Proteome analysis heavily relies on a broad mixture of analytical techniques, starting from sample preparation, to separation and enrichment and last but certainly not in the least mass spectrometry. Through developments in these enabling technologies MS-based proteomics has matured and start to deliver biological relevant information. Still our measurements are still far from comprehensive, and the optimal matured workflow does not (yet) exist for proteomics. In my laboratory we try to explore alternative complementary and/or hybrid methods to explore better the richness of the proteome. In this lecture I will primarily focus on alternative and hybrid peptides fragmentation technologies, such as higher energy collision induced dissociation (HCD) electron transfer induced dissociation (ETD) and ultra-violet photodissociation (UVPD) and hybrid combinations thereof (EThcD). In more detail I will describe methods enabling 1) enhanced peptide coverage based on a combination of HCD and ETD that leads to improved analysis of phosphopeptides, MHC peptides 1,2, protein disulfide bridges 3, and middle-down proteomics analysis 2) implementation of UVPD on an Orbitrap for improved phosphopeptide site analysis and 3) hybrid methods essential for proteome-wide cross-linking studies in human cell lysates4. 1. Mommen et al. PNAS 111 (2013) 4507-4512 2. Marino et al. JACS 137 (2015) 10922-10925 3. Liu et al. Mol Cell Prot 13 (2014) 2776-2786 4. Liu et al. Nature Methods 12 (2015) in press

Award Address (Frank H. Field and Joe L. Franklin Award for Outstanding Achievement in Mass Spectrometry sponsored by Waters Corporation). Exploiting electron impact phenomena on gaseous ions to create hybrid peptide fragmentation methods of usage in structural proteomics and signaling

251st National Meeting (2016)

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