Mass spectrometry-based peptide quantification: applications and limitations

Abstract

In various areas of research, proteomics and particularly the quantification of proteins and peptides renders a useful addition to biochemical experiments. The range of possible applications varies from supervision of concentration changes of relevant proteins during biogenesis to differential proteomics approaches, distinguishing, for instance, healthy and diseased states. Furthermore, mass spectrometry-based peptide quantification yields the possibility of using highly sensitive bottom-up approaches for determination of protein regulations as well as multiplexing capability. Thereby, changes in protein abundances may be linked to specific cellular states bearing the opportunity to reveal marker proteins for several diseases.

Identification of Novel Centrosomal Proteins in Dictyostelium discoideum by Comparative Proteomic Approaches

“…Furthermore, the iTRAQ-label, required for relative quantification by mass spectrometry, is introduced at a rather late stage of the analysis. 11 Thereby, specific protein loss prior to pooling of the respective samples cannot be fully excluded and the identification of an utmost complete protein inventory of an entire cell organelle by a single proteomics approach is rather difficult.…”

Derivatisation of arginine residues with malondialdehyde for the analysis of peptides and protein digests by LC‐ESI‐MS/MS

“…1 Chemical modification of proteins has found numerous applications for the enrichment of subclasses of peptides/proteins from a sample and for many other purposes. 2 Ingenious methods during the sample preparation stage allow researchers to perform relative or absolute quantification of protein levels in multiple samples 3,4 and target post-translational modifications like phosphorylation. 5,6 Frequently, hundreds to thousands of proteins are identified in large-scale proteomic studies, in particular when multidimensional separation techniques like 2D LC are employed.…”

Development of Metrology for Modern Biology

“…After that, another research team described the use of this approach for the absolute protein quantification where a target protein was proteolyzed and quantified using LC-MS/MS with a stable isotope labeled peptide as an internal standard through (Barr et al, 1996). The rapid advances in mass spectrometry based proteomics have greatly improved the analytical sensitivity and made peptide based analysis possible to detect targets in a complex matrix (Anderson et al, 2004;Gerber et al, 2003;Kirkpatrick et al, 2005;Mayya et al, 2006;Putz et al, 2005;Stahl-Zeng et al, 2007). The principal of this approach is that the isotopically labeled synthetic peptide is spiked to the sample, and the mixture is subjected to enzymatic digestion followed by LC-MS/MS.…”