{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,28]],"date-time":"2025-11-28T17:11:00Z","timestamp":1764349860379},"reference-count":30,"publisher":"Springer Science and Business Media LLC","issue":"7","license":[{"start":{"date-parts":[[2006,6,21]],"date-time":"2006-06-21T00:00:00Z","timestamp":1150848000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Nat Methods"],"published-print":{"date-parts":[[2006,7]]},"DOI":"10.1038\/nmeth891","type":"journal-article","created":{"date-parts":[[2006,6,21]],"date-time":"2006-06-21T18:34:09Z","timestamp":1150914849000},"page":"533-539","source":"Crossref","is-referenced-by-count":101,"title":["Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software"],"prefix":"10.1038","volume":"3","author":[{"given":"Patrick G A","family":"Pedrioli","sequence":"first","affiliation":[]},{"given":"Brian","family":"Raught","sequence":"additional","affiliation":[]},{"given":"Xiang-Dong","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Richard","family":"Rogers","sequence":"additional","affiliation":[]},{"given":"John","family":"Aitchison","sequence":"additional","affiliation":[]},{"given":"Michael","family":"Matunis","sequence":"additional","affiliation":[]},{"given":"Ruedi","family":"Aebersold","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2006,6,21]]},"reference":[{"key":"BFnmeth891_CR1","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1021\/cr990076h","volume":"101","author":"R Aebersold","year":"2001","unstructured":"Aebersold, R. & Goodlett, D.R. Mass spectrometry in proteomics. Chem. Rev. 101, 269\u2013295 (2001).","journal-title":"Chem. Rev."},{"key":"BFnmeth891_CR2","doi-asserted-by":"publisher","first-page":"699","DOI":"10.1038\/nrm1468","volume":"5","author":"H Steen","year":"2004","unstructured":"Steen, H. & Mann, M. The ABC's (and XYZ's) of peptide sequencing. Nat. Rev. Mol. Cell Biol. 5, 699\u2013711 (2004).","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"BFnmeth891_CR3","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1016\/S0968-0004(03)00113-0","volume":"28","author":"DC Schwartz","year":"2003","unstructured":"Schwartz, D.C. & Hochstrasser, M. A superfamily of protein tags: ubiquitin, SUMO and related modifiers. Trends Biochem. Sci. 28, 321\u2013328 (2003).","journal-title":"Trends Biochem. Sci."},{"key":"BFnmeth891_CR4","doi-asserted-by":"publisher","first-page":"599","DOI":"10.1038\/nrm1700","volume":"6","author":"RL Welchman","year":"2005","unstructured":"Welchman, R.L., Gordon, C. & Mayer, R.J. Ubiquitin and ubiquitin-like proteins as multifunctional signals. Nat. Rev. Mol. Cell Biol. 6, 599\u2013609 (2005).","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"BFnmeth891_CR5","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1146\/annurev.cellbio.16.1.591","volume":"16","author":"F Melchior","year":"2000","unstructured":"Melchior, F. SUMO\u2013nonclassical ubiquitin. Annu. Rev. Cell Dev. Biol. 16, 591\u2013626 (2000).","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"BFnmeth891_CR6","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1146\/annurev.biochem.73.011303.074118","volume":"73","author":"ES Johnson","year":"2004","unstructured":"Johnson, E.S. Protein modification by SUMO. Annu. Rev. Biochem. 73, 355\u2013382 (2004).","journal-title":"Annu. Rev. Biochem."},{"key":"BFnmeth891_CR7","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1074\/mcp.M400149-MCP200","volume":"4","author":"G Rosas-Acosta","year":"2005","unstructured":"Rosas-Acosta, G., Russell, W.K., Deyrieux, A., Russell, D.H. & Wilson, V.G. A universal strategy for proteomic studies of SUMO and other ubiquitin-like modifiers. Mol. Cell. Proteomics 4, 56\u201372 (2005).","journal-title":"Mol. Cell. Proteomics"},{"key":"BFnmeth891_CR8","doi-asserted-by":"publisher","first-page":"33791","DOI":"10.1074\/jbc.M404201200","volume":"279","author":"AC Vertegaal","year":"2004","unstructured":"Vertegaal, A.C. et al. A proteomic study of SUMO-2 target proteins. J. Biol. Chem. 279, 33791\u201333798 (2004).","journal-title":"J. Biol. Chem."},{"key":"BFnmeth891_CR9","doi-asserted-by":"publisher","first-page":"20999","DOI":"10.1074\/jbc.M401541200","volume":"279","author":"Y Zhao","year":"2004","unstructured":"Zhao, Y., Kwon, S.W., Anselmo, A., Kaur, K. & White, M.A. Broad spectrum identification of cellular small ubiquitin-related modifier (SUMO) substrate proteins. J. Biol. Chem. 279, 20999\u201321002 (2004).","journal-title":"J. Biol. Chem."},{"key":"BFnmeth891_CR10","doi-asserted-by":"publisher","first-page":"8551","DOI":"10.1073\/pnas.0402889101","volume":"101","author":"T Li","year":"2004","unstructured":"Li, T. et al. Sumoylation of heterogeneous nuclear ribonucleoproteins, zinc finger proteins, and nuclear pore complex proteins: a proteomic analysis. Proc. Natl. Acad. Sci. USA 101, 8551\u20138556 (2004).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"BFnmeth891_CR11","doi-asserted-by":"publisher","first-page":"5004","DOI":"10.1074\/jbc.M411718200","volume":"280","author":"C Gocke","year":"2005","unstructured":"Gocke, C., Yu, H. & Kang, J. Systematic identification and analysis of mammalian SUMO substrates. J. Biol. Chem. 280, 5004\u20135012 (2005).","journal-title":"J. Biol. Chem."},{"key":"BFnmeth891_CR12","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1074\/mcp.M400154-MCP200","volume":"4","author":"C Denison","year":"2005","unstructured":"Denison, C. et al. A proteomic strategy for gaining insights into protein sumoylation in yeast. Mol. Cell. Proteomics 4, 246\u2013254 (2005).","journal-title":"Mol. Cell. Proteomics"},{"key":"BFnmeth891_CR13","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1074\/mcp.M400166-MCP200","volume":"4","author":"D Wykoff","year":"2005","unstructured":"Wykoff, D. & O'Shea, E. Identification of sumoylated proteins by systematic immunoprecipitation of the budding yeast proteome. Mol. Cell. Proteomics 4, 73\u201383 (2005).","journal-title":"Mol. Cell. Proteomics"},{"key":"BFnmeth891_CR14","doi-asserted-by":"publisher","first-page":"41346","DOI":"10.1074\/jbc.M407950200","volume":"279","author":"VG Panse","year":"2004","unstructured":"Panse, V.G., Hardeland, U., Werner, T., Kuster, B. & Hurt, E. A proteome-wide approach identifies sumoylated substrate proteins in yeast. J. Biol. Chem. 279, 41346\u201341351 (2004).","journal-title":"J. Biol. Chem."},{"key":"BFnmeth891_CR15","doi-asserted-by":"publisher","first-page":"4102","DOI":"10.1074\/jbc.M413209200","volume":"280","author":"JT Hannich","year":"2005","unstructured":"Hannich, J.T. et al. Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae. J. Biol. Chem. 280, 4102\u20134110 (2005).","journal-title":"J. Biol. Chem."},{"key":"BFnmeth891_CR16","doi-asserted-by":"publisher","first-page":"45662","DOI":"10.1074\/jbc.M409203200","volume":"279","author":"JA Wohlschlegel","year":"2004","unstructured":"Wohlschlegel, J.A., Johnson, E.S., Reed, S.I. & Yates, J.R., III. Global analysis of protein sumoylation in Saccharomyces cerevisiae. J. Biol. Chem. 279, 45662\u201345668 (2004).","journal-title":"J. Biol. Chem."},{"key":"BFnmeth891_CR17","doi-asserted-by":"publisher","first-page":"12654","DOI":"10.1074\/jbc.M009476200","volume":"276","author":"MS Rodriguez","year":"2001","unstructured":"Rodriguez, M.S., Dargemont, C. & Hay, R.T. SUMO-1 conjugation in vivo requires both a consensus modification motif and nuclear targeting. J. Biol. Chem. 276, 12654\u201312659 (2001).","journal-title":"J. Biol. Chem."},{"key":"BFnmeth891_CR18","doi-asserted-by":"publisher","first-page":"21664","DOI":"10.1074\/jbc.M100006200","volume":"276","author":"DA Sampson","year":"2001","unstructured":"Sampson, D.A., Wang, M. & Matunis, M.J. The small ubiquitin-like modifier-1 (SUMO-1) consensus sequence mediates Ubc9 binding and is essential for SUMO-1 modification. J. Biol. Chem. 276, 21664\u201321669 (2001).","journal-title":"J. Biol. Chem."},{"key":"BFnmeth891_CR19","doi-asserted-by":"publisher","first-page":"26675","DOI":"10.1074\/jbc.273.41.26675","volume":"273","author":"T Kamitani","year":"1998","unstructured":"Kamitani, T. et al. Identification of three major sentrinization sites in PML. J. Biol. Chem. 273, 26675\u201326682 (1998).","journal-title":"J. Biol. Chem."},{"key":"BFnmeth891_CR20","doi-asserted-by":"publisher","first-page":"976","DOI":"10.1016\/1044-0305(94)80016-2","volume":"5","author":"JK Eng","year":"1994","unstructured":"Eng, J.K., McCormack, A.L. & Yates, J.R., III. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976\u2013989 (1994).","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"BFnmeth891_CR21","doi-asserted-by":"publisher","first-page":"4646","DOI":"10.1021\/ac0341261","volume":"75","author":"AI Nesvizhskii","year":"2003","unstructured":"Nesvizhskii, A.I., Keller, A., Kolker, E. & Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646\u20134658 (2003).","journal-title":"Anal. Chem."},{"key":"BFnmeth891_CR22","doi-asserted-by":"publisher","first-page":"1457","DOI":"10.1083\/jcb.135.6.1457","volume":"135","author":"MJ Matunis","year":"1996","unstructured":"Matunis, M.J., Coutavas, E. & Blobel, G. A novel ubiquitin-like modification modulates the partitioning of the Ran-GTPase-activating protein RanGAP1 between the cytosol and the nuclear pore complex. J. Cell Biol. 135, 1457\u20131470 (1996).","journal-title":"J. Cell Biol."},{"key":"BFnmeth891_CR23","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1083\/jcb.140.3.499","volume":"140","author":"MJ Matunis","year":"1998","unstructured":"Matunis, M.J., Wu, J. & Blobel, G. SUMO-1 modification and its role in targeting the Ran GTPase-activating protein, RanGAP1, to the nuclear pore complex. J. Cell Biol. 140, 499\u2013509 (1998).","journal-title":"J. Cell Biol."},{"key":"BFnmeth891_CR24","doi-asserted-by":"publisher","first-page":"30091","DOI":"10.1074\/jbc.M301344200","volume":"278","author":"RS Rogers","year":"2003","unstructured":"Rogers, R.S., Horvath, C.M. & Matunis, M.J. SUMO modification of STAT1 and its role in PIAS-mediated inhibition of gene activation. J. Biol. Chem. 278, 30091\u201330097 (2003).","journal-title":"J. Biol. Chem."},{"key":"BFnmeth891_CR25","doi-asserted-by":"publisher","first-page":"35368","DOI":"10.1074\/jbc.M104214200","volume":"276","author":"MH Tatham","year":"2001","unstructured":"Tatham, M.H. et al. Polymeric chains of SUMO-2 and SUMO-3 are conjugated to protein substrates by SAE1\/SAE2 and Ubc9. J. Biol. Chem. 276, 35368\u201335374 (2001).","journal-title":"J. Biol. Chem."},{"key":"BFnmeth891_CR26","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/S0092-8674(01)00633-X","volume":"108","author":"A Pichler","year":"2002","unstructured":"Pichler, A., Gast, A., Seeler, J.S., Dejean, A. & Melchior, F. The nucleoporin RanBP2 has SUMO1 E3 ligase activity. Cell 108, 109\u2013120 (2002).","journal-title":"Cell"},{"key":"BFnmeth891_CR27","doi-asserted-by":"publisher","first-page":"8264","DOI":"10.1074\/jbc.M510364200","volume":"281","author":"M Yang","year":"2006","unstructured":"Yang, M., Hsu, C-T., Ting, C-Y., Liu, L.F. & Hwang, J. Assembly of a polymeric chain of SUMO1 on human topoisomerase I in vitro. J. Biol. Chem. 281, 8264\u20138274 (2006).","journal-title":"J. Biol. Chem."},{"key":"BFnmeth891_CR28","doi-asserted-by":"publisher","first-page":"1459","DOI":"10.1038\/nbt1031","volume":"22","author":"PG Pedrioli","year":"2004","unstructured":"Pedrioli, P.G. et al. A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 22, 1459\u20131466 (2004).","journal-title":"Nat. Biotechnol."},{"key":"BFnmeth891_CR29","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1021\/pr015509n","volume":"1","author":"SP Gygi","year":"2002","unstructured":"Gygi, S.P., Rist, B., Griffin, T.J., Eng, J. & Aebersold, R. Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags. J. Proteome Res. 1, 47\u201354 (2002).","journal-title":"J. Proteome Res."},{"key":"BFnmeth891_CR30","doi-asserted-by":"publisher","first-page":"5383","DOI":"10.1021\/ac025747h","volume":"74","author":"A Keller","year":"2002","unstructured":"Keller, A., Nesvizhskii, A.I., Kolker, E. & Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS\/MS and database search. Anal. Chem. 74, 5383\u20135392 (2002).","journal-title":"Anal. Chem."}],"container-title":["Nature Methods"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/nmeth891.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/nmeth891","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/nmeth891.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,19]],"date-time":"2023-05-19T00:00:32Z","timestamp":1684454432000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/nmeth891"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,6,21]]},"references-count":30,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2006,7]]}},"alternative-id":["BFnmeth891"],"URL":"https:\/\/doi.org\/10.1038\/nmeth891","relation":{},"ISSN":["1548-7091","1548-7105"],"issn-type":[{"value":"1548-7091","type":"print"},{"value":"1548-7105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,6,21]]}}}