Mining the human plasma proteome with three-dimensional strategies by high-resolution Quadrupole Orbitrap Mass Spectrometry

Zhao, Yan; Chang, Cheng; Qin, Peibin; Cao, Qin; Tian, Fang; Jiang, Jing; Li, Xianyu; Yu, Wenfeng; Zhu, Yunping; He, Fuchu; Ying, Wantao; Qian, Xiaohong

doi:10.1016/j.aca.2015.11.001

Cited by 18 publications

(9 citation statements)

References 34 publications

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“…Human blood plasma has been considered as the main source of biomarkers in clinical studies as it contains circulating markers reflecting associated physiological changes . Current technologies can be used to generate detailed and quantitative proteomics profiles of samples derived from tissue, bio‐fluid and cells . Among available proteomics technologies, shotgun proteomics has been extensively used to analyze large numbers of candidate protein biomarkers associated with specific pathologies …”

Section: Introductionmentioning

confidence: 99%

Plasma Proteome Profiles of Stable CAD Patients Stratified According to Total Apo C‐III Levels

Manfredi

Chiariello

Conte

et al. 2018

Proteomics Clinical Apps

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Section: Introductionmentioning

confidence: 99%

Plasma Proteome Profiles of Stable CAD Patients Stratified According to Total Apo C‐III Levels

Manfredi

Chiariello

Conte

et al. 2018

Proteomics Clinical Apps

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“…A comparison of CPLL technology with other protein depletion strategies such as a single Seppro IgY14 immunodepletion and tandem Seppro IgY14 immunodepletion for human plasma proteome profiling has been recently reported . In each strategy, three dimensions were combined with three processes namely HAP depletion/equalization (in the first dimension), protein fractionation (in the second dimension), and LC–MS/MS analysis (in the third dimension).…”

Section: Methodologies Used To Reduce the Complexity Of Proteomic Sammentioning

confidence: 99%

Liquid‐phase based separation systems for depletion, prefractionation, and enrichment of proteins in biological fluids and matrices for in‐depth proteomics analysis—An update covering the period 2014–2016

Rassi

Puangpila

2016

Electrophoresis

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This review article is an update of our previous one by C. Puangpila, E. Mayadunne, and Z. El Rassi, Electrophoresis 2015, 36, 238-252. Similarly to the previous article, this review has two main topics, including (i) proteomic sample preparation (e.g., depletion of high-abundance proteins, reduction of the protein dynamic concentration range, and enrichment of a particular subproteome), and (ii) the subsequent chromatographic and/or electrophoretic prefractionation prior to protein separation and identification by LC-MS/MS. More than 70 papers published in the period extending from mid-2014 to the present have been reviewed. Although an effort was made to yield a comprehensive review article, one may safely state that this review article is by no means thorough, and the aim was to rather provide a concise description of the latest developments in the field.

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“…Zhao et al. used a homemade C18 GEAgel precolumn coupled with an Easy nano‐LC system as an on‐line desalting method and they compared combinations of five 3D strategies for human plasma proteome profiling. The strategies employed were proteome equalization (Strategy A), tandem removal of high‐abundance proteins by Seppro IgY14 (Strategy B), deglycosylation before high‐pH RPLC separation (Strategy D), SDS‐PAGE separation (Strategy E), and combination of strategies B, high‐pH reverse phase‐LC fractionation and positive scan LC‐MS/MS analysis (Strategy C).…”

Section: Desaltingmentioning

confidence: 99%

Sample Clean‐up Strategies for ESI Mass Spectrometry Applications in Bottom‐up Proteomics: Trends from 2012 to 2016

2017

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Bottom-up proteomics is a mass spectrometric (MS)-based approach for the characterization of peptides obtained from in-solution protein digestion. MS is favored over other methods for peptide and protein analysis because of its better sensitivity and high throughput. Inorganic ions and surfactants present in the sample or produced during tryptic digestion are detrimental in MS analysis and affect the proteome data, thus sample preparation for removal of these unwanted components has become essential. Here, we review 48 research papers on strategies for removal of salts and surfactants (in particular, SDS) prior to ESI-MS analysis in bottom-up proteomics from 2012 to 2016. The strategies were mostly based on SPE and membrane-based filter-aided sample preparation for salt and SDS removal, respectively. Some known limitations of SPE and filter-aided sample preparation procedures are that they can be time consuming, laborious, and require the use of organic solvents before a concentrated extract suitable for analysis is obtained. The development of faster analytical methods by reducing the sample preparation time and thereby, increasing sample throughput, and in a solvent-less and membrane-less operation, is a significant contribution to proteome research.

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Mining the human plasma proteome with three-dimensional strategies by high-resolution Quadrupole Orbitrap Mass Spectrometry

Cited by 18 publications

References 34 publications

Plasma Proteome Profiles of Stable CAD Patients Stratified According to Total Apo C‐III Levels

Plasma Proteome Profiles of Stable CAD Patients Stratified According to Total Apo C‐III Levels

Liquid‐phase based separation systems for depletion, prefractionation, and enrichment of proteins in biological fluids and matrices for in‐depth proteomics analysis—An update covering the period 2014–2016

Sample Clean‐up Strategies for ESI Mass Spectrometry Applications in Bottom‐up Proteomics: Trends from 2012 to 2016

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