Harnessing chromatographic information in proteomics: comprehensive coverage of peptide post-translational and chemical modifications

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Rapid developments in bioanalytical chemistry have provided enormous benefits for many applied fields of modern science including human health, agriculture, energy, and environmental studies. Liquid chromatography – mass spectrometry (LC-MS) has become the method of choice for proteomic applications, as it is the most powerful technique for protein/peptide analysis. This technique relies on LC separation and MS analysis of smaller peptides: products of protein proteolytic digestion. Most of the developmental emphasis in recent years has been on the MS-component of the system. At the same time many researchers have recognized the ability of the LC component to provide very valuable information, given the ability to compute the retention properties of analyzed molecules. Overall this makes LC-MS a “double-edged sword”, where the outcomes from both methods can be used to improve the analysis output and design of the methods themselves. Several research teams have been developing peptide retention prediction models. My laboratory has been at the forefront of these developments: our Sequence Specific Retention Calculator (SSRCalc) model has become a benchmark tool in the field, attracting attention both from the proteomic/chromatographic community and from major vendors of proteomics equipment and software.