Comprehensive Overview of Bottom-Up Proteomics using Mass Spectrometry.

Autor: Jiang Y; Department of Computational Biomedicine, Cedars Sinai Medical Center., Rex DAB; Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India., Schuster D; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland; Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8093, Switzerland; Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland., Neely BA; Chemical Sciences Division, National Institute of Standards and Technology, NIST Charleston · Funded by NIST., Rosano GL; Mass Spectrometry Unit, Institute of Molecular and Cellular Biology of Rosario, Rosario, Argentina · Funded by Grant PICT 2019-02971 (Agencia I+D+i)., Volkmar N; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland., Momenzadeh A; Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, California, USA., Peters-Clarke TM; Department of Pharmaceutical Chemistry, University of California-San Francisco., Egbert SB; Department of Chemistry, University of Manitoba, Winnipeg, Cananda., Kreimer S; Smidt Heart Institute, Cedars Sinai Medical Center; Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center., Doud EH; Center for Proteome Analysis, Indiana University School of Medicine, Indianapolis, Indiana, USA., Crook OM; Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom., Yadav AK; Translational Health Science and Technology Institute · Funded by Grant BT/PR16456/BID/7/624/2016 (Department of Biotechnology, India); Grant Translational Research Program (TRP) at THSTI funded by DBT., Vanuopadath M; School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam-690 525, Kerala, India · Funded by Department of Health Research, Indian Council of Medical Research, Government of India (File No.R.12014/31/2022-HR)., Mayta ML; School of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martín 3103, Argentina; Molecular Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina., Duboff AG; Department of Chemistry, University of Washington · Funded by Summer Research Acceleration Fellowship, Department of Chemistry, University of Washington., Riley NM; Department of Chemistry, University of Washington · Funded by National Institutes of Health Grant R00 GM147304., Moritz RL; Institute for Systems biology, Seattle, WA, USA, 98109 · Funded by National Institutes of Health Grants R01GM087221, R24GM127667, U19AG023122, S10OD026936; National Science Foundation Award 1920268., Meyer JG; Department of Computational Biomedicine, Cedars Sinai Medical Center · Funded by National Institutes of Health Grant R21 AG074234; National Institutes of Health Grant R35 GM142502.
Jazyk: angličtina
Zdroj: ArXiv [ArXiv] 2023 Nov 13. Date of Electronic Publication: 2023 Nov 13.
Abstrakt: 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 to aid the novice and experienced researcher. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this work to serve as a basic resource for new practitioners in the field of shotgun or bottom-up proteomics.
Databáze: MEDLINE