Neuroproteomics — LC-MS Quantitative Approaches

Abstract

Neuroproteomics is a scientific field that aims to study all the proteins of the central nervous system, their expression, function, and interactions. The central nervous system is intricate and heterogeneous, and the study of its proteome is consequently complex, with many biological questions still requiring deep investigation. For this, mass spectrometry approaches, most often coupled with liquid chromatography (LC-MS), have been the number one choice in proteomics, and over the years it has added many important findings to the field. At this point it is important that proteomics turns to the quantitative expression of proteins instead of only identifying which proteins are present in a given sample, much because the most important alterations may be slight alterations in the quantity of a protein in a given situation. Therefore, many LC-MS quantitative approaches have been developed relying on the labeling of the proteins or even by using label-free techniques.In this chapter, a brief description of the principles and procedures of several approaches used for relative and absolute, targeted and untargeted quantification of proteins is presented, complemented with a literature revision of their application in the neurosciences field.

oxSWATH: An integrative method for a comprehensive redox-centered analysis combined with a generic differential proteomics screening

“…Thus allowing to isolate the fragmentation spectrum of very similar peptides within different SWATH windows and to obtain the quantification of those peptides at the fragmentation levels without interference, as performed in MRM. In addition to that, the SWATH-MS pipeline comprises an informed/targeted data analysis (extraction of quantitative data) limited to the peptides confidently identified in a previous conventional proteomics approach, ensuring that potentially all the proteins/peptides that have been identified could be quantified [18] , [19] . These characteristics of the SWATH-MS make it an appealing strategy to quantify PTMs, in particular for the study of cysteine modifications using differential alkylation that relies on the tagging of the cysteines with different reagents to induce a mass shift between reduced and oxidized peptides.…”

Systematic Review and Meta-Analysis of Mass Spectrometry Proteomics Applied to Human Peripheral Fluids to Assess Potential Biomarkers of Schizophrenia

“…The CNS proteome can change even with minimal alterations in the normal course of its development and/or function [39,40]. To understand the alterations and the mechanisms related to a disorder, we should analyze qualitative and quantitative changes in the complete set of proteins encoded by an organism's genome at different or specific points in time [23,41]. Proteomics can be a powerful tool since it can give a real-time evaluation of an individual state, health vs. disease, and, in an ideal scenario, predict the susceptibility to develop a specific mental disorder [4,39].…”

Recent Advances in Proteomics Research

“…DiART was designed as a less expensive 6-plex isobaric labeling reagent to label amine groups of proteins and peptides and is, once more, based in a very similar structure as iTRAQ and TMT using an amine-reactive group, a balancer group, and a reporter group in the mass range of 114-119 Da. [111,117] In a study comparing DiART and iTRAQ, the authors found that DiART leads to more intense reporter ions and consequently less ratio compression, however with the DiART approach, the common fragmentation method is not advisable due to easy reporter ion fragmentation [118]. DiART has also proven to be compatible and valuable for PTM analysis as quantitative phosphoproteomic studies [119].…”