PNNL

Abstract

Introduction Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been a leading method for proteomics analysis since the turn of the century. The clear advantages provided by LC-MS/MS are offset by significant disadvantages, including cost. Recently, several emerging non-mass spectrometric methods have become more visible, but little information is available about their capacity to analyze the complex mixtures that are routine for mass spectrometry. Areas Covered We review recent non-mass-spectrometric methods for sequencing proteins and peptides, including those using nanopores, sequencing by degradation, fluorescence, reverse translation, and short-epitope mapping, with comments on bioinformatics challenges, fundamental limitations, and areas where new technologies will be more or less competitive with LC-MS/MS. In addition to conventional literature searches (Web of Science database), instrument vendor websites, patents, webinars, and preprints were also consulted to give a more up-to-date picture. Expert Opinion Many of these new technologies are quite promising. However, demonstrations that they outperform mass spectrometry in terms of peptides and proteins identified have not yet been published, and astute observers note important disadvantages, especially relating to the dynamic range of single-molecule measurements of complex mixtures. However, even if the performance of emerging methods proves to be inferior to LC-MS/MS, their low cost could create a different kind of proteomics revolution: a dramatic increase in the number of biology laboratories engaging in new forms of proteomics research.