{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T16:57:38Z","timestamp":1791305858669,"version":"4.3.1"},"reference-count":29,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2014,2,1]],"date-time":"2014-02-01T00:00:00Z","timestamp":1391212800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2014,2,1]],"date-time":"2014-02-01T00:00:00Z","timestamp":1391212800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"}],"funder":[{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006590","name":"Ministerium f\u00c3\u00bcr Wissenschaft und Wirtschaft, Land Sachsen-Anhalt","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006590","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","award":["W21004490"],"award-info":[{"award-number":["W21004490"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Proteomics"],"published-print":{"date-parts":[[2014,2]]},"DOI":"10.1016\/j.jprot.2013.12.007","type":"journal-article","created":{"date-parts":[[2013,12,19]],"date-time":"2013-12-19T04:50:15Z","timestamp":1387428615000},"page":"79-89","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":46,"special_numbering":"C","title":["Protein identification and quantification by data-independent acquisition and multi-parallel collision-induced dissociation mass spectrometry (MSE) in the chloroplast stroma proteome"],"prefix":"10.1016","volume":"98","author":[{"given":"Stefan","family":"Helm","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dirk","family":"Dobritzsch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anja","family":"R\u00f6diger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Birgit","family":"Agne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sacha","family":"Baginsky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jprot.2013.12.007_bb0005","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1007\/978-1-61779-885-6_7","article-title":"Quantitative mass spectrometry-based proteomics: an overview","volume":"893","author":"Nikolov","year":"2012","journal-title":"Methods Mol Biol"},{"key":"10.1016\/j.jprot.2013.12.007_bb0010","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1002\/mas.20183","article-title":"Plant proteomics: concepts, applications, and novel strategies for data interpretation","volume":"28","author":"Baginsky","year":"2009","journal-title":"Mass Spectrom Rev"},{"key":"10.1016\/j.jprot.2013.12.007_bb0015","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1042\/BJ20110363","article-title":"The proteomic future: where mass spectrometry should be taking us","volume":"444","author":"Thelen","year":"2012","journal-title":"Biochem J"},{"key":"10.1016\/j.jprot.2013.12.007_bb0020","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1038\/nmeth.2015","article-title":"Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions","volume":"9","author":"Picotti","year":"2012","journal-title":"Nat Methods"},{"key":"10.1016\/j.jprot.2013.12.007_bb0025","doi-asserted-by":"crossref","first-page":"756","DOI":"10.1002\/pmic.201000426","article-title":"Quantitative plant proteomics","volume":"11","author":"Bindschedler","year":"2011","journal-title":"Proteomics"},{"issue":"7436","key":"10.1016\/j.jprot.2013.12.007_bb0030","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1038\/nature11835","article-title":"A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis","volume":"494","author":"Picotti","year":"2013","journal-title":"Nature"},{"issue":"1","key":"10.1016\/j.jprot.2013.12.007_bb0035","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/nbt1270","article-title":"Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation","volume":"25","author":"Lu","year":"2007","journal-title":"Nat Biotechnol"},{"issue":"5878","key":"10.1016\/j.jprot.2013.12.007_bb0040","doi-asserted-by":"crossref","first-page":"938","DOI":"10.1126\/science.1157956","article-title":"Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics","volume":"320","author":"Baerenfaller","year":"2008","journal-title":"Science"},{"key":"10.1016\/j.jprot.2013.12.007_bb0045","doi-asserted-by":"crossref","first-page":"4193","DOI":"10.1021\/ac0498563","article-title":"A model for random sampling and estimation of relative protein abundance in shotgun proteomics","volume":"76","author":"Liu","year":"2004","journal-title":"Anal Chem"},{"issue":"4","key":"10.1016\/j.jprot.2013.12.007_bb0050","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1002\/pmic.201000553","article-title":"Less label, more free: Approaches in label-free quantitative mass spectrometry","volume":"11","author":"Neilson","year":"2011","journal-title":"Proteomics"},{"issue":"1","key":"10.1016\/j.jprot.2013.12.007_bb0055","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1074\/mcp.M500230-MCP200","article-title":"Absolute quantification of proteins by LCMSE - A virtue of parallel MS acquisition","volume":"5","author":"Silva","year":"2006","journal-title":"Mol Cell Proteomics"},{"issue":"6","key":"10.1016\/j.jprot.2013.12.007_bb0060","doi-asserted-by":"crossref","first-page":"2340","DOI":"10.1021\/pr300776t","article-title":"Improving qualitative and quantitative performance for MS(E)-based label-free proteomics","volume":"12","author":"Bond","year":"2013","journal-title":"J Proteome Res"},{"issue":"9","key":"10.1016\/j.jprot.2013.12.007_bb0065","doi-asserted-by":"crossref","first-page":"1740","DOI":"10.1016\/j.jprot.2010.05.011","article-title":"Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods","volume":"73","author":"Grossmann","year":"2010","journal-title":"J Proteomics"},{"issue":"23","key":"10.1016\/j.jprot.2013.12.007_bb0070","doi-asserted-by":"crossref","first-page":"4245","DOI":"10.1002\/pmic.200700474","article-title":"A workflow to increase the detection rate of proteins from unsequenced organisms in high-throughput proteomics experiments","volume":"7","author":"Grossmann","year":"2007","journal-title":"Proteomics"},{"key":"10.1016\/j.jprot.2013.12.007_bb0075","doi-asserted-by":"crossref","first-page":"1578","DOI":"10.1104\/pp.111.172932","article-title":"Plastid proteomics in higher plants: current state and future goals","volume":"155","author":"van Wijk","year":"2011","journal-title":"Plant Physiol"},{"issue":"1","key":"10.1016\/j.jprot.2013.12.007_bb0080","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1021\/pr300952g","article-title":"Construction of plastid reference proteomes for maize and Arabidopsis and evaluation of their orthologous relationships; the concept of orthoproteomics","volume":"12","author":"Huang","year":"2013","journal-title":"J Proteome Res"},{"issue":"11","key":"10.1016\/j.jprot.2013.12.007_bb0085","doi-asserted-by":"crossref","first-page":"3911","DOI":"10.1105\/tpc.111.092882","article-title":"Plastid proteome assembly without Toc159: photosynthetic protein import and accumulation of N-acetylated plastid precursor proteins","volume":"23","author":"Bischof","year":"2011","journal-title":"Plant Cell"},{"issue":"4","key":"10.1016\/j.jprot.2013.12.007_bb0090","doi-asserted-by":"crossref","first-page":"2189","DOI":"10.1104\/pp.112.204032","article-title":"Common and specific protein accumultation patterns in different albino\/pale-green mutants reveals regulon organization at the proteome level","volume":"160","author":"Motohashi","year":"2012","journal-title":"Plant Physiol"},{"issue":"6","key":"10.1016\/j.jprot.2013.12.007_bb0095","doi-asserted-by":"crossref","first-page":"1669","DOI":"10.1105\/tpc.108.063784","article-title":"Subunits of the plastid ClpPR protease complex have differential contributions to embryogenesis, plastid biogenesis, and plant development in Arabidopsis","volume":"21","author":"Kim","year":"2009","journal-title":"Plant Cell"},{"issue":"8","key":"10.1016\/j.jprot.2013.12.007_bb0100","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1074\/mcp.O111.014704","article-title":"PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life","volume":"11","author":"Wang","year":"2012","journal-title":"Mol Cell Proteomics"},{"issue":"3","key":"10.1016\/j.jprot.2013.12.007_bb0105","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1371\/journal.pbio.1000048","article-title":"Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes","volume":"7","author":"Schrimpf","year":"2009","journal-title":"PLoS Biol"},{"issue":"6","key":"10.1016\/j.jprot.2013.12.007_bb0110","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1074\/mcp.M900325-MCP200","article-title":"AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins","volume":"9","author":"Ferro","year":"2010","journal-title":"Mol Cell Proteomics"},{"key":"10.1016\/j.jprot.2013.12.007_bb0115","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1016\/0003-2697(76)90527-3","article-title":"A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding","volume":"72","author":"Bradford","year":"1976","journal-title":"Anal Biochem"},{"key":"10.1016\/j.jprot.2013.12.007_bb0120","doi-asserted-by":"crossref","first-page":"2323","DOI":"10.1021\/pr300775k","article-title":"Effects of traveling wave ion mobility separation on data independent acquisition in proteomics studies","volume":"12","author":"Shliaha","year":"2013","journal-title":"J Proteome Res"},{"issue":"D1","key":"10.1016\/j.jprot.2013.12.007_bb0125","doi-asserted-by":"crossref","first-page":"D1185","DOI":"10.1093\/nar\/gks1151","article-title":"SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis","volume":"41","author":"Tanz","year":"2013","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"10.1016\/j.jprot.2013.12.007_bb0130","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1093\/mp\/ssp058","article-title":"The chloroplast kinase network: new insights from large-scale phosphoproteome profiling","volume":"2","author":"Baginsky","year":"2009","journal-title":"Mol Plant"},{"issue":"6","key":"10.1016\/j.jprot.2013.12.007_bb0135","doi-asserted-by":"crossref","first-page":"914","DOI":"10.1111\/j.1365-313X.2004.02016.x","article-title":"MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes","volume":"37","author":"Thimm","year":"2004","journal-title":"Plant J"},{"issue":"5","key":"10.1016\/j.jprot.2013.12.007_bb0140","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1016\/j.cub.2004.02.039","article-title":"The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions","volume":"14","author":"Kleffmann","year":"2004","journal-title":"Curr Biol"},{"issue":"7","key":"10.1016\/j.jprot.2013.12.007_bb0145","doi-asserted-by":"crossref","first-page":"2678","DOI":"10.1073\/pnas.88.7.2678","article-title":"Biosynthetic Threonine Deaminase Gene of Tomato - Isolation, Structure, and up-Regulation in Floral Organs","volume":"88","author":"Samach","year":"1991","journal-title":"Proc Natl Acad Sci U S A"}],"container-title":["Journal of Proteomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1874391913006428?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1874391913006428?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T11:56:33Z","timestamp":1761738993000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1874391913006428"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,2]]},"references-count":29,"alternative-id":["S1874391913006428"],"URL":"https:\/\/doi.org\/10.1016\/j.jprot.2013.12.007","relation":{},"ISSN":["1874-3919"],"issn-type":[{"value":"1874-3919","type":"print"}],"subject":[],"published":{"date-parts":[[2014,2]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Protein identification and quantification by data-independent acquisition and multi-parallel collision-induced dissociation mass spectrometry (MSE) in the chloroplast stroma proteome","name":"articletitle","label":"Article Title"},{"value":"Journal of Proteomics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jprot.2013.12.007","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"Copyright \u00a9 2013 Elsevier B.V. All rights reserved.","name":"copyright","label":"Copyright"}]}}