FigsharePub Date : 2024-08-23DOI: 10.1021/acs.jproteome.4c00177.s002
CassandraN. Fuller (19474750), Lilian Valadares Tose (19474753), Francisca N. L. Vitorino (5080508), Natarajan V. Bhanu (8762832), Erin M. Panczyk (8339259), Melvin A. Park (1308141), Benjamin A. Garcia (205670), Francisco Fernandez-Lima (761320)
{"title":"Bottom-upnHistone Post-translational ModificationnAnalysis using Liquid Chromatography, Trapped Ion Mobility Spectrometry,nand Tandem Mass Spectrometry","authors":"CassandraN. Fuller (19474750), Lilian Valadares Tose (19474753), Francisca N. L. Vitorino (5080508), Natarajan V. Bhanu (8762832), Erin M. Panczyk (8339259), Melvin A. Park (1308141), Benjamin A. Garcia (205670), Francisco Fernandez-Lima (761320)","doi":"10.1021/acs.jproteome.4c00177.s002","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00177.s002","url":null,"abstract":"The amino acid position within a histone sequence andnthe chemicalnnature of post-translational modifications (PTMs) are essential fornelucidating the “Histone Code”. Previous work has shownnthat PTMs induce specific biological responses and are good candidatesnas biomarkers for diagnostics. Here, we evaluate the analytical advantagesnof trapped ion mobility (TIMS) with parallel accumulation-serial fragmentationn(PASEF) and tandem mass spectrometry (MS/MS) for bottom-up proteomicsnof model cancer cells. The study also considered the use of nanoliquidnchromatography (LC) and traditional methods: LC-TIMS-PASEF-ToF MS/MSnvs nLC-TIMS-PASEF-ToF MS/MS vs nLC-MS/MS. The addition of TIMS andnPASEF-MS/MS increased the number of detected peptides due to the addednseparation dimension. All three methods showed high reproducibilitynand low RSD in the MS domain (<5 ppm). While the LC, nLC and TIMSnseparations showed small RSD across samples, the accurate mobilityn(1/K<sub>0</sub>) measurements (<0.6% RSD) increased the confidencenof peptide assignments. Trends were observed in the retention timenand mobility concerning the number and type of PTMs (e.g., ac, me<sub>1–3</sub>) and their corresponding unmodified, propionylatednpeptide that aided in peptide assignment. Mobility separation permittednthe annotation of coeluting structural and positional isomers andncompared with nLC-MS/MS showed several advantages due to reduced chemicalnnoise.","PeriodicalId":522032,"journal":{"name":"Figshare","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147890146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}