List of mass spectrometry software
Mass spectrometry software is software used for data acquisition, analysis, or representation in mass spectrometry.
Proteomics software
For more details on this topic, see protein mass spectrometry.
In protein mass spectrometry, tandem mass spectrometry (also known as MS/MS or MS2) experiments are used for protein/peptide identification. Peptide identification algorithms fall into two broad classes: database search and de novo search. The former search takes place against a database containing all amino acid sequences assumed to be present in the analyzed sample, whereas the latter infers peptide sequences without knowledge of genomic data.
Database search algorithms
Name | Type | Description | Link |
---|---|---|---|
Byonic | Database search program released in 2011 by Protein Metrics Inc. with original developments at PARC[1] that searches MS/MS data from all types of instruments and internally employs the program Combyne,[2] which combines peptide identifications to produce protein scores and identification probabilities. | server | |
Greylag | open source | Database search program developed at the Stowers Institute for Medical Research designed to perform large searches on computational clusters having hundreds of nodes. | server |
InsPecT | A MS-alignment search engine available at the Center for Computational Mass Spectrometry at the University of California, San Diego[3] | download | |
Mascot | proprietary | Performs mass spectrometry data analysis through a statistical evaluation of matches between observed and projected peptide fragments.[4] | |
MassMatrix | MassMatrix is a database search software package for tandem mass spectrometric data. It uses a mass accuracy sensitive probabilistic scoring model to rank peptide and protein matches. | download | |
MassWiz | open source | Search algorithm developed at Institute of Genomics and Integrative Biology available as a windows commandline tool. | download, server |
MyriMatch | open source | Database search program developed at the Vanderbilt University Medical Center designed to run in a single-computer environment or across an entire cluster of processing nodes.[5] | download |
OMSSA | open source | database search program developed at the National Center for Biotechnology Information.[6][7] | |
PEAKS DB | proprietary | Database search engine, run in parallel with de novo sequencing to automatically validate search results, allowing for a higher number of found sequences for a given false discovery rate. In addition to providing an independent database search, results can be incorporated as part of the software’s multi-engine (Sequest, Mascot, X!Tandem, OMSSA, PEAKS DB) consensus reporting tool, inChorus.[8] The tool also provides a list of sequences identified exclusively by de novo sequencing. | |
Phenyx | Developed by Geneva Bioinformatics (GeneBio) in collaboration with the Swiss Institute of Bioinformatics (SIB). Phenyx incorporates OLAV, a family of statistical scoring models, to generate and optimize scoring schemes that can be tailored for all kinds of instruments, instrumental set-ups and general sample treatments.[9] | ||
ProteinPilot Software | Uses Paragon database search algorithm that combines the generation of short sequence tags (‘taglets’) for computation of sequence temperature values and estimates of feature probabilities to enable the peptide identification considering hundreds of modifications, non-tryptic cleavages and amino acid substitutions. Uses the Pro Group Algorithm for protein inference analysis to report the minimal set of proteins justified based on the peptide evidence. Supports quantification for label-based workflows (iTRAQ reagents, mTRAQ reagents and SILAC labeling). A translation layer translates user interface controls in the language of the proteomics experimental scientist to underlying complex informatics parameters.[10] pate/content/6/9/1638.short | ||
Protein Prospector | open source | Protein Prospector is a package of about twenty proteomic analysis tools developed at the University of California San Francisco. The tandem mass spectrometry searching software is Batch-Tag / Batch-Tag Web, with the results processed and displayed using Search Compare. It uses scoring systems tailored to instrument and fragmentation mode to optimize analysis of different types of fragmentation data. | server |
RAId | Developed at the National Center for Biotechnology Information, Robust Accurate Identification (RAId)[11] is a suite of proteomics tools for analyzing tandem mass spectrometry data with accurate statistics.[12] | ||
SEQUEST | proprietary | Identifies collections of tandem mass spectra to peptide sequences that have been generated from databases of protein sequences.[13] | |
SIMS | SIMS (Sequential Interval Motif Search) is a software tool design to perform unrestrictive PTM search over tandem mass spectra; users do not have to characterize the potential PTMs. Instead, users only need to specify the range of modification mass for each individual amino acid. | server | |
SimTandem | freeware | A database search engine for identification of peptide sequences from LC/MS/MS data; the engine can be used as an external tool in OpenMS/TOPP.[14] | download |
SQID | open source | SeQuence IDentification (SQID) is an intensity-incorporated protein identification algorithm for tandem mass spectrometry. | download |
X!Tandem | open source | Matches tandem mass spectra with peptide sequences. | server |
pFind | pFind Studio is a computational solution for mass spectrometry-based proteomics, it germinated in 2002 in Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China. | download |
De novo sequencing algorithms
De novo peptide sequencing algorithms are based, in general, on the approach proposed in Bartels et al. (1990).[15]
Name | Type | Description | Link |
---|---|---|---|
CycloBranch | open source | A stand-alone, cross-platform and open-source de novo engine for identification of nonribosomal peptides (linear, cyclic, branched and branch-cyclic) from accurate product ion spectra.[16] | download |
DeNovoX | De novo sequencing on CID spectra acquired with ion trap mass spectrometers delivering complete and/or partial peptide sequences (sequence tags).[17] | ||
DeNoS | Sequencing of peptides using all information from CAD and ECD spectra; part of the software tool Proteinmatching Analysis Software (PAS) which in turn is part of the software package Medicwave Bioinformatics Suite (MBS).[18] | server | |
Lutefisk | open source | Software for the de novo interpretation of peptide CID spectra. | server |
Novor | proprietary, free for academic research | Real-time de novo peptide sequencing engine that is fast, accurate and easy to be integrated into research pipelines. Novor can de novo sequence more than 300 MS/MS spectra per second on a Macbook Pro laptop computer.[19] | download server |
PEAKS | proprietary | De novo sequencing for each peptide, confidence scores on individual amino acid assignments with manually assisted modeand automated de novo sequencing on an entire LC run processed data faster than 1 spectrum per second.[20][21] | |
Supernovo | proprietary | A unique, hands-free solution for end-to-end de novo sequencing of monoclonal antibodies | server |
Homology searching algorithms
Name | Type | Description | Link |
---|---|---|---|
MS-Homology | open source | MS-Homology is a database search program within the Protein Prospector package that permits searching with strings that combine masses and amino acid stretches, where one can specify the number of amino acid mismatches allowed. | server |
SPIDER | proprietary | The SPIDER algorithm matches sequence tags with errors to database sequences for the purpose of protein and peptide identification and can be used in conjunction with PEAKS mass spectrometry data analysis software. | server |
MS/MS peptide quantification
For more details on this topic, see Quantitative proteomics.
Name | Type | Description | Link |
---|---|---|---|
MarkerView Software | proprietary | Commercial software for statistical analysis for quantitative mass spec data sets from metabolomics and proteomic profiling applications. | download |
MassChroQ | open source | Peptide quantification analysis of label free or various isotopic labeling methods (SILAC, ICAT, N-15, C-13 …), works with high and low resolution spectrometer systems, supports complex data treatments as peptide or protein fractionation prior to LC-MS analysis (SCX, SDS-PAGE, etc.). | server, download |
MaxQuant | freeware | Quantitative proteomics 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. | download |
MultiQuant Software | proprietary | Can process quantitative data sets from TripleTOF or QTRAP systems, including MRM and SWATH Acquisition. | download |
OpenMS | open source | Software C++ library for LC-MS/MS data management and analysis that offers an infrastructure for the development of mass spectrometry related software. 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.[22] | server, download |
ProtMax | freeware | ProtMAX[23] is a software tool for analyzing shotgun proteomics mass spectrometry data sets, developed by Volker Egelhofer at the University of Vienna. | download |
Spectronaut | proprietary | Commercial software for quantitative proteomics developed by Biognosys AG (Schlieren, Switzerland) based on the mProphet algorithm[24] that allows the targeted analysis of data independent acquisition (DIA) data sets for label-free peptide quantitation, also called SWATH acquisition.[25] | website |
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. | website |
Other software
Name | Type | Description | Link |
---|---|---|---|
Advanced Chemistry Development | proprietary | Commercial solutions for the interpretation of MS and xC/MS data with spectrum/structure matching, identification of known and unknown metabolites, as well as for the identification of compounds through spectral comparison. | |
Analyst | proprietary | Software by AB Sciex, a division of The Danaher Corporation. | |
AnalyzerPro | proprietary | A vendor independent software application for processing mass spectrometry data that can analyze both GC-MS and LC-MS data using both qualitative and quantitative data processing and is used for metabolomics data processing using MatrixAnalyzer for the comparison of multiple data sets. | |
Chromeleon | proprietary | Software by Thermo Fisher Scientific used with mass spectrometry instruments, as well as chromatography instruments. | |
Easotope | open source | Software for archiving, organizing, and analyzing mass spectrometer data. Currently oriented toward clumped CO2 analysis but also useful for bulk CO2 work and expandable to other isotopic systems. | website |
ESIprot | Enables the charge state determination and molecular weight calculation for low resolution electrospray ionization (ESI) mass spectrometry (MS) data of proteins.[26] | server, online | |
LabSolutions LCMS | proprietary | Software by Shimadzu Corporation used with mass spectrometry and HPLC instruments. | |
Mass++ | open source | Analysis software for mass spectrometry that can import and export files with open-formats (mzXML, mzML) and load some instrument vendor formats; users can develop and add original functions as Mass++ plug-ins. | website |
MassBank.jp | website | website hosted by the Institute for Advanced Biosciences, in Keio University, Tsuruoka City, Yamagata, Japan with mass spectrometric data for organic compounds. | website |
MassBank.eu | website | European MassBank server with mirrored mass spectral data from MassBank.jp and special mass spectral data related to environmental organic compounds and pollutants. The website is provided by the NORMAN Network and hosted by the Helmholtz Centre for Environmental Research (Leipzig, Germany) | website |
MassBank | open source | MassBank and RMassBank development website provided by the MassBank consortium | github |
MassCenter | proprietary | Software by JEOL used with mass spectrometry instruments. | |
Mass Frontier | proprietary | Software by HighChem used for interpretation and management of mass spectra of small molecules. | website |
MassLynx | proprietary | Software by Waters Corporation. | |
Mass-Up | open-source | Utility for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data that loads data from mzML, mzXML and CSV files and allows users to apply baseline correction, normalization, smoothing, peak detection and peak matching.[27] | download |
massXpert | Graphical user interface-based (GUI) software for simulating and analyzing mass spectrometric data obtained on known bio-polymer sequences.[28] | manual | |
mMass | open source | Multi-platform package of tools for mass spectrometric data analysis and interpretation written in Python. | website |
MolAna | MolAna was developed by Phenomenome Discoveries Inc, (PDI) for use in IONICS Mass Spectrometry Group's 3Q Molecular Analyzer, Triple quadrupole mass spectrometer | ||
ms2mz | freeware | Utility for converting between mass spectrometer file formats, e.g. to convert proprietary binary files to MGF peak list files to prepare files for upload to Proteome Cluster. | download |
MSGraph | open source | sourceforge | |
MSight | freeware | Software for mass spectrometry imaging developed by the Swiss Institute of Bioinformatics.[29] | |
MSiReader | freeware | Vendor-neutral interface built on the Matlab platform designed to view and perform data analysis of mass spectrometry imaging (MSI) data.[30] Matlab is not required to use MSiReader. | download |
mspire | open-source | Mass spectrometry informatics developers toolbox written in ruby that includes an mzML reader/writer, in-silico digestion and isotopic pattern calculation etc.; submodules such as mspire-lipidomics, mspire-sequest, and mspire-simulator extend the functionality.[31] | |
Multimaging | Software for mass spectrometry imaging designed to normalize, validate and interpret MS images. | website | |
multiMS-toolbox | open source | ms-alone and multiMS-toolbox is a tool chain for mass spectrometry data peak extraction and statistical analysis. | website |
mzCloud | website | Web-based mass spectral database that comprises a collection of high and low resolution tandem mass spectrometry data acquired under a number of experimental conditions. | website |
MZmine 2 | open source | An open-source software for mass-spectrometry data processing, with the main focus on LC-MS data. | website |
OmicsHub Proteomics | OmicsHub Proteomics combines a LIMS for mass spec information management with data analysis functionalities on one platform. | ||
OpenChrom | open source | Chromatography and mass spectrometry software that can be extended using plug-ins and is available for several operating systems (Microsoft Windows, Linux, Unix, Mac OS X) and processor architectures (x86, x86_64, ppc). with converters for the native access of various data files, e.g. converters for mzXML, netCDF, Agilent, Finnigan and Varian file formats. | website, sourceforge |
PatternLab | freeware | Software for post-analysis of SEQUEST, ProLuCID or Comet database search results filtered by DTASelect or Census.[32] | website |
SIM-XL | freeware | Spectrum Identification Machine for Cross-linked Peptides (SIM-XL) is a fast and sensitive XL search engine which is part of the PatternLab for proteomics environment, to analyze tandem mass spectrometry data derived from cross-linked peptides.[33] | website |
Peacock | open source | Mac OS X application developed by Johan Kool that can be used to interpret gas-chromatography/mass-spectrometry (GC/MS) data files. | Google Code |
PeakInvestigator | proprietary | 3-4X effective resolution improvement in post-processing of raw profile data output from mass specs. Veritomyx advanced signal processing software for peak detection, deconvolution, and centroiding of raw profile mass spec data reveals multiple peaks hidden in overlapped data. Notable features: order-of-magnitude improvements in mass and abundance precision for deconvolved peaks; local dynamic baselining; advanced thresholding algorithm increases sensitivity across wide dynamic range; statistically-driven and completely automated (no user-to-user variation). More complete and precise resulting mass lists facilitate faster and cost-efficient subsequent determination of correct biomolecular identifications. | website |
PIQMIe | web | Proteomics Identifications/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.[34] | websitedownload |
POTAMOS | open source | Web application that provides calculated mass spectrometry data independently of instrumentation focused on a well known protein family of histones whose PTMs are believed to play a crucial role in gene regulation; calculates the kind, the number and the combinations of the possible PTMs corresponding to a given peptide sequence and a given mass. | download |
PROTRAWLER | LC/MS data reduction application that reads raw mass spectrometry vendor data (from a variety of well-known instrument companies) and creates lists of {mass, retention time, integrated signal intensity} triplets summarizing the LC/MS chromatogram. | ||
ProteoIQ | proprietary | Software for the post-analysis of Mascot, SEQUEST, or X!Tandem database search results.[35][36][37] | |
Proteomatic | Freeware | Data processing pipeline created for the purpose of evaluating mass spectrometric proteomics experiments.[38] | |
ProteomicsTools | open source | Software for the post-analysis of MASCOT, SEQUEST, Comet, XTandem, PFind, PeptidePhophet, MyriMatch, MSGF, OMSSA, MSAmanda or Percolator database search result.[39] | GitHub |
ProteoWizard | open source | Link library and tools athat re a set of modular and extensible open-source, cross-platform tools and software libraries that facilitate proteomics data analysis. | sourceforge |
pymzML | open source | Python module to interface mzML data in Python based on cElementTree with additional tools for MS-informatics.[40] | download |
Quantinetix | Software for mass spectrometry imaging designed to quantify and normalize MS images in various study types that is compatible with a variety of MSI instruments, including Bruker, Sciex, Thermo and with iMZML. | server; website | |
Rational Numbers Excel Add-In | proprietary | De novo identification tool that works with Microsoft Excel 2010, Excel 2013, and Excel 2016. | |
Rational Numbers Search | proprietary | Identification of small molecules by comparison of accurate-mass fragmentation data to a database of 250000 molecules represented as mathematical partitions | |
REGATTA | LC/MS list comparison application that works with ProTrawler (but accepts input in Excel/CSV form) to provide an environment for LC/MS results list filtering and normalization {mass, retention time, integrated intensity} lists. | ||
RemoteAnalyzer | proprietary | Software by SpectralWorks Limited for vendor independent 'Open Access' client/server based solutions to provide a walk-up and use LC-MS and GC-MS data system; instrument control and data processing support for multiple vendors' hardware is provided. | |
Scaffold | proprietary | Suite of proteomics tools for analyzing spectra, peptides and proteins across multiple samples. | server |
SCiLS Lab | Statistical analysis of MALDI imaging mass spectrometry data that integrates with Bruker MALDI imaging. | server | |
SimGlycan | proprietary | Predicts the structure of glycans and glycopeptides using mass spectrometry MS/MS data. | server |
SIMION | proprietary | Ion optics simulation program | server |
Spectrolyzer | Spectrolyzer is a Microsoft Windows-based software package that provides bioinformatics data analysis tools for different mass spectrometers that focuses on finding protein biomarkers and detecting protein deviations. | server | |
Spectromania | proprietary | Software for analysis and visualization of mass spectrometric data.[41] | |
StavroX | proprietary | Software to identify cross-linked peptides from mass spectrometric data written in Java that can be used for a wide variety of cross linkers and proteases used in the cross linking MS experiment; it compares theoretical peptide-peptide cross link combinations for the analyzed proteins to MS/MS data.[42] | |
TOF-DS | proprietary | Software by Markes International used with BenchTOF time-of-flight mass spectrometers | |
TurboMass | proprietary | GC/MS software by PerkinElmer. | |
Universal Mass Calculator | Universal Mass Calculator (UMC) for Windows written in C++ is a proprietary toolbox for calculating relevant information from sum formulae, e.g. isotope distribution, mass differences, mass deviations and mass/isotope information of the elements, degree of deuteration. | server | |
VIPER | Analysis of accurate mass and chromatography retention time analysis of LC-MS features (accurate mass and time tag approach).[43] | ||
Xcalibur | proprietary | Software by Thermo Fisher Scientific used with mass spectrometry instruments. | |
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. | website |
See also
- Mass spectrometry data format: for a list of mass spectrometry data viewers and format converters.
- List of protein structure prediction software
References
- ↑ 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.
- ↑ 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.
- ↑ "Inspect and MS-Alignment".
- ↑ 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.
- ↑ Tabb, David L.; Fernando, Christopher G.; Chambers, Matthew C. (2007). "MyriMatch: Highly Accurate Tandem Mass Spectral Peptide Identification by Multivariate Hypergeometric Analysis". Journal of Proteome Research. 6 (2): 654–61. doi:10.1021/pr0604054. PMC 2525619. PMID 17269722.
- ↑ "OMSSA ms/ms search engine". Pubchem.ncbi.nlm.nih.gov. Retrieved 2011-09-27.
- ↑ Geer, Lewis Y.; Markey, Sanford P.; Kowalak, Jeffrey A.; Wagner, Lukas; Xu, Ming; Maynard, Dawn M.; Yang, Xiaoyu; Shi, Wenyao; Bryant, Stephen H. (2004). "Open Mass Spectrometry Search Algorithm". Journal of Proteome Research. 3 (5): 958–64. doi:10.1021/pr0499491. PMID 15473683.
- ↑ Liang, C; Smith, JC; Hendrie, Christopher (2003). "A Comparative Study of Peptide Sequencing Software Tools for MS/MS".
- ↑ 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.
- ↑ Molecular & Cellular Proteomics
- ↑ "RAId MS/MS search engine". QMBP NCBI NLM NIH. Retrieved 2008-01-01.
- ↑ Alves, Gelio; Ogurtsov, Aleksey Y.; Yu, Yi-Kuo (2007). "RAId_DbS: peptide identification using database searches with realistic statistics". Biol Direct. 2: 25. doi:10.1186/1745-6150-2-25. PMC 2211744. PMID 17961253.
- ↑ Jimmy K. Eng, Ashley L. McCormack, and John R. Yates, III (1994). "An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database". J Am Soc Mass Spectrom. 5 (11): 976–989. doi:10.1016/1044-0305(94)80016-2. PMID 24226387.
- ↑ 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).
- ↑ 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.
- ↑ 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.
- ↑ thermo finnigan introduces denovox – Search results from HighBeam Business
- ↑ 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.
- ↑ Ma, Bin (30 June 2015). "Novor: Real-Time Peptide de Novo Sequencing Software". Journal of the American Society for Mass Spectrometry. 26: 1885–1894. doi:10.1007/s13361-015-1204-0. Retrieved 3 July 2015.
- ↑ Ma, Bin; Zhang, Kaizhong; Hendrie, Christopher; Liang, Chengzhi; Li, Ming; Doherty-Kirby, Amanda; Lajoie, Gilles (2003). "PEAKS: powerful software for peptidede novo sequencing by tandem mass spectrometry". Rapid Communications in Mass Spectrometry. 17 (20): 2337–42. doi:10.1002/rcm.1196. PMID 14558135.
- ↑ Tannu, Nilesh S; Hemby, Scott E (2007). "De novo protein sequence analysis of Macaca mulatta". BMC Genomics. 8: 270. doi:10.1186/1471-2164-8-270. PMC 1965481. PMID 17686166.
- ↑ Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O (2016). "OpenMS: a flexible open-source software platform for mass spectrometry data analysis". Nat. Methods. 13 (9): 741–8. doi:10.1038/nmeth.3959. PMID 27575624.
- ↑ Egelhofer V, Hoehenwarter W, Lyon D, Weckwerth W, Wienkoop S (2013). "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. doi:10.1038/nprot.2013.013. PMID 23449253.
- ↑ Reiter, L; et al. (2011). "mProphet: automated data processing and statistical validation for large-scale SRM experiments". Nat Methods. 8 (5): 430–435. doi:10.1038/nmeth.1584.
- ↑ 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.
- ↑ 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.
- ↑ "Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery". BMC Bioinformatics. 16. doi:10.1186/s12859-015-0752-4.
- ↑ Rusconi, F. (2009). "massXpert 2: a cross-platform software environment for polymer chemistry modelling and simulation/analysis of mass spectrometric data". Bioinformatics. 25 (20): 2741–2. doi:10.1093/bioinformatics/btp504. PMID 19740912.
- ↑ Palagi, Patricia M.; Walther, Daniel; Quadroni, Manfredo; Catherinet, SéBastien; Burgess, Jennifer; Zimmermann-Ivol, Catherine G.; Sanchez, Jean-Charles; Binz, Pierre-Alain; Hochstrasser, Denis F.; Appel, Ron D. (2005). "MSight: An image analysis software for liquid chromatography-mass spectrometry". Proteomics. 5 (9): 2381–4. doi:10.1002/pmic.200401244. PMID 15880814.
- ↑ Robichaud, Guillaume; Garrard, Kenneth P.; Barry, Jeremy A.; Muddiman, David C. (March 2013). "MSiReader: An Open-Source Interface to View and Analyze High Resolving Power MS Imaging Files on Matlab Platform". Journal of the American Society for Mass Spectrometry. Springer. 24 (5): 718–721. doi:10.1007/s13361-013-0607-z. PMID 23536269.
- ↑ Prince, J. T.; Marcotte, E. M. (2008). "Mspire: Mass spectrometry proteomics in Ruby". Bioinformatics. 24 (23): 2796–2797. doi:10.1093/bioinformatics/btn513. PMC 2639276. PMID 18930952.
- ↑ Carvalho, Paulo C; Fischer, Juliana SG; Chen, Emily I; Yates, John R; Barbosa, Valmir C (2008). "PatternLab for proteomics: a tool for differential shotgun proteomics". BMC Bioinformatics. 9: 316. doi:10.1186/1471-2105-9-316. PMC 2488363. PMID 18644148.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ Götze, Michael; Pettelkau J; Schaks S; Bosse K; Ihling CH; Krauth F; Fritzsche R; Kühn U; Sinz A. (January 2012). "StavroX--a software for analyzing crosslinked products in protein interaction studies". J Am Soc Mass Spectrom. 23 (1): 76–87. doi:10.1007/s13361-011-0261-2. PMID 22038510.
- ↑ 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.
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