Yuming Jiang, Devasahayam Arokia Balaya Rex, Dina Schuster, Benjamin A. Neely, Germán L. Rosano, Norbert Volkmar, Amanda Momenzadeh, Trenton M. Peters-Clarke, Susan B. Egbert, Simion Kreimer, Emma H. Doud, Oliver M. Crook, Amit Kumar Yadav, Muralidharan Vanuopadath, Adrian D. Hegeman, Martín L. Mayta, Anna G. Duboff, Nicholas M. Riley, Robert L. Moritz, Jesse G. Meyer
{"title":"Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry","authors":"Yuming Jiang, Devasahayam Arokia Balaya Rex, Dina Schuster, Benjamin A. Neely, Germán L. Rosano, Norbert Volkmar, Amanda Momenzadeh, Trenton M. Peters-Clarke, Susan B. Egbert, Simion Kreimer, Emma H. Doud, Oliver M. Crook, Amit Kumar Yadav, Muralidharan Vanuopadath, Adrian D. Hegeman, Martín L. Mayta, Anna G. Duboff, Nicholas M. Riley, Robert L. Moritz, Jesse G. Meyer","doi":"10.1021/acsmeasuresciau.3c00068","DOIUrl":null,"url":null,"abstract":"Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. “Shotgun proteomics” or “bottom-up proteomics” is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.","PeriodicalId":29800,"journal":{"name":"ACS Measurement Science Au","volume":null,"pages":null},"PeriodicalIF":4.6000,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"ACS Measurement Science Au","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1021/acsmeasuresciau.3c00068","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, ANALYTICAL","Score":null,"Total":0}
引用次数: 0
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. “Shotgun proteomics” or “bottom-up proteomics” is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
期刊介绍:
ACS Measurement Science Au is an open access journal that publishes experimental computational or theoretical research in all areas of chemical measurement science. Short letters comprehensive articles reviews and perspectives are welcome on topics that report on any phase of analytical operations including sampling measurement and data analysis. This includes:Chemical Reactions and SelectivityChemometrics and Data ProcessingElectrochemistryElemental and Molecular CharacterizationImagingInstrumentationMass SpectrometryMicroscale and Nanoscale systemsOmics (Genomics Proteomics Metabonomics Metabolomics and Bioinformatics)Sensors and Sensing (Biosensors Chemical Sensors Gas Sensors Intracellular Sensors Single-Molecule Sensors Cell Chips Arrays Microfluidic Devices)SeparationsSpectroscopySurface analysisPapers dealing with established methods need to offer a significantly improved original application of the method.