MS software by PerkinElmer.
Universal Mass Calculator freeware UMC is programmed as a tool for use in Mass Spectrometry in order to give useful assistance in interpreting measurement results, mainly derived from molecular or quasi molecular ions.

It can be used for the calculation of:

  • Mass deviation (mmu or ppm) of measured mass from given empirical formula
  • Mass differences of two empirical formulas
  • Elemental compositions (also taking into account the measured intensity pattern, "most abundant" algorithm[83] included)
  • Isotope pattern simulation from empirical formulas
  • Analysis of the degree of isotope labelling with D, 13C, 15N or 18O
VIPER Analysis of accurate mass and chromatography retention time analysis of LC-MS features (accurate mass and time tag approach).[84]
Xcalibur proprietary Software by Thermo Fisher Scientific used with mass spectrometry instruments.
XCMS Online (Cloud-Based) proprietary Freely available and the most widely used metabolomic and lipidomic data processing platform with over 21,000 users as of 2017.

See also

References

  1. ↑ Cox, Jürgen; Neuhauser, Nadin; Michalski, Annette; Scheltema, Richard A.; Olsen, Jesper V.; Mann, Matthias (2011). "Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment". Journal of Proteome Research 10 (4): 1794–1805. doi:10.1021/pr101065j. ISSN 1535-3893. PMID 21254760. 
  2. ↑ 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. 
  3. ↑ 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. 
  4. ↑ Eng, Jimmy K.; Jahan, Tahmina A.; Hoopmann, Michael R. (2013). "Comet: An open-source MS/MS sequence database search tool". Proteomics 13 (1): 22–24. doi:10.1002/pmic.201200439. ISSN 1615-9853. PMID 23148064. 
  5. ↑ "Inspect and MS-Alignment". 
  6. ↑ 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. 
  7. ↑ Kong, Andy T.; Leprevost, Felipe V.; Avtonomov, Dmitry M.; Mellacheruvu, Dattatreya; Nesvizhskii, Alexey I. (2017). "MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics". Nature Methods 14 (5): 513–520. doi:10.1038/nmeth.4256. PMID 28394336. 
  8. ↑ Sabareesh, Varatharajan; Singh, Gurpreet (2013). "Mass spectrometry-based lipid(ome) analyzer and molecular platform: a new software to interpret and analyze electrospray and/or matrix-assisted laser desorption/ionization mass spectrometric data of lipids: a case study from Mycobacterium tuberculosis". Journal of Mass Spectrometry 48 (4): 465–477. doi:10.1002/jms.3163. ISSN 1096-9888. PMID 23584940. Bibcode: 2013JMSp...48..465S. 
  9. ↑ 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. PMID 17269722. 
  10. ↑ "OMSSA ms/ms search engine". Pubchem.ncbi.nlm.nih.gov. https://pubchem.ncbi.nlm.nih.gov/omssa/. 
  11. ↑ Geer, Lewis Y.; Markey, Sanford P.; Kowalak, Jeffrey A.; Wagner, Lukas; Xu, Ming; Maynard, Dawn M.; Yang, Xiaoyu; Shi, Wenyao et al. (2004). "Open Mass Spectrometry Search Algorithm". Journal of Proteome Research 3 (5): 958–64. doi:10.1021/pr0499491. PMID 15473683. Bibcode: 2004q.bio.....6002G. 
  12. ↑ Liang, C; Smith, JC; Hendrie, Christopher (2003). "A Comparative Study of Peptide Sequencing Software Tools for MS/MS". American Society for Mass Spectrometry. 
  13. ↑ 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. 
  14. ↑ Zhang, Zhuo; Sun, Shiwei; Zhu, Xiaopeng; Chang, Suhua; Liu, Xiaofei; Yu, Chungong; Bu, Dongbo; Chen, Runsheng (2006). "A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data". BMC Bioinformatics 7 (1): 222. doi:10.1186/1471-2105-7-222. ISSN 1471-2105. PMID 16638152. 
  15. ↑ Xu, T.; Park, S.K.; Venable, J.D.; Wohlschlegel, J.A.; Diedrich, J.K.; Cociorva, D.; Lu, B.; Liao, L. et al. (2015). "ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity". Journal of Proteomics 129: 16–24. doi:10.1016/j.jprot.2015.07.001. ISSN 1874-3919. PMID 26171723. 
  16. ↑ Shilov, Ignat V.; Seymour, Sean L.; Patel, Alpesh A.; Loboda, Alex; Tang, Wilfred H.; Keating, Sean P.; Hunter, Christie L.; Nuwaysir, Lydia M. et al. (2007). "The Paragon Algorithm, a Next Generation Search Engine That Uses Sequence Temperature Values and Feature Probabilities to Identify Peptides from Tandem Mass Spectra". Molecular & Cellular Proteomics 6 (9): 1638–1655. doi:10.1074/mcp.T600050-MCP200. ISSN 1535-9476. PMID 17533153. 
  17. ↑ "RAId MS/MS search engine". QMBP NCBI NLM NIH. https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/raid/index.html. 
  18. ↑ 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. PMID 17961253. 
  19. ↑ Jimmy K. Eng; Ashley L. McCormack; 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. 
  20. ↑ Hricovíni, Miloš; Tvaroška, Igor; Hirsch, Ján; Duben, Anthony J. (1991). "Nuclear overhauser effects and the flexibility of saccharides: methyl β-xylobioside". Carbohydrate Research 210: 13–20. doi:10.1016/0008-6215(91)80109-Z. ISSN 0008-6215. PMID 1878875. 
  21. ↑ 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): 1–15. doi:10.1515/jib-2013-228. PMID 24231142. 
  22. ↑ Diament, Benjamin J.; Noble, William Stafford (2011). "Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra". Journal of Proteome Research 10 (9): 3871–3879. doi:10.1021/pr101196n. ISSN 1535-3893. PMID 21761931. 
  23. ↑ kou, Qiang; Wu, Si; Tolić, Nikola; Paša-Tolić, Ljiljana; Liu, Yunlong; Liu, Xiaowen (2017). "A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra.". Bioinformatics 33 (9): 1309–1316. doi:10.1093/bioinformatics/btw806. ISSN 1460-2059. PMID 28453668. 
  24. ↑ kou, Qiang; Xun, Likun; Liu, Xiaowen (2016). "TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization.". Bioinformatics 32 (22): 3495–3497. doi:10.1093/bioinformatics/btw398. ISSN 1460-2059. PMID 27423895. 
  25. ↑ 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. PMID 24730078. 
  26. ↑ Novak, Jiri; Lemr, Karel; Schug, Kevin A.; Havlicek, Vladimir (2015). "CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra". J. Am. Soc. Mass Spectrom. 26 (10): 1780–1786. doi:10.1007/s13361-015-1211-1. PMID 26195308. Bibcode: 2015JASMS..26.1780N. 
  27. ↑ 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. 
  28. ↑ thermo finnigan introduces denovox – Search results [|permanent dead link|dead link}}]
  29. ↑ Ma, Bin (30 June 2015). "Novor: Real-Time Peptide de Novo Sequencing Software". Journal of the American Society for Mass Spectrometry 26 (11): 1885–1894. doi:10.1007/s13361-015-1204-0. PMID 26122521. Bibcode: 2015JASMS..26.1885M. 
  30. ↑ Ma, Bin; Zhang, Kaizhong; Hendrie, Christopher; Liang, Chengzhi; Li, Ming; Doherty-Kirby, Amanda; Lajoie, Gilles (2003). "PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry". Rapid Communications in Mass Spectrometry 17 (20): 2337–42. doi:10.1002/rcm.1196. PMID 14558135. Bibcode: 2003RCMS...17.2337M. 
  31. ↑ 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. PMID 17686166. 
  32. ↑ Sen, K. Ilker; Tang, Wilfred H; Nayak, Shruti; Kil, Yong J; Bern, Marshall; Ozoglu, Berk; Ueberheide, Beatrix; Davis, Darryl et al. (2017-05-01). "Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery" (in en). Journal of the American Society for Mass Spectrometry 28 (5): 803–810. doi:10.1007/s13361-016-1580-0. ISSN 1044-0305. PMID 28105549. 
  33. ↑ Messner, Christoph B.; Demichev, Vadim; Bloomfield, Nic; Yu, Jason S. L.; White, Matthew; Kreidl, Marco; Egger, Anna-Sophia; Freiwald, Anja et al. (July 2021). "Ultra-fast proteomics with Scanning SWATH" (in en). Nature Biotechnology 39 (7): 846–854. doi:10.1038/s41587-021-00860-4. ISSN 1546-1696. PMID 33767396. 
  34. ↑ Demichev, Vadim; Yu, Fengchao; Teo, Guo Ci; Szyrwiel, Lukasz; Rosenberger, George A.; Decker, Jens; Kaspar-Schoenefeld, Stephanie; Lilley, Kathryn S. et al. (2021-03-09). "High sensitivity dia-PASEF proteomics with DIA-NN and FragPipe" (in en). bioRxiv: 2021.03.08.434385. doi:10.1101/2021.03.08.434385. https://www.biorxiv.org/content/10.1101/2021.03.08.434385v1. 
  35. ↑ Demichev, Vadim; Messner, Christoph B.; Vernardis, Spyros I.; Lilley, Kathryn S.; Ralser, Markus (January 2020). "DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput" (in en). Nature Methods 17 (1): 41–44. doi:10.1038/s41592-019-0638-x. ISSN 1548-7105. PMID 31768060. 
  36. ↑ "OpenMS: a flexible open-source software platform for mass spectrometry data analysis". Nat. Methods 13 (9): 741–8. 2016. doi:10.1038/nmeth.3959. PMID 27575624. http://edoc.mdc-berlin.de/15966/13/15966oa.pdf. 
  37. ↑ "Using ProtMAX to create high-mass-accuracy precursor alignments from label-free quantitative mass spectrometry data generated in shotgun proteomics experiments". Nat Protoc 8 (3): 595–601. 2013. doi:10.1038/nprot.2013.013. PMID 23449253. 
  38. ↑ Maclean, B (2010). "Skyline: An Open Source Document Editor for Creating and Analyzing Targeted Proteomics Experiments". Bioinformatics 26 (7): 966–968. doi:10.1093/bioinformatics/btq054. PMID 20147306. 
  39. ↑ Reiter, L (2011). "mProphet: automated data processing and statistical validation for large-scale SRM experiments". Nat Methods 8 (5): 430–435. doi:10.1038/nmeth.1584. PMID 21423193. 
  40. ↑ 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. PMID 24206228. 
  41. ↑ Ozawa, SI; Bald, T; Onishi, T; Xue, H; Matsumura, T; Kubo, R; Takahashi, H; Hippler, M et al. (October 2018). "Configuration of Ten Light-Harvesting Chlorophyll a/b Complex I Subunits in Chlamydomonas reinhardtii Photosystem I.". Plant Physiology 178 (2): 583–595. doi:10.1104/pp.18.00749. PMID 30126869. 
  42. ↑ Muth, Thilo; Weilnböck, Lisa; Rapp, Erdmann; Huber, Christian G.; Martens, Lennart; Vaudel, Marc; Barsnes, Harald (2014). "DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra". Journal of Proteome Research 13 (2): 1143–1146. doi:10.1021/pr4008078. ISSN 1535-3893. PMID 24295440. 
  43. ↑ Sahil; Shubhra Agrawal; GeorgeSabu; Rishabh Gupta; Pankaj Kumar; Saiful B. Khan; kailash yadav; Naman Gupta et al. (2019-01-11), ElucidataInc/ElMaven: v0.6.1, doi:10.5281/zenodo.2537593 
  44. ↑ 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. Bibcode: 2010RCMS...24..285W. 
  45. ↑ Malioutov, Dmitry; Chen, Tianchi; Airoldi, Edoardo; Jaffe, Jacob; Budnik, Bogdan; Slavov, Nikolai (2019-01-01). "Quantifying Homologous Proteins and Proteoforms" (in en). Molecular & Cellular Proteomics 18 (1): 162–168. doi:10.1074/mcp.TIR118.000947. ISSN 1535-9476. PMID 30282776. PMC 6317479. https://www.mcponline.org/content/18/1/162. 
  46. ↑ "LIFS LipidXplorer Wiki". https://lifs-tools.org/wiki/index.php/Main_Page. 
  47. ↑ López-Fernández, H; Santos, HM; Capelo, JL; Fdez-Riverola, F; Glez-Peña, D; Reboiro-Jato, M (2015). "Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery". BMC Bioinformatics 16: 318. doi:10.1186/s12859-015-0752-4. PMID 26437641. 
  48. ↑ Rusconi, F. (2009). "massXpert 2: a cross-platform software environment for polymer chemistry modeling and simulation/analysis of mass spectrometric data". Bioinformatics 25 (20): 2741–2. doi:10.1093/bioinformatics/btp504. PMID 19740912. 
  49. ↑ Huber, Florian; Verhoeven, Stefan; Meijer, Christiaan; Spreeuw, Hanno; Villanueva, Efrain; Geng, Cunliang; van der Hooft, Justin J.J.; Rogers, Simon et al. (2020). "matchms - processing and similarity evaluation of mass spectrometry data". Journal of Open Source Software 5 (52): 2411. doi:10.21105/joss.02411. Bibcode: 2020JOSS....5.2411H. https://joss.theoj.org/papers/10.21105/joss.02411. 
  50. ↑ "The Analytical Scientist Innovation Awards 2023" (in en). 2023-12-12. https://theanalyticalscientist.com/techniques-tools/the-analytical-scientist-innovation-awards-2023. 
  51. ↑ Xue, Jingchuan; Guijas, Carlos; Benton, H. Paul; Warth, Benedikt; Siuzdak, Gary (October 2020). "METLIN MS2 molecular standards database: a broad chemical and biological resource" (in en). Nature Methods 17 (10): 953–954. doi:10.1038/s41592-020-0942-5. ISSN 1548-7105. PMID 32839599. PMC 8802982. https://www.nature.com/articles/s41592-020-0942-5. 
  52. ↑ Baker, Erin S.; Hoang, Corey; Uritboonthai, Winnie; Heyman, Heino M.; Pratt, Brian; MacCoss, Michael; MacLean, Brendan; Plumb, Robert et al. (December 2023). "METLIN-CCS: an ion mobility spectrometry collision cross section database" (in en). Nature Methods 20 (12): 1836–1837. doi:10.1038/s41592-023-02078-5. ISSN 1548-7105. https://www.nature.com/articles/s41592-023-02078-5. 
  53. ↑ Aisporna, Aries; Benton, H. Paul; Chen, Andy; Derks, Rico J. E.; Galano, Jean Marie; Giera, Martin; Siuzdak, Gary (2022-03-02). "Neutral Loss Mass Spectral Data Enhances Molecular Similarity Analysis in METLIN" (in en). Journal of the American Society for Mass Spectrometry 33 (3): 530–534. doi:10.1021/jasms.1c00343. ISSN 1044-0305. PMID 35174708. PMC 10131246. https://pubs.acs.org/doi/10.1021/jasms.1c00343. 
  54. ↑ "METLIN - Database Commons". https://ngdc.cncb.ac.cn/databasecommons/database/id/5907. 
  55. ↑ Domingo-Almenara, Xavier; Guijas, Carlos; Billings, Elizabeth; Montenegro-Burke, J. Rafael; Uritboonthai, Winnie; Aisporna, Aries E.; Chen, Emily; Benton, H. Paul et al. (2019-12-20). "The METLIN small molecule dataset for machine learning-based retention time prediction" (in en). Nature Communications 10 (1): 5811. doi:10.1038/s41467-019-13680-7. ISSN 2041-1723. PMID 31862874. PMC 6925099. https://www.nature.com/articles/s41467-019-13680-7. 
  56. ↑ Rusconi, F. (2019). "mineXpert: Biological Mass Spectrometry Data Visualization and Mining with Full JavaScript Ability". J. Proteome Res. 18 (5): 2254–2259. doi:10.1021/acs.jproteome.9b00099. PMID 30950277. https://hal-cnrs.archives-ouvertes.fr/hal-02379614/file/minexpert-filippo-rusconi-jproteomeres-2019.pdf. 
  57. ↑ Palagi, Patricia M.; Walther, Daniel; Quadroni, Manfredo; Catherinet, SéBastien; Burgess, Jennifer; Zimmermann-Ivol, Catherine G.; Sanchez, Jean-Charles; Binz, Pierre-Alain et al. (2005). "MSight: An image analysis software for liquid chromatography-mass spectrometry". Proteomics 5 (9): 2381–4. doi:10.1002/pmic.200401244. PMID 15880814. 
  58. ↑ 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 24 (5): 718–721. doi:10.1007/s13361-013-0607-z. PMID 23536269. Bibcode: 2013JASMS..24..718R. 
  59. ↑ Prince, J. T.; Marcotte, E. M. (2008). "Mspire: Mass spectrometry proteomics in Ruby". Bioinformatics 24 (23): 2796–2797. doi:10.1093/bioinformatics/btn513. PMID 18930952. 
  60. ↑ Goeminne, L. J. E.; Gevaert, K.; Clement, L. (2016). "Peptide-level Robust Ridge Regression Improves Estimation, Sensitivity, and Specificity in Data-dependent Quantitative Label-free Shotgun Proteomics.". Molecular & Cellular Proteomics 15 (2): 657–668. doi:10.1074/mcp.M115.055897. PMID 26566788. 
  61. ↑ Goeminne, L. J. E.; Gevaert, K.; Clement, L. (2018). "Experimental design and data analysis in label-free quantitative LC/MS proteomics: A tutorial with MSqRob.". Journal of Proteomics 171: 23–26. doi:10.1016/j.jprot.2017.04.004. PMID 28391044. https://zenodo.org/record/7541882. 
  62. ↑ Goeminne, L. J. E.; Sticker, A.; Martens, M.; Gevaert, K.; Clement, L. (2020). "MSqRob takes the missing hurdle: uniting intensity- and count-based proteomics". Analytical Chemistry XXXX (XX): 6278–6287. doi:10.1021/acs.analchem.9b04375. PMID 32227882. https://biblio.ugent.be/publication/8671265. 
  63. ↑ Migas, Lukasz G.; France, Aidan P.; Bellina, Bruno; Barran, Perdita E. (April 2018). "ORIGAMI : A software suite for activated ion mobility mass spectrometry (aIM-MS) applied to multimeric protein assemblies". International Journal of Mass Spectrometry 427: 20–28. doi:10.1016/j.ijms.2017.08.014. ISSN 1387-3806. Bibcode: 2018IJMSp.427...20M. https://www.research.manchester.ac.uk/portal/en/publications/origami-a-software-suite-for-activated-ion-mobility-mass-spectrometry-aimms-applied-to-multimeric-protein-assemblies(36cd403d-e95c-4294-beb8-b03ef318f98a).html. 
  64. ↑ 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. PMID 18644148. 
  65. ↑ Ackerman, Miranda; Jacobo, Eduardo (2017). Peak Strainer. doi:10.17617/1.47. 
  66. ↑ Laboratory, National High Magnetic Field. "ICR Software - MagLab" (in en). https://nationalmaglab.org/user-facilities/icr/software/#:~:text=PetroOrg%20was%20developed%20specifically%20for,contaminants%20and%20natural%20organic%20matter.. 
  67. ↑ 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. 
  68. ↑ 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. 
  69. ↑ 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. 
  70. ↑ 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. 
  71. ↑ 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. 
  72. ↑ Sheng, Quanhu; Dai, Jie; Wu, Yibo; Tang, Haixu; Zeng, Rong (2012). "BuildSummary: using a group-based approach to improve the sensitivity of peptide/protein identification in shotgun proteomics". J Proteome Res 11 (3): 1494–1502. doi:10.1021/pr200194p. PMID 22217156. 
  73. ↑ Gallant, James; Heunis, Tiaan; Sampson, Samantha; Bitter, Wilbert (2020). "ProVision: A web based platform for rapid analysis of proteomics data processed by MaxQuant". Bioinformatics 36 (19): 4965–4967. doi:10.1093/bioinformatics/btaa620. PMID 32638008. 
  74. ↑ 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. 
  75. ↑ Goloborodko, Anton; Levitsky, Lev; Ivanov, Mark; Gorshkov, Mikhail (2013). "Pyteomics — a Python framework for exploratory data analysis and rapid software prototyping in proteomics". J Am Soc Mass Spectrom 24 (2): 301–4. doi:10.1007/s13361-012-0516-6. PMID 23292976. Bibcode: 2013JASMS..24..301G. 
  76. ↑ 76.0 76.1 Titeca, Kevin; Meysman, Pieter; Gevaert, Kris; Tavernier, Jan; Laukens, Kris; Martens, Lennart; Eyckerman, Sven (2016-01-04). "SFINX: Straightforward Filtering Index for Affinity Purification-Mass Spectrometry Data Analysis". Journal of Proteome Research 15 (1): 332–338. doi:10.1021/acs.jproteome.5b00666. ISSN 1535-3907. PMID 26616242. https://pubmed.ncbi.nlm.nih.gov/26616242. 
  77. ↑ Titeca, Kevin; Van Quickelberghe, Emmy; Samyn, Noortje; De Sutter, Delphine; Verhee, Annick; Gevaert, Kris; Tavernier, Jan; Eyckerman, Sven (May 2017). "Analyzing trapped protein complexes by Virotrap and SFINX". Nature Protocols 12 (5): 881–898. doi:10.1038/nprot.2017.014. ISSN 1750-2799. PMID 28358392. https://pubmed.ncbi.nlm.nih.gov/28358392. 
  78. ↑ Titeca, Kevin; Meysman, Pieter; Laukens, Kris; Martens, Lennart; Tavernier, Jan; Eyckerman, Sven (2017-06-15). "sfinx: an R package for the elimination of false positives from affinity purification-mass spectrometry datasets". Bioinformatics 33 (12): 1902–1904. doi:10.1093/bioinformatics/btx076. ISSN 1367-4811. PMID 28186257. https://pubmed.ncbi.nlm.nih.gov/28186257. 
  79. ↑ 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 129: 51–5. doi:10.1016/j.jprot.2015.01.013. PMID 25638023. 
  80. ↑ 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. PMID 16464158. 
  81. ↑ Pedrioli, Patrick G. A. (2010). "Trans-Proteomic Pipeline: A Pipeline for Proteomic Analysis". Proteome Bioinformatics. Methods in Molecular Biology. 604. pp. 213–238. doi:10.1007/978-1-60761-444-9_15. ISBN 978-1-60761-443-2. 
  82. ↑ Deutsch, Eric W.; Mendoza, Luis; Shteynberg, David; Farrah, Terry; Lam, Henry; Tasman, Natalie; Sun, Zhi; Nilsson, Erik et al. (2010). "A guided tour of the Trans-Proteomic Pipeline". Proteomics 10 (6): 1150–1159. doi:10.1002/pmic.200900375. ISSN 1615-9853. PMID 20101611. 
  83. ↑ Cody, Robert B.; Fouquet, Thierry (2019-07-01). "Elemental Composition Determinations Using the Abundant Isotope" (in en). Journal of the American Society for Mass Spectrometry 30 (7): 1321–1324. doi:10.1007/s13361-019-02203-9. ISSN 1044-0305. https://pubs.acs.org/doi/10.1007/s13361-019-02203-9. 
  84. ↑ 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



Retrieved from "https://handwiki.org/wiki/index.php?title=Biology:List_of_mass_spectrometry_software&oldid=3526063"