{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T05:34:15Z","timestamp":1770269655839,"version":"3.49.0"},"reference-count":12,"publisher":"Springer Science and Business Media LLC","issue":"S7","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/1471-2105-16-s7-s1","type":"journal-article","created":{"date-parts":[[2015,6,18]],"date-time":"2015-06-18T09:53:16Z","timestamp":1434621196000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["A coherent mathematical characterization of isotope trace extraction, isotopic envelope extraction, and LC-MS correspondence"],"prefix":"10.1186","volume":"16","author":[{"given":"Rob","family":"Smith","sequence":"first","affiliation":[]},{"given":"John T","family":"Prince","sequence":"additional","affiliation":[]},{"given":"Dan","family":"Ventura","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2015,4,23]]},"reference":[{"issue":"12","key":"6926_CR1","doi-asserted-by":"publisher","first-page":"2373","DOI":"10.1074\/mcp.M800203-MCP200","volume":"7","author":"H Choi","year":"2008","unstructured":"Choi H, Fermin D, Nesvizhskii AI: Significance analysis of spectral count data in label-free shotgun proteomics. Mol Cell Proteomics. 2008, 7 (12): 2373-2385. 10.1074\/mcp.M800203-MCP200.","journal-title":"Mol Cell Proteomics"},{"issue":"3","key":"6926_CR2","doi-asserted-by":"publisher","first-page":"340","DOI":"10.1002\/pmic.200600422","volume":"7","author":"S Wiese","year":"2007","unstructured":"Wiese S, Reidegeld KA, Meyer HE, Warscheid B: Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research. Proteomics. 2007, 7 (3): 340-350. 10.1002\/pmic.200600422.","journal-title":"Proteomics"},{"key":"6926_CR3","doi-asserted-by":"publisher","first-page":"1785","DOI":"10.1021\/pr101060v","volume":"10","author":"A Michalski","year":"2011","unstructured":"Michalski A, Cox J, Mann M: More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Marjority is Inaccessible to Data-Dependent LC-MS\/MS. Journal of Proteome Research. 2011, 10: 1785-1793. 10.1021\/pr101060v.","journal-title":"Journal of Proteome Research"},{"issue":"3","key":"6926_CR4","doi-asserted-by":"publisher","first-page":"1087","DOI":"10.1007\/s00726-012-1289-8","volume":"43","author":"S Cappadona","year":"2012","unstructured":"Cappadona S, Baker PR, Cutillas PR, Heck AJ, van Breukelen B: Current challenges in software solutions for mass spectrometry-based quantitative proteomics. Amino Acids. 2012, 43 (3): 1087-1108. 10.1007\/s00726-012-1289-8.","journal-title":"Amino Acids"},{"issue":"1","key":"6926_CR5","doi-asserted-by":"publisher","first-page":"504","DOI":"10.1186\/1471-2105-9-504","volume":"9","author":"R Tautenhahn","year":"2008","unstructured":"Tautenhahn R, Bottcher C, Neumann S: Highly sensitive feature detection for high resolution LC\/MS. BMC Bioinformatics. 2008, 9 (1): 504-10.1186\/1471-2105-9-504.","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"6926_CR6","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1186\/1471-2105-11-395","volume":"11","author":"T Pluskal","year":"2010","unstructured":"Pluskal T, Castillo S, Villar-Briones A, Oresic M: MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics. 2010, 11 (1): 395-10.1186\/1471-2105-11-395.","journal-title":"BMC Bioinformatics"},{"key":"6926_CR7","first-page":"359","volume-title":"Bioinformatics","author":"CJ Conley","year":"2014","unstructured":"Conley CJ, Smith R, Torgrip RJ, Taylor RM, Tautenhahn R, Prince JT: Massifquant: open-source Kalman filter based XC-MS isotope trace feature detection. Bioinformatics. 2014, 359-"},{"issue":"12","key":"6926_CR8","doi-asserted-by":"publisher","first-page":"1367","DOI":"10.1038\/nbt.1511","volume":"26","author":"J Cox","year":"2008","unstructured":"Cox J, Mann M: MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification. Nature Biotechnology. 2008, 26 (12): 1367-1372. 10.1038\/nbt.1511.","journal-title":"Nature Biotechnology"},{"key":"6926_CR9","volume-title":"Journal of Proteome Research","author":"H Weisser","year":"2013","unstructured":"Weisser H, Nahnsen S, Grossmann J, Nilse L, Quandt A, Brauer H, Sturm M, Kenar E, Kohlbacher O, Aebersold R, et al: An automated pipeline for high-throughput label-free quantitative proteomics. Journal of Proteome Research. 2013"},{"issue":"15","key":"6926_CR10","doi-asserted-by":"publisher","first-page":"1902","DOI":"10.1093\/bioinformatics\/btl276","volume":"22","author":"M Bellew","year":"2006","unstructured":"Bellew M, Coram M, Fitzgibbon M, Igra M, Randolph T, Wang P, May D, Eng J, Fang R, Lin C, et al: A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics. 2006, 22 (15): 1902-1909. 10.1093\/bioinformatics\/btl276.","journal-title":"Bioinformatics"},{"key":"6926_CR11","volume-title":"Briefings in Bioinformatics","author":"R Smith","year":"2013","unstructured":"Smith R, Ventura D, Prince JT: LC-MS Alignment in Theory and Practice: A Comprehensive Algorithmic Review. Briefings in Bioinformatics. 2013"},{"issue":"2","key":"6926_CR12","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1093\/bioinformatics\/btl326","volume":"23","author":"J Listgarten","year":"2007","unstructured":"Listgarten J, Neal RM, Roweis ST, Wong P, Emili A: Difference detection in LC-MS data for protein biomarker discovery. Bioinformatics. 2007, 23 (2): 198-204. 10.1093\/bioinformatics\/btl553.","journal-title":"Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-16-S7-S1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T06:21:59Z","timestamp":1548224519000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-16-S7-S1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,4,23]]},"references-count":12,"journal-issue":{"issue":"S7","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["6926"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-16-s7-s1","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,4,23]]},"assertion":[{"value":"23 April 2015","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S1"}}