Literature DB >> 33950486

Quantitative Mass Spectrometry-Based Proteomics: An Overview.

Svitlana Rozanova1,2, Katalin Barkovits1,2, Miroslav Nikolov3, Carla Schmidt4, Henning Urlaub3,5,6, Katrin Marcus7,8.   

Abstract

In recent decades, mass spectrometry has moved more than ever before into the front line of protein-centered research. After being established at the qualitative level, the more challenging question of quantification of proteins and peptides using mass spectrometry has become a focus for further development. In this chapter, we discuss and review actual strategies and problems of the methods for the quantitative analysis of peptides, proteins, and finally proteomes by mass spectrometry. The common themes, the differences, and the potential pitfalls of the main approaches are presented in order to provide a survey of the emerging field of quantitative, mass spectrometry-based proteomics.

Keywords:  Absolute quantification; Chemical labeling; Isotope labeling; Label-free; Mass spectrometry; Metabolic labeling; Proteomics; Relative quantification

Year:  2021        PMID: 33950486     DOI: 10.1007/978-1-0716-1024-4_8

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  126 in total

1.  Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry.

Authors:  Pavel V Bondarenko; Dirk Chelius; Thomas A Shaler
Journal:  Anal Chem       Date:  2002-09-15       Impact factor: 6.986

2.  A model for random sampling and estimation of relative protein abundance in shotgun proteomics.

Authors:  Hongbin Liu; Rovshan G Sadygov; John R Yates
Journal:  Anal Chem       Date:  2004-07-15       Impact factor: 6.986

3.  Options and considerations when selecting a quantitative proteomics strategy.

Authors:  Bruno Domon; Ruedi Aebersold
Journal:  Nat Biotechnol       Date:  2010-07-09       Impact factor: 54.908

4.  Maximizing peptide identification events in proteomic workflows using data-dependent acquisition (DDA).

Authors:  Nicholas W Bateman; Scott P Goulding; Nicholas J Shulman; Avinash K Gadok; Karen K Szumlinski; Michael J MacCoss; Christine C Wu
Journal:  Mol Cell Proteomics       Date:  2013-07-02       Impact factor: 5.911

5.  More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS.

Authors:  Annette Michalski; Juergen Cox; Matthias Mann
Journal:  J Proteome Res       Date:  2011-02-28       Impact factor: 4.466

Review 6.  Using data-independent, high-resolution mass spectrometry in protein biomarker research: perspectives and clinical applications.

Authors:  Tatjana Sajic; Yansheng Liu; Ruedi Aebersold
Journal:  Proteomics Clin Appl       Date:  2015-02-23       Impact factor: 3.494

7.  Fast Proteome Identification and Quantification from Data-Dependent Acquisition-Tandem Mass Spectrometry (DDA MS/MS) Using Free Software Tools.

Authors:  Jesse G Meyer
Journal:  Methods Protoc       Date:  2019-01-17

8.  Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues.

Authors:  Roland Bruderer; Oliver M Bernhardt; Tejas Gandhi; Saša M Miladinović; Lin-Yang Cheng; Simon Messner; Tobias Ehrenberger; Vito Zanotelli; Yulia Butscheid; Claudia Escher; Olga Vitek; Oliver Rinner; Lukas Reiter
Journal:  Mol Cell Proteomics       Date:  2015-02-27       Impact factor: 5.911

Review 9.  Shotgun proteomics and biomarker discovery.

Authors:  W Hayes McDonald; John R Yates
Journal:  Dis Markers       Date:  2002       Impact factor: 3.434

10.  Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ.

Authors:  Jürgen Cox; Marco Y Hein; Christian A Luber; Igor Paron; Nagarjuna Nagaraj; Matthias Mann
Journal:  Mol Cell Proteomics       Date:  2014-06-17       Impact factor: 5.911

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  5 in total

1.  Shotgun Proteomics Revealed Preferential Degradation of Misfolded In Vivo Obligate GroE Substrates by Lon Protease in Escherichia coli.

Authors:  Tatsuya Niwa; Yuhei Chadani; Hideki Taguchi
Journal:  Molecules       Date:  2022-06-11       Impact factor: 4.927

2.  Evaluation of acquisition modes for semi-quantitative analysis by targeted and untargeted mass spectrometry.

Authors:  Hannah M Britt; Tristan Cragnolini; Suniya Khatun; Abubakar Hatimy; Juliette James; Nathanael Page; Jonathan P Williams; Christopher Hughes; Richard Denny; Konstantinos Thalassinos; Johannes P C Vissers
Journal:  Rapid Commun Mass Spectrom       Date:  2022-07-15       Impact factor: 2.586

Review 3.  "Omic" Approaches to Bacteria and Antibiotic Resistance Identification.

Authors:  Daria Janiszewska; Małgorzata Szultka-Młyńska; Paweł Pomastowski; Bogusław Buszewski
Journal:  Int J Mol Sci       Date:  2022-08-24       Impact factor: 6.208

4.  CCIVR facilitates comprehensive identification of cis-natural antisense transcripts with their structural characteristics and expression profiles.

Authors:  Tatsuya Ohhata; Maya Suzuki; Satoshi Sakai; Kosuke Ota; Hazuki Yokota; Chiharu Uchida; Hiroyuki Niida; Masatoshi Kitagawa
Journal:  Sci Rep       Date:  2022-09-15       Impact factor: 4.996

Review 5.  Recent Developments in Clinical Plasma Proteomics-Applied to Cardiovascular Research.

Authors:  Nicolai Bjødstrup Palstrøm; Rune Matthiesen; Lars Melholt Rasmussen; Hans Christian Beck
Journal:  Biomedicines       Date:  2022-01-12
  5 in total

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