{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T17:24:06Z","timestamp":1778693046883,"version":"3.51.4"},"reference-count":28,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,7,1]],"date-time":"2019-07-01T00:00:00Z","timestamp":1561939200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,7,1]],"date-time":"2019-07-01T00:00:00Z","timestamp":1561939200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100014989","name":"Chan Zuckerberg Initiative","doi-asserted-by":"crossref","award":["2018-182799"],"award-info":[{"award-number":["2018-182799"]}],"id":[{"id":"10.13039\/100014989","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2019,12]]},"DOI":"10.1186\/s12859-019-2962-7","type":"journal-article","created":{"date-parts":[[2019,7,1]],"date-time":"2019-07-01T10:03:21Z","timestamp":1561975401000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["MassComp, a lossless compressor for mass spectrometry data"],"prefix":"10.1186","volume":"20","author":[{"given":"Ruochen","family":"Yang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xi","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1864-7868","authenticated-orcid":false,"given":"Idoia","family":"Ochoa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,7,1]]},"reference":[{"issue":"1","key":"2962_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/(SICI)1098-2787(1998)17:1<1::AID-MAS1>3.0.CO;2-K","volume":"17","author":"AG Marshall","year":"1998","unstructured":"Marshall AG, et al. Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom Rev. 1998; 17(1):1\u201335.","journal-title":"Mass Spectrom Rev"},{"issue":"6928","key":"2962_CR2","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1038\/nature01511","volume":"422","author":"R Aebersold","year":"2003","unstructured":"Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature. 2003; 422(6928):198\u2013207.","journal-title":"Nature"},{"issue":"1","key":"2962_CR3","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1002\/mas.20108","volume":"26","author":"K Dettmer","year":"2007","unstructured":"Dettmer K, Aronov PA, Hammock BD. Mass spectrometry-based metabolomics. Mass Spectrom Rev. 2007; 26(1):51\u201378.","journal-title":"Mass Spectrom Rev"},{"issue":"7","key":"2962_CR4","doi-asserted-by":"publisher","first-page":"1751","DOI":"10.1074\/mcp.M800588-MCP200","volume":"8","author":"FS Oppermann","year":"2009","unstructured":"Oppermann FS, Gnad F, et al. Large-scale proteomics analysis of the human kinome. Mol Cel Proteomics. 2009; 8(7):1751\u201364.","journal-title":"Mol Cel Proteomics"},{"issue":"7","key":"2962_CR5","doi-asserted-by":"publisher","first-page":"1742","DOI":"10.1039\/C5MB00158G","volume":"11","author":"M Bakar","year":"2015","unstructured":"Bakar M, et al. Metabolomics\u2013the complementary field in systems biology: a review on obesity and type 2 diabetes. Mol BioSyst. 2015; 11(7):1742\u201374.","journal-title":"Mol BioSyst"},{"issue":"4","key":"2962_CR6","doi-asserted-by":"publisher","first-page":"29","DOI":"10.3390\/proteomes4040029","volume":"4","author":"TT Duarte","year":"2016","unstructured":"Duarte TT, Spencer CT. Personalized proteomics: the future of precision medicine. Proteomes. 2016; 4(4):29.","journal-title":"Proteomes"},{"key":"2962_CR7","doi-asserted-by":"publisher","first-page":"D1063","DOI":"10.1093\/database\/bas004","volume":"2012","author":"A Csordas","year":"2012","unstructured":"Csordas A, Ovelleiro D, et al. Pride: quality control in a proteomics data repository. Database. 2012; 2012:D1063\u2013D1069.","journal-title":"Database"},{"issue":"6","key":"2962_CR8","doi-asserted-by":"publisher","first-page":"1234","DOI":"10.1021\/pr049882h","volume":"3","author":"R Craig","year":"2004","unstructured":"Craig R, et al. Open source system for analyzing, validating, and storing protein identification data. J Proteome Res. 2004; 3(6):1234\u201342.","journal-title":"J Proteome Res"},{"issue":"suppl_1","key":"2962_CR9","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1093\/nar\/gkj040","volume":"34","author":"F Desiere","year":"2006","unstructured":"Desiere F, Deutsch EW, et al. The peptideatlas project. Nucleic Acids Res. 2006; 34(suppl_1):655\u20138.","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"2962_CR10","doi-asserted-by":"publisher","first-page":"1170","DOI":"10.1002\/pmic.201100515","volume":"12","author":"T Farrah","year":"2012","unstructured":"Farrah T, Deutsch EW, et al. Passel: the peptideatlas srmexperiment library. Proteomics. 2012; 12(8):1170\u20135.","journal-title":"Proteomics"},{"issue":"13","key":"2962_CR11","doi-asserted-by":"publisher","first-page":"3537","DOI":"10.1002\/pmic.200401303","volume":"5","author":"L Martens","year":"2005","unstructured":"Martens L, Hermjakob H, Jones P, et al. Pride: the proteomics identifications database. Proteomics. 2005; 5(13):3537\u201345.","journal-title":"Proteomics"},{"issue":"suppl_1","key":"2962_CR12","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1093\/nar\/gkj138","volume":"34","author":"P Jones","year":"2006","unstructured":"Jones P, C\u00f4t\u00e9 RG, et al. Pride: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res. 2006; 34(suppl_1):659\u201363.","journal-title":"Nucleic Acids Res"},{"key":"2962_CR13","unstructured":"massIVE. Mass Spectrometry Interactive Virtual Environment. \n                    https:\/\/massive.ucsd.edu\/ProteoSAFe\/static\/massive.jsp\n                    \n                  . Accessed: Aug 2017."},{"issue":"11","key":"2962_CR14","doi-asserted-by":"publisher","first-page":"1459","DOI":"10.1038\/nbt1031","volume":"22","author":"PG Pedrioli","year":"2004","unstructured":"Pedrioli PG, Eng JK, et al. A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol. 2004; 22(11):1459\u201366.","journal-title":"Nat Biotechnol"},{"issue":"S2","key":"2962_CR15","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1002\/pmic.200600537","volume":"6","author":"H Hermjakob","year":"2006","unstructured":"Hermjakob H. The hupo proteomics standards initiative\u2013overcoming the fragmentation of proteomics data. Proteomics. 2006; 6(S2):34\u20138.","journal-title":"Proteomics"},{"issue":"6","key":"2962_CR16","doi-asserted-by":"publisher","first-page":"1537","DOI":"10.1074\/mcp.O114.037879","volume":"13","author":"J Teleman","year":"2014","unstructured":"Teleman J, et al. Numerical compression schemes for proteomics mass spectrometry data. Mol Cel Proteomics. 2014; 13(6):1537\u201342.","journal-title":"Mol Cel Proteomics"},{"issue":"12","key":"2962_CR17","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.1038\/nmeth.4037","volume":"13","author":"I Numanagi\u0107","year":"2016","unstructured":"Numanagi\u0107 I, et al. Comparison of high-throughput sequencing data compression tools. Nat Methods. 2016; 13(12):1005.","journal-title":"Nat Methods"},{"key":"2962_CR18","doi-asserted-by":"publisher","first-page":"2748","DOI":"10.1093\/bioinformatics\/bty205","volume":"34.16","author":"\u0141 Roguski","year":"2018","unstructured":"Roguski \u0141, et al.FaStore: a space-saving solution for raw sequencing data. Bioinformatics. 2018; 34.16:2748\u201356.","journal-title":"Bioinformatics"},{"issue":"19","key":"2962_CR19","doi-asserted-by":"publisher","first-page":"3122","DOI":"10.1093\/bioinformatics\/btv330","volume":"31","author":"G Malysa","year":"2015","unstructured":"Malysa G, Hernaez M, et al. Qvz: lossy compression of quality values. Bioinformatics. 2015; 31(19):3122\u20139.","journal-title":"Bioinformatics"},{"issue":"1","key":"2962_CR20","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1109\/TC.2008.131","volume":"58","author":"M Burtscher","year":"2009","unstructured":"Burtscher M, Ratanaworabhan P. Fpc: A high-speed compressor for double-precision floating-point data. IEEE Trans Comput. 2009; 58(1):18\u201331.","journal-title":"IEEE Trans Comput"},{"issue":"1","key":"2962_CR21","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1002\/0471250953.bi1323s44","volume":"44","author":"NJ Edwards","year":"2013","unstructured":"Edwards NJ. Peparml: A meta-search peptide identification platform for tandem mass spectra. Curr Protoc Bioinforma. 2013; 44(1):13\u201323.","journal-title":"Curr Protoc Bioinforma"},{"issue":"1","key":"2962_CR22","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1038\/nrg2626","volume":"11","author":"ML Metzker","year":"2010","unstructured":"Metzker ML. Sequencing technologies\u2014the next generation. Nat Rev Genet. 2010; 11(1):31.","journal-title":"Nat Rev Genet"},{"issue":"16","key":"2962_CR23","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, et al. The sequence alignment\/map format and samtools. Bioinformatics. 2009; 25(16):2078\u20139.","journal-title":"Bioinformatics"},{"key":"2962_CR24","unstructured":"MSconverter. Data Conversion to GNPS Compatible Formats -.mzXML and.mzML. \n                    https:\/\/bix-lab.ucsd.edu\/display\/Public\/Data+Conversion+to+GNPS+Compatible+Formats+-+.mzXML+and+.mzML\n                    \n                  . Accessed: Aug 2017."},{"issue":"7","key":"2962_CR25","doi-asserted-by":"publisher","first-page":"620","DOI":"10.1109\/TCSVT.2003.815173","volume":"13","author":"D Marpe","year":"2003","unstructured":"Marpe D, Schwarz H, Wiegand T. Context-based adaptive binary arithmetic coding in the h. 264\/avc video compression standard. IEEE Trans Circ Syst Video Technol. 2003; 13(7):620\u201336.","journal-title":"IEEE Trans Circ Syst Video Technol"},{"issue":"2","key":"2962_CR26","first-page":"183","volume":"18","author":"I Ochoa","year":"2016","unstructured":"Ochoa I, Hernaez M, Goldfeder R, Weissman T, Ashley E. Effect of lossy compression of quality scores on variant calling. Brief Bioinforma. 2016; 18(2):183\u201394.","journal-title":"Brief Bioinforma"},{"key":"2962_CR27","unstructured":"FileConverter. FileConverter \u2013 Converts between different MS file formats. \n                    http:\/\/ftp.mi.fu-berlin.de\/pub\/OpenMS\/release1.9-documentation\/html\/TOPPFileConverter.html\n                    \n                  . Accessed: Aug 2017."},{"key":"2962_CR28","unstructured":"TinyXML-2. \n                    http:\/\/www.grinninglizard.com\/tinyxml2\/\n                    \n                  . Accessed: Aug 2017."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2962-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-019-2962-7\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2962-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,29]],"date-time":"2020-06-29T19:08:14Z","timestamp":1593457694000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-019-2962-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,7,1]]},"references-count":28,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2019,12]]}},"alternative-id":["2962"],"URL":"https:\/\/doi.org\/10.1186\/s12859-019-2962-7","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/542894","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,7,1]]},"assertion":[{"value":"6 February 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 June 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 July 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"368"}}