Correlation between peak capacity and protein sequence coverage in proteomics analysis by liquid chromatography-mass spectrometry/mass spectrometry

Liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) allows the acquisition of a vast amount of analytical data in the aim of identifying peptides and proteins. Difficulties arise when attempting to identify proteins from the results of analyses of their peptide digests. We investigated possible quantitative correlations between the peak capacity achieved in chromatographic analyses and the protein sequence coverage. For this purpose, we used high performance liquid chromatography (HPLC) columns packed with fully and superficially porous (shell) particles of average sizes ranging from 2.6 to 15μm in diameter. We found that the sequence coverage of bovine serum albumin obtained with a 10-min gradient elution run on a column packed with 2.6μm shell particles is greater than that provided by 40-min gradients run on columns packed with 15 or 10μm particles and equal to those yielded by the same 40-min gradient run on columns packed with 3 and 5μm particles.