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

Abstract

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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