{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T04:11:48Z","timestamp":1775016708768,"version":"3.50.1"},"reference-count":31,"publisher":"Springer Science and Business Media LLC","issue":"1","funder":[{"DOI":"10.13039\/100008762","name":"Genome Canada","doi-asserted-by":"publisher","award":["214PRO"],"award-info":[{"award-number":["214PRO"]}],"id":[{"id":"10.13039\/100008762","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["MOP77688"],"award-info":[{"award-number":["MOP77688"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12859-017-1865-8","type":"journal-article","created":{"date-parts":[[2017,10,23]],"date-time":"2017-10-23T14:47:18Z","timestamp":1508770038000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":66,"title":["A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE)"],"prefix":"10.1186","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4496-8131","authenticated-orcid":false,"given":"R. Greg","family":"Stacey","sequence":"first","affiliation":[]},{"given":"Michael A.","family":"Skinnider","sequence":"additional","affiliation":[]},{"given":"Nichollas E.","family":"Scott","sequence":"additional","affiliation":[]},{"given":"Leonard J.","family":"Foster","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,10,23]]},"reference":[{"key":"1865_CR1","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1101\/gr.4527806","volume":"16","author":"M Arifuzzaman","year":"2006","unstructured":"Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, et al. Large-scale identification of protein\u2013protein interaction of Escherichia Coli K-12. Genome Res. 2006;16:686\u201391.","journal-title":"Genome Res"},{"key":"1865_CR2","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1038\/nature04532","volume":"440","author":"A-C Gavin","year":"2006","unstructured":"Gavin A-C, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, et al. Proteome survey reveals modularity of the yeast cell machinery. Nature. 2006;440:631\u20136.","journal-title":"Nature"},{"key":"1865_CR3","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1038\/nature04670","volume":"440","author":"NJ Krogan","year":"2006","unstructured":"Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, et al. Global landscape of protein complexes in the yeast Saccharomyces Cerevisiae. Nature. 2006;440:637\u201343.","journal-title":"Nature"},{"key":"1865_CR4","doi-asserted-by":"crossref","first-page":"1235","DOI":"10.1126\/science.1176343","volume":"326","author":"S K\u00fchner","year":"2009","unstructured":"K\u00fchner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, et al. Proteome organization in a genome-reduced bacterium. Science. 2009;326:1235\u201340.","journal-title":"Science"},{"key":"1865_CR5","doi-asserted-by":"crossref","first-page":"1576","DOI":"10.1002\/pmic.201100523","volume":"12","author":"WH Dunham","year":"2012","unstructured":"Dunham WH, Mullin M, Gingras A-C. Affinity-purification coupled to mass spectrometry: basic principles and strategies. Proteomics. 2012;12:1576\u201390.","journal-title":"Proteomics"},{"key":"1865_CR6","doi-asserted-by":"crossref","first-page":"1068","DOI":"10.1016\/j.cell.2012.08.011","volume":"150","author":"PC Havugimana","year":"2012","unstructured":"Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, et al. A census of human soluble protein complexes. Cell. 2012;150:1068\u201381.","journal-title":"Cell"},{"key":"1865_CR7","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1016\/j.cmet.2012.08.009","volume":"16","author":"H Heide","year":"2012","unstructured":"Heide H, Bleier L, Steger M, Ackermann J, Dr\u00f6se S, Schwamb B, et al. Complexome profiling identifies TMEM126B as a component of the mitochondrial complex I assembly complex. Cell Metab. 2012;16:538\u201349.","journal-title":"Cell Metab"},{"key":"1865_CR8","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/nmeth.2131","volume":"9","author":"AR Kristensen","year":"2012","unstructured":"Kristensen AR, Gsponer J, Foster LJA. High-throughput approach for measuring temporal changes in the interactome. Nat Methods. 2012;9:907\u20139.","journal-title":"Nat Methods"},{"key":"1865_CR9","doi-asserted-by":"crossref","first-page":"2763","DOI":"10.3390\/ijms10062763","volume":"10","author":"A Br\u00fcckner","year":"2009","unstructured":"Br\u00fcckner A, Polge C, Lentze N, Auerbach D, Schlattner U. Yeast two-hybrid, a powerful tool for systems biology. Int J Mol Sci. 2009;10:2763\u201388.","journal-title":"Int J Mol Sci"},{"key":"1865_CR10","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1038\/nmeth.1541","volume":"8","author":"H Choi","year":"2011","unstructured":"Choi H, Larsen B, Lin Z-Y, Breitkreutz A, Mellacheruvu D, Fermin D, et al. SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat Methods. 2011;8:70\u20133.","journal-title":"Nat Methods"},{"key":"1865_CR11","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.jprot.2014.10.024","volume":"118","author":"NE Scott","year":"2015","unstructured":"Scott NE, Brown LM, Kristensen AR, Foster LJ. Development of a computational framework for the analysis of protein correlation profiling and spatial proteomics experiments. J Proteome. 2015;118:112\u201329.","journal-title":"J Proteome"},{"key":"1865_CR12","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1016\/j.jprot.2012.10.001","volume":"81","author":"C Wan","year":"2013","unstructured":"Wan C, Liu J, Fong V, Lugowski A, Stoilova S, Bethune-Waddell D, et al. ComplexQuant: high-throughput computational pipeline for the global quantitative analysis of endogenous soluble protein complexes using high resolution protein HPLC and precision label-free LC\/MS\/MS. J Proteome. 2013;81:102\u201311.","journal-title":"J Proteome"},{"key":"1865_CR13","unstructured":"PrInCE: Bioinformatics pipeline for predicting protein interactomes via co-elution. Matlab. Foster lab; 2016. \nhttps:\/\/github.com\/fosterlab\/PrInCE\n\n. Accessed 26 May 2017."},{"issue":"suppl 1","key":"1865_CR14","doi-asserted-by":"crossref","first-page":"D497","DOI":"10.1093\/nar\/gkp914","volume":"38","author":"A Ruepp","year":"2010","unstructured":"Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, Fobo G, et al. CORUM: the comprehensive resource of mammalian protein complexes\u20142009. Nucleic Acids Res. 2010;38(suppl 1):D497\u2013501.","journal-title":"Nucleic Acids Res"},{"key":"1865_CR15","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1038\/nature14877","volume":"525","author":"C Wan","year":"2015","unstructured":"Wan C, Borgeson B, Phanse S, Tu F, Drew K, Clark G, et al. Panorama of ancient metazoan macromolecular complexes. Nature. 2015;525:339\u201344.","journal-title":"Nature"},{"key":"1865_CR16","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1038\/nmeth.1938","volume":"9","author":"T Nepusz","year":"2012","unstructured":"Nepusz T, Yu H, Paccanaro A. Detecting overlapping protein complexes in protein-protein interaction networks. Nat Methods. 2012;9:471\u20132.","journal-title":"Nat Methods"},{"key":"1865_CR17","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1186\/1471-2105-7-488","volume":"7","author":"S Brohee","year":"2006","unstructured":"Brohee S, Van Helden J. Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinf. 2006;7:488.","journal-title":"BMC Bioinf"},{"key":"1865_CR18","doi-asserted-by":"crossref","first-page":"906","DOI":"10.15252\/msb.20167067","volume":"13","author":"NE Scott","year":"2017","unstructured":"Scott NE, Rogers LD, Prudova A, Brown NF, Fortelny N, Overall CM, et al. Interactome disassembly during apoptosis occurs independent of caspase cleavage. Mol Syst Biol. 2017;13:906.","journal-title":"Mol Syst Biol"},{"key":"1865_CR19","doi-asserted-by":"crossref","first-page":"D479","DOI":"10.1093\/nar\/gku975","volume":"43","author":"BH Meldal","year":"2014","unstructured":"Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, et al. The complex portal-an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 2014;43:D479\u201384.","journal-title":"Nucleic Acids Res"},{"key":"1865_CR20","doi-asserted-by":"crossref","first-page":"932","DOI":"10.15252\/msb.20167490","volume":"13","author":"K Drew","year":"2017","unstructured":"Drew K, Lee C, Huizar RL, Tu F, Borgeson B, McWhite CD, et al. Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes. Mol Syst Biol. 2017;13:932.","journal-title":"Mol Syst Biol"},{"key":"1865_CR21","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25:25\u20139.","journal-title":"Nat Genet"},{"key":"1865_CR22","doi-asserted-by":"crossref","first-page":"D1049","DOI":"10.1093\/nar\/gku1179","volume":"43","author":"GO Consortium","year":"2015","unstructured":"Consortium GO. Gene ontology consortium: going forward. Nucleic Acids Res. 2015;43:D1049\u201356.","journal-title":"Nucleic Acids Res"},{"key":"1865_CR23","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1038\/nature13302","volume":"509","author":"M-S Kim","year":"2014","unstructured":"Kim M-S, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, et al. A draft map of the human proteome. Nature. 2014;509:575\u201381.","journal-title":"Nature"},{"key":"1865_CR24","doi-asserted-by":"crossref","first-page":"1260419","DOI":"10.1126\/science.1260419","volume":"347","author":"M Uhl\u00e9n","year":"2015","unstructured":"Uhl\u00e9n M, Fagerberg L, Hallstr\u00f6m BM, Lindskog C, Oksvold P, Mardinoglu A, et al. Tissue-based map of the human proteome. Science. 2015;347:1260419.","journal-title":"Science"},{"key":"1865_CR25","doi-asserted-by":"crossref","first-page":"D374","DOI":"10.1093\/nar\/gkt887","volume":"42","author":"R Mosca","year":"2013","unstructured":"Mosca R, C\u00e9ol A, Stein A, Olivella R, Aloy P. 3did: a catalog of domain-based interactions of known three-dimensional structure. Nucleic Acids Res. 2013;42:D374\u20139.","journal-title":"Nucleic Acids Res"},{"key":"1865_CR26","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1016\/j.cell.2015.09.053","volume":"163","author":"MY Hein","year":"2015","unstructured":"Hein MY, Hubner NC, Poser I, Cox J, Nagaraj N, Toyoda Y, et al. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell. 2015;163:712\u201323.","journal-title":"Cell"},{"key":"1865_CR27","doi-asserted-by":"crossref","first-page":"1971","DOI":"10.1101\/gr.206701","volume":"11","author":"R Mrowka","year":"2001","unstructured":"Mrowka R, Patzak A, Herzel H. Is there a bias in proteome research? Genome Res. 2001;11:1971\u20133.","journal-title":"Genome Res"},{"key":"1865_CR28","doi-asserted-by":"crossref","first-page":"3905","DOI":"10.1093\/emboj\/19.15.3905","volume":"19","author":"A Eugster","year":"2000","unstructured":"Eugster A, Frigerio G, Dale M, Duden R. COP I domains required for coatomer integrity, and novel interactions with ARF and ARF-GAP. EMBO J. 2000;19:3905\u201317.","journal-title":"EMBO J"},{"key":"1865_CR29","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1083\/jcb.135.1.53","volume":"135","author":"D Faulstich","year":"1996","unstructured":"Faulstich D, Auerbach S, Orci L, Ravazzola M, Wegehingel S, Lottspeich F, et al. Architecture of coatomer: molecular characterization of d-COP and protein interactions within the complex. J Cell Biol. 1996;135:53\u201362.","journal-title":"J Cell Biol"},{"key":"1865_CR30","doi-asserted-by":"crossref","first-page":"11649","DOI":"10.1073\/pnas.95.20.11649","volume":"95","author":"C Harter","year":"1998","unstructured":"Harter C, Wieland FTA. Single binding site for dilysine retrieval motifs and p23 within the \u03b3 subunit of coatomer. Proc Natl Acad Sci. 1998;95:11649\u201354.","journal-title":"Proc Natl Acad Sci"},{"key":"1865_CR31","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1038\/nmeth.1279","volume":"6","author":"N Simonis","year":"2009","unstructured":"Simonis N, Rual J-F, Carvunis A-R, Tasan M, Lemmens I, Hirozane-Kishikawa T, et al. Empirically controlled mapping of the Caenorhabditis Elegans protein-protein interactome network. Nat Methods. 2009;6:47\u201354.","journal-title":"Nat Methods"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1865-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,10,23]],"date-time":"2017-10-23T14:47:36Z","timestamp":1508770056000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1865-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,10,23]]},"references-count":31,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["1865"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1865-8","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/152355","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,10,23]]},"article-number":"457"}}