Advances and Challenges in Liquid Chromatography-Mass Spectrometry-based Proteomics Profiling for Clinical Applications

Qian, Weijun; Jacobs, Jon; Liu, Tao; Camp, David G.; Smith, Richard D.

doi:10.1074/mcp.m600162-mcp200

Cited by 327 publications

(294 citation statements)

References 121 publications

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“…14,15 While albumin, the most abundant plasma protein, accounts for ∼60% of the plasma protein weight, this number increases to 96%whenthe12mostabundantplasmaproteinsareconsidered. 14,15 Thus, the discovery of very low abundance glycated proteins represents the proverbial "needle in a haystack".…”

Section: Discussionmentioning

confidence: 99%

“…This trend is more apparent for the glycated proteins from whole plasma than for the glycated proteins from the low-abundance protein fraction of plasma (data not shown). A possible explanation for this observation is that low-abundance proteins, which have higher turn-over rates compared with the classical plasma proteins and account for less than 4% of the plasma protein weight, 15 do not accumulate significant amounts of the Amadori compound before in vivo proteolytic digestion. Similarly, the observed quantitative difference (based on HPLCUV) in levels of enriched glycated plasma peptides was not as readily distinguished among the three sample groups as the enrichment on the protein level (data not shown).…”

Section: Bac Enrichment Of Glycated Peptidesmentioning

confidence: 99%

“…Currently, human blood plasma is the most commonly used clinical sample in such analyses, potentially including specific biomarkers for virtually every human disease as a result of either direct or indirect interaction with all the cellular components of the body, for example, tissue-or tumorspecific proteins may be released into the blood stream upon cell damage or cell death. 14,15 With an average life span of 21 days, 14 the abundant classical plasma proteins are suitable indicators for short to midterm glycemic control. In this respect, glycated albumin, which reflects the status of blood glucose more rapidly and more efficiently than glycated hemoglobin (HbA1c), 16 has been suggested as a biomarker for monitoring midterm glycemic control.…”

Section: Introductionmentioning

confidence: 99%

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Proteomic Profiling of Nonenzymatically Glycated Proteins in Human Plasma and Erythrocyte Membranes

et al. 2008

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Nonenzymatic glycation of peptides and proteins by D-glucose has important implications in the pathogenesis of diabetes mellitus, particularly in the development of diabetic complications. In this work, we report the first proteomics-based characterization of nonenzymatically glycated proteins in human plasma and erythrocyte membranes from individuals with normal glucose tolerance, impaired glucose tolerance, and type 2 diabetes mellitus. Phenylboronate affinity chromatography was used to enrich glycated proteins and glycated tryptic peptides from both human plasma and erythrocyte membranes. The enriched peptides were subsequently analyzed by liquid chromatography coupled with electron transfer dissociation-tandem mass spectrometry, resulting in the confident identification of 76 and 31 proteins from human plasma and erythrocyte membranes, respectively. Although most of the glycated proteins could be identified in samples from individuals with normal glucose tolerance, slightly higher numbers of glycated proteins and more glycation sites were identified in samples from individuals with impaired glucose tolerance and type 2 diabetes mellitus.

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Section: Discussionmentioning

confidence: 99%

Section: Bac Enrichment Of Glycated Peptidesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Proteomic Profiling of Nonenzymatically Glycated Proteins in Human Plasma and Erythrocyte Membranes

et al. 2008

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“…In proteomics, diseased tissue samples or proximal fluids are often a more straightforward material for analysis to reach clinically relevant results due to higher analyte concentrations compared to plasma and serum 1,2 which, because of dilution and clearance, carry lower concentration of pertinent proteins. However, it has been shown that, following tissue sampling, substantial alterations of the proteome occurs.…”

Section: Introductionmentioning

confidence: 99%

Heat Stabilization of the Tissue Proteome: A New Technology for Improved Proteomics

et al. 2009

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After tissue or body fluid sampling, proteases and other protein-modifying enzymes can rapidly change composition of the proteome. As a direct consequence, analytical results will reflect a mix of in vivo proteome and ex vivo degradation products. Vital information about the presampling state may be destroyed or distorted, leading to variation between samples and incorrect conclusions. Sample stabilization and standardization of sample handling can reduce or eliminate this problem. Here, a novel tissue stabilization system which utilizes a combination of heat and pressure under vacuum was used to stop degradation in mouse brain tissue immediately after sampling. It was found by biochemical assays that enzymatic activity was reduced to background levels in stabilized samples. Western blot analysis confirmed that post-translational phosphorylations of analyzed proteins were stable and conserved for up to 2 h at room temperature and that peptide extracts were devoid of abundant protein degradation fragments. The combination of reduced complexity and proteolytic inactivation enabled mass spectrometric identification of several neuropeptides and endogenous peptides including modified species at higher levels compared to nonstabilized samples. The tissue stabilizing system ensures reproducible and rapid inactivation of enzymes. Therefore, the system provides a powerful improvement to proteomics by greatly reducing the complexity and dynamic range of the proteome in tissue samples and enables enhanced possibilities for discovery and analysis of clinically relevant protein/peptide biomarkers.

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“…(LC-MS/MS), for greatly improved speed and efficiency. The high throughput and sensitive nature of this technique has made it an increasingly popular approach for (comparative) proteome profiling (Link et al, 1999;Qian et al, 2006).…”

Section: Complementing 2-de: the Emergence Of Non-gel Based Approachesmentioning

confidence: 99%

Two-dimensional gel electrophoresis in bacterial proteomics

et al. 2012

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Two-dimensional gel electrophoresis (2-DE) is a gel-based technique widely used for analyzing the protein composition of biological samples. It is capable of resolving complex mixtures containing more than a thousand protein components into individual protein spots through the coupling of two orthogonal biophysical separation techniques: isoelectric focusing (first dimension) and polyacrylamide gel electrophoresis (second dimension). 2-DE is ideally suited for analyzing the entire expressed protein complement of a bacterial cell: its proteome. Its relative simplicity and good reproducibility have led to 2-DE being widely used for exploring proteomics within a wide range of environmental and medically-relevant bacteria. Here we give a broad overview of the basic principles and historical development of gel-based proteomics, and how this powerful approach can be applied for studying bacterial biology and physiology. We highlight specific 2-DE applications that can be used to analyze when, where and how much proteins are expressed. The links between proteomics, genomics and mass spectrometry are discussed. We explore how proteomics involving tandem mass spectrometry can be used to analyze (post-translational) protein modifications or to identify proteins of unknown origin by de novo peptide sequencing. The use of proteome fractionation techniques and non-gel-based proteomic approaches are also discussed. We highlight how the analysis of proteins secreted by bacterial cells (secretomes or exoproteomes) can be used to study infection processes or the immune response. This review is aimed at non-specialists who wish to gain a concise, comprehensive and contemporary overview of the nature and applications of bacterial proteomics.

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Advances and Challenges in Liquid Chromatography-Mass Spectrometry-based Proteomics Profiling for Clinical Applications

Cited by 327 publications

References 121 publications

Proteomic Profiling of Nonenzymatically Glycated Proteins in Human Plasma and Erythrocyte Membranes

Proteomic Profiling of Nonenzymatically Glycated Proteins in Human Plasma and Erythrocyte Membranes

Heat Stabilization of the Tissue Proteome: A New Technology for Improved Proteomics

Two-dimensional gel electrophoresis in bacterial proteomics

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