Back to the future-The value of single protein species investigations

Abstract

In proteomics, in the past years, there was a focus on high throughput and reaching of large numbers of identified proteins with the basic discourse of protein expression. To avoid the impression of producing pure lists attempts are usually made to correlate proteins changed in amount between two biological situations to different pathways or protein interactions. This discourse is based on two simplifications, which limit the applicability of proteomics drastically: (i) it is sufficient to quantify a protein from several enzymatic digestion products; (ii) a biological situation is sufficiently described, if a peptide with its PTM is identified, resulting in long lists of modified peptides with data amounts, which are not anymore made accessible for the reader of a publication. The elucidation of N-terminal methylation of proteasome subunit Rpt1 in yeast by Kimura et al. (Proteomics 2013, 13, 3167-3174), which represents the focus on one protein, shows the value of solid chemical analysis with a complete data documentation and paves the way to proteomics based on the protein speciation discourse.

Homogenization of tissues via picosecond-infrared laser (PIRL) ablation: Giving a closer view on the in-vivo composition of protein species as compared to mechanical homogenization

“…Due to a dysregulation of the fine-tuned protein processing machinery or pathological effects such as oxidative stress, proteins are modified, potentially leading to harmful protein species [4] , [5] , [6] , [7] . Therefore, to better understand disease-related proteomes on a functional level, tissue proteome must be analyzed with respect to protein species [8] , [9] , [10] . In the past decade, significant progress has been made in the field of proteomics that have now made protein species accessible to be studied.…”

Comparative proteomics analysis of host cells infected with Brucella abortusA19

“…Among the identified proteins, several proteins (Fig. 2) were identified in more than one spot, we speculate that these proteins may be proteolytically or environmentally processed, modified, and/or transported to organelles or outside the cell, spliced, or degraded [18,36]. Interestingly, Thiede et al [37] found that more than 50% of the spots investigated contained more than one protein.…”

Fourteen years of plant proteomics reflected in Proteomics: Moving from model species and 2DE‐based approaches to orphan species and gel‐free platforms

“…Finally, within this section, we will mention some papers included in the proteinomics category. Proteomics through simple protein extracts’ preparation and a combination of chemical analysis and data documentation offers the possibility for protein speciation discourse, as reviewed by Jungblut . The analysis of different gene products (splicing variants, PTMs), allelic variants, and isoforms (it is curious to note how these terms are used in the literature in a rather confused way and sometimes as synonymous) is of great relevance for biological knowledge, and this thought requires keeping our mind away from the high‐throughput concept.…”