Top Down proteomics: Facts and perspectives

Abstract

The rise of the “Top Down” method in the field of mass spectrometry-based proteomics has ushered in a new age of promise and challenge for the characterization and identification of proteins. Injecting intact proteins into the mass spectrometer allows for better characterization of post-translational modifications and avoids several of the serious “inference” problems associated with peptide-based proteomics. However, successful implementation of a Top Down approach to endogenous or other biologically relevant samples often requires the use of one or more forms of separation prior to mass spectrometric analysis, which have only begun to mature for whole protein MS. Recent advances in instrumentation have been used in conjunction with new ion fragmentation using photons and electrons that allow for better (and often complete) protein characterization on cases simply not tractable even just a few years ago. Finally, the use of native electrospray mass spectrometry has shown great promise for the identification and characterization of whole protein complexes in the 100 kDa to 1 MDa regime, with prospects for complete compositional analysis for endogenous protein assemblies a viable goal over the coming few years.

Theory and Practice of UHPLC and UHPLC–MS

“…In contrast, when intact protein molecular ions are introduced in the MS, the strategy is called topdown (Tran et al, 2011;Catherman et al, 2014). In this case, the use of an ESI source requires coupling with a highly accurate mass analyzer for unique identification, to locate and characterize posttranslational modifications.…”

Insights into autosomal dominant polycystic kidney disease by quantitative mass spectrometry-based proteomics

“…In contrast, Btopdown proteomics^analysis characterizes entire proteins. This approach allows, among others, the study of posttranslational modification (PTM) crosstalk (Catherman et al 2014). However, because of the unique characteristics of each protein, top-down proteomics is technically rather challenging and experimental conditions have to be adopted for each protein-of-interest or each protein group-of-interest.…”

Top-down proteomics: applications, recent developments and perspectives

“…A nice review has been presented with details of different methodological approaches used so far to quantify all proteoforms present in any given snake venom [131,132]. The recent advancements in mass spectrometric instrumentation, dissociation strategies, and bioinformatic tools including top-down mass spectrometry instrumentation is increasingly attaining momentum in proteomic analysis [133][134][135][136][137][138][139][140][141][142]. More recently, Daniel P. et al was the first person who applied top-down mass spectrometry for the snake (Indonesian King Cobra, Ophiophagus Hannah) Venomic proteomics applications [143].…”