The comparison between 2DE‐MS and bottom‐up LC‐MS demands high‐end techniques for both technologies

Abstract

In contrast to bottom-up LC-MS only 2DE-MS can separate and detect a huge number of human protein species. Kwiatkowski et al. (in this issue) established parameters to estimate the amount of protein speciation for each human protein. Proteins identified in 2DE-MS approaches showed more protein speciation than in bottom-up LC-MS. The authors state that protein speciation is likely to increase the chance of proteins to be determined in 2-DE/MS, though admitting that low-sensitivity 2DE-MS methods were used in this study. In agreement with Kwiatkowski et al., we are convinced that the difference between 2DE-MS and bottom-up LC-MS will disappear, if high-resolution 2DE is combined with identification by a high-sensitivity LC-Orbitrap-MS. Meta-analysis of proteomic data is surely a promising tool, though the technological progress in 2DE and MS has to reach a plateau to enable useful comparisons.

Personalized Drug Therapy: Innovative Concept Guided With Proteoformics

“…For ESI-LC/MS analysis, tandem mass spectrometry data are produced and used for search protein database for identification of protein amino acid sequence and PTMs. For 2DE-LC/MS approach, it has superhigh throughput in analysis human proteoforms, which can reach up to half million to one million of proteoforms ( 23 , 24 , 61 , 63 ). 2DE coupled with TD-MS (2DE-TD-MS): For 2DE-TD-MS approach, the common procedure is that the 2DE-separated therapeutic proteins or drug-targeted proteins are purified, and then the purified proteins are subjected to TD-MS analysis.…”

“…For ESI-LC/MS analysis, tandem mass spectrometry data are produced and used for search protein database for identification of protein amino acid sequence and PTMs. For 2DE-LC/MS approach, it has superhigh throughput in analysis human proteoforms, which can reach up to half million to one million of proteoforms ( 23 , 24 , 61 , 63 ).…”