{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T14:53:56Z","timestamp":1786978436242,"version":"build-2736575974"},"reference-count":28,"publisher":"Wiley","issue":"17","license":[{"start":{"date-parts":[[2019,7,31]],"date-time":"2019-07-31T00:00:00Z","timestamp":1564531200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/501100010843","name":"Guangzhou Science, Technology and Innovation Commission","doi-asserted-by":"publisher","award":["201802020016"],"award-info":[{"award-number":["201802020016"]}],"id":[{"id":"10.13039\/501100010843","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["91839302, 31670834, 31870824 &31700723"],"award-info":[{"award-number":["91839302, 31670834, 31870824 &31700723"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["analyticalsciencejournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Rapid Comm Mass Spectrometry"],"published-print":{"date-parts":[[2019,9,15]]},"abstract":"<jats:sec>\n                    <jats:title>Rationale<\/jats:title>\n                    <jats:p>Formalin\u2010Fixed Paraffin\u2010Embedded (FFPE) samples are valuable for proteomic studies of disease. However, the crosslink among proteins, protein vs nucleic acid, and other covalent chemical modifications like methylation introduced by formaldehyde can interfere with trypsin digestion in proteomics studies. LysargiNase was reported to have a better full\u2010cleavage rate at methylation and b ion coverage than trypsin. The contribution of LysargiNase in the proteomic study of FFPE samples was assessed and compared with trypsin in this study for the first time to facilitate proteomic research on FFPE samples.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>The FFPE proteins were extracted with an \u201cantigen retrieval\u201d method. Digestion parameters were optimized by visualization of the digests on the tricine gel by silver staining. Then the FFPE proteins were separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS\u2010PAGE) and cut into 16 gel bands and in\u2010gel digested by trypsin and LysargiNase, respectively. Peptides were desalted with Stage\u2010Tips and separated via liquid chromatography. Electrospray ionization was conducted and peptide mass was measured in the LTQ Orbitrap Velos in the data\u2010dependent mode.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>High concentrations of enzyme facilitate the digestion efficiency of FFPE samples. A total of 32,294 peptides and 3445 proteins were identified with LysargiNase and trypsin combined in two replicates. LysargiNase increased peptide identification by 18.9% and protein identification by 13.4% on the basis of trypsin. Consistently, LysargiNase increased C\u2010terminal peptide identification by 47.7%. Moreover, LysargiNase showed better full\u2010cleavage rate (49.3%) at methylated sites than trypsin (23.9%). LysargiNase and trypsin combined can improve the b\u2010ion coverage by 50% on FFPE samples.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>FFPE samples can be more efficiently digested at high concentrations of LysargiNase and trypsin. LysargiNase can better digest methylated peptides and improve the proteome identification by 13.4% and the b\u2010ion coverage by 50% on the basis of trypsin in FFPE samples.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1002\/rcm.8479","type":"journal-article","created":{"date-parts":[[2019,5,8]],"date-time":"2019-05-08T05:28:16Z","timestamp":1557293296000},"page":"1381-1389","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["LysargiNase enhances protein identification on the basis of trypsin on formalin\u2010fixed paraffin\u2010embedded samples"],"prefix":"10.1002","volume":"33","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9812-7821","authenticated-orcid":false,"given":"Shu","family":"Liu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) Beijing Institute of Lifeomics  Beijing 102206 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Xu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) Beijing Institute of Lifeomics  Beijing 102206 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanan","family":"Yin","sequence":"additional","affiliation":[{"name":"Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of the Ministry of Education, School of Pharmaceutical Sciences Wuhan University  Wuhan 430072 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5138-3510","authenticated-orcid":false,"given":"Junling","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) Beijing Institute of Lifeomics  Beijing 102206 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fuqiang","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) Beijing Institute of Lifeomics  Beijing 102206 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanchang","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) Beijing Institute of Lifeomics  Beijing 102206 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ping","family":"Xu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) Beijing Institute of Lifeomics  Beijing 102206 China"},{"name":"Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of the Ministry of Education, School of Pharmaceutical Sciences Wuhan University  Wuhan 430072 China"},{"name":"Anhui Medical University  Hefei 230032 China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2019,7,31]]},"reference":[{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.O115.056515"},{"key":"e_1_2_6_3_1","doi-asserted-by":"publisher","DOI":"10.1369\/jhc.2010.957191"},{"key":"e_1_2_6_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.euprot.2015.10.001"},{"key":"e_1_2_6_5_1","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.201100550"},{"key":"e_1_2_6_6_1","doi-asserted-by":"publisher","DOI":"10.1155\/2010\/927585"},{"key":"e_1_2_6_7_1","doi-asserted-by":"publisher","DOI":"10.4172\/jpb.1000315"},{"key":"e_1_2_6_8_1","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.201400454"},{"key":"e_1_2_6_9_1","doi-asserted-by":"publisher","DOI":"10.1002\/prca.201200046"},{"key":"e_1_2_6_10_1","doi-asserted-by":"publisher","DOI":"10.1186\/1559-0275-11-4"},{"key":"e_1_2_6_11_1","doi-asserted-by":"publisher","DOI":"10.1021\/pr200019m"},{"key":"e_1_2_6_12_1","doi-asserted-by":"publisher","DOI":"10.1021\/pr100234w"},{"key":"e_1_2_6_13_1","doi-asserted-by":"publisher","DOI":"10.1021\/pr400960r"},{"key":"e_1_2_6_14_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.6b02872"},{"key":"e_1_2_6_15_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3177"},{"key":"e_1_2_6_16_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.7b03673"},{"key":"e_1_2_6_17_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky869"},{"key":"e_1_2_6_18_1","doi-asserted-by":"publisher","DOI":"10.1002\/rcm.7535"},{"key":"e_1_2_6_19_1","doi-asserted-by":"publisher","DOI":"10.1021\/pr900251d"},{"key":"e_1_2_6_20_1","doi-asserted-by":"publisher","DOI":"10.1021\/pr0603396"},{"key":"e_1_2_6_21_1","doi-asserted-by":"publisher","DOI":"10.1021\/pr900748n"},{"key":"e_1_2_6_22_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0115862"},{"key":"e_1_2_6_23_1","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2006.468"},{"key":"e_1_2_6_24_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2009.01.041"},{"key":"e_1_2_6_25_1","doi-asserted-by":"publisher","DOI":"10.1021\/ac026117i"},{"key":"e_1_2_6_26_1","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.201200591"},{"key":"e_1_2_6_27_1","doi-asserted-by":"publisher","DOI":"10.18632\/oncotarget.12372"},{"key":"e_1_2_6_28_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1511"},{"key":"e_1_2_6_29_1","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M600469-MCP200"}],"container-title":["Rapid 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