Quantitative Proteomics of Changes in Energy Metabolism-Related Proteins in Atrial Tissue From Valvular Disease Patients With Permanent Atrial Fibrillation

Tu, Tao; Zhou, Shenghua; Liu, Zhenjiang; Li, Xuping; Liu, Qiming

doi:10.1253/circj.cj-13-1365

Cited by 52 publications

(42 citation statements)

References 45 publications

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“…We instead developed a PRM-based method to quantify pSer825 in vivo: a sortilin peptide library was generated using a stable isotope-labeled cell-free synthesized full-length sortilin standard atrium, from patients with valvular disease with and without atrial fibrillation. 47 In the latter study, the left atrial tissues of atrial fibrillation patients exhibited a decrease in several proteins related to energy metabolism, such as electron transport and ATP metabolism, demonstrating that the proteome can be a readout for the electrical status of the atrium. Itou et al from our laboratory investigated the processes that regulate osteoclastogenesis using the TMT method.…”

Section: Tandem Mass Taggingmentioning

confidence: 82%

Current Trends and Future Perspectives of State-of-the-Art Proteomics Technologies Applied to Cardiovascular Disease Research

Singh

Aikawa

2016

Circ J

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The ongoing development of MS is in part influenced by the drive to identify and quantify as many proteins as possible in a given sample. 1,15-17 A major challenge in proteomics, however, is that the dynamic range of a typical deep sequencing analysis (5-6 orders in magnitude) does not reflect the more extensive dynamic range of protein abundance that is as extensive as 12 orders in plasma. 18-20 In addition, cytoskeletal and extracellular matrix proteins dominate samples, masking the less abundant transcription factors and signaling molecules that are usually of interest. 1,18,19 Depletion of these highly abundant proteins, such as albumin from plasma, is required to sequence deep into the proteome ( Figure 1C). 21-23 Also, the less abundant proteins can be enriched by cellular fractionation methods such as those that separate cellular compartments or those that use immunopurification strategies ( Figure 1C). 24, 25 The dynamic range capabilities of MS continually improve, but the identification and quantification of low-abundance proteins still depend on sample preparation procedures that shift these low signals into the detection range of the instrument either by depletion and/or enrichment approaches.any developments in the field of proteomics have come from the yeast model system 1-3 and from cancer research ( Figure 1A). In addition, immortalized cells (eg, HeLa, HEK293T, RAW264.7, THP-1) have provided mass spectrometrists ample protein with limited variability across biological replicates, factors that are important to establish technical reproducibility when novel workflows are being developed. The cardiovascular sciences have also influenced and benefited from developments in unbiased and targeted mass spectrometry (MS) approaches ( Figure 1B). Research pertaining to the heart and its metabolism, 4,5 extracellular matrix remodeling 6,7 posttranslational modification in vascular development. 8 lipoprotein content and metabolism, 9-11 and platelet function 12,13 have thrived as a result of the application of MS technologies. Recently, cardiovascular disease research has taken advantage of the readily accessible plasma pool for biomarker-and target-based studies. Tissues affected by heart failure, atherosclerosis and aortic aneurysms are in direct contact with the circulatory system, which increases the likelihood that proteins either causal or consequential to these pathologies can be detected in plasma. The use of mass spectrometry (MS)-dependent protein research is increasing in the cardiovascular sciences. A major reason for this is the versatility of and ability for MS technologies to accommodate a variety of biological questions such as those pertaining to basic research and clinical applications. In addition, mass spectrometers are becoming easier to operate, and require less expertise to run standard proteomics experiments. Nonetheless, despite the increasing interest in proteomics, many non-expert end users may not be as familiar with the variety of mass spectrometric tools and workflows available...

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Section: Tandem Mass Taggingmentioning

confidence: 82%

Current Trends and Future Perspectives of State-of-the-Art Proteomics Technologies Applied to Cardiovascular Disease Research

Singh

Aikawa

2016

Circ J

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“…Using these methods we can evaluate the different amounts of 1,000 or more proteins in crude samples. 1, 2 Comprehensive quantitative evaluation of the amount of protein gives valuable information that cannot be obtained by the evaluation of the level of expression of mRNA; for example, information on the degradation or transport of proteins. Specifically, determination of marker genes contained in the blood cannot be performed other than by mass spectrometry.…”

Section: Usefulness and Limitation Of Protein Mass Analysismentioning

confidence: 99%

Usefulness and Limitation of Protein Mass Analysis

Takashima

2015

Circ J

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“…9 Usually, these tags are incorporated via the reaction of primary amines of peptide N-termini and lysine residues with a reactive NHS-ester group of the tagging reagent. Whereas labeling reactions at the levels of isolated proteins or peptides derived from a proteolytic digestion are well established and applied to tackle various research questions, [10][11][12][13][14][15][16][17] the introduction of tandem mass tags at the level of intact cells has not been reported yet, even though labeling of whole cells with amine-reactive reagents is widely used and described. In the context of gel-based proteome analysis, for example, Mayrhofer et al performed labeling of intact cells with amine-reactive CyDye DIGE fluorophors enabling for a specific and more sensitive quantification of surface proteins.…”

Section: Introductionmentioning

confidence: 99%

NHS-based Tandem Mass Tagging of Proteins at the Level of Whole Cells: A Critical Evaluation in Comparison to Conventional TMT-Labeling Approaches for Quantitative Proteome Analysis

et al. 2017

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Tandem mass tags (TMT) are usually introduced at the levels of isolated proteins or peptides. Here, for the first time, we report the labeling of whole cells and a critical evaluation of its performance in comparison to conventional labeling approaches. The obtained results indicated that TMT protein labeling using intact cells is generally possible, if it is coupled to a subsequent enrichment using anti-TMT antibody. The quantitative results were similar to those obtained after labeling of isolated proteins and both were found to be slightly complementary to peptide labeling. Furthermore, when using NHS-based TMT, no specificity towards cell surface proteins was observed in the case of cell labeling. In summary, the conducted study revealed first evidence for the general possibility of TMT cell labeling and highlighted limitations of NHS-based labeling reagents. Future studies should therefore focus on the synthesis and investigation of membrane impermeable TMTs to increase specificity towards cell surface proteins.

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Quantitative Proteomics of Changes in Energy Metabolism-Related Proteins in Atrial Tissue From Valvular Disease Patients With Permanent Atrial Fibrillation

Cited by 52 publications

References 45 publications

Current Trends and Future Perspectives of State-of-the-Art Proteomics Technologies Applied to Cardiovascular Disease Research

Current Trends and Future Perspectives of State-of-the-Art Proteomics Technologies Applied to Cardiovascular Disease Research

Usefulness and Limitation of Protein Mass Analysis

NHS-based Tandem Mass Tagging of Proteins at the Level of Whole Cells: A Critical Evaluation in Comparison to Conventional TMT-Labeling Approaches for Quantitative Proteome Analysis

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