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 2011–2014

Abstract

This review article expands on the previous one (S. Selvaraju and Z. El Rassi, Electrophoresis 2012, 33, 74-88) by reviewing pertinent literature in the period extending from early 2011 to present. As the previous review article, the present one is concerned with proteomic sample preparation (e.g., depletion of high abundance proteins, reduction of the protein dynamic concentration range, enrichment of a particular sub-proteome), and the subsequent chromatographic and/or electrophoretic pre-fractionation prior to peptide separation and identification by LC-MS/MS. This review article is distinguished from its second version published in Electrophoresis 2012, 33, 74-88 by expanding on capturing/enriching sub-phosphoproteomes by immobilized metal affinity chromatography and metal oxide affinity chromatography. Seventy-seven papers published in the period extending from mid 2011 to the present have been reviewed. By no means this review article is exhaustive, given the fact that its aim is to give a concise treatment of the latest developments in the field.

Sensitive measurement of total protein phosphorylation level in complex protein samples

“…Before performing a phosphoproteomic experiment, it is important to estimate how much phosphorylation is in a test sample so that a proper sample preparation protocol can be applied, including potential fractionations and phosphopeptide enrichment. 25, 36, 37 Samples like yeast and plant cell extracts are typically lower in phosphorylation than human samples and thus increasing the starting amount of yeast or plant samples for analysis is desirable for a global phosphoproteomic profiling. However, there is no simple solution to estimate the starting sample amount except performing a series of preliminary experiments, which can be both costly and inefficient.…”

Clinical mass spectrometry proteomics (cMSP) for medical laboratory: What does the future hold?

“…However, comparisons between these methods showed that HAP removal was more efficient when an ACN-precipitation step was performed [34]. In the case of proteins present in very low concentrations, it may be necessary to enrich the analyte using more advanced methods [35]. For instance, HAP can be removed before the digestion step using the commercially available immunoaffinity columns now covering up to 20 proteins.…”

Cardiovascular proteomics in the era of big data: experimental and computational advances

“…Whereas the now-dethroned 2D electrophoresis was limited to detecting a few hundred proteins, contemporary LC–MS experiments can resolve peptides from >10,000 proteins to allow their identification and quantification. Since 2001, separation science has led in a relentless pursuit to increase protein coverage [12, 13], with the success of strong cation exchange-reversed phase based MudPIT approaches followed successively by other 2D-LC approaches including reversed-phase-reversed-phase separation [14] as well as very-long separation columns with high peak capacity, nano-scale microfluidic devices driven by ultra-high pressure LC systems [15] and capillary electrophoresis separation (see [16, 17] for reviews on separation science developments). By separating the peptide samples into smaller subset based on their chemistry, a simpler mixture of peptides is introduced into the mass spectrometer in any given time, which decreases ion competition and increases sensitivity.

Fig.

…”