Open Search of Peptide Glycation Products from Tandem Mass Spectra

Abstract

Identification of chemically modified peptides in mass spectrometry (MS)-based glycation studies is a crucial yet challenging task. There is a need to establish a mode for matching tandem mass spectrometry (MS/MS) data, allowing for both known and unknown peptide glycation modifications. We present an open search approach that uses classic and modified peptide fragment ions. The latter are shifted by the mass delta of the modification. Both provide key structural information that can be used to assess the peptide core structure of the glycation product. We also leverage redundant neutral losses from the modification side chain, introducing a third ion class for matching referred to as characteristic fragment ions. We demonstrate that peptide glycation product MS/MS spectra contain multidimensional information and that most often, more than half of the spectral information is ignored if no attempt is made to use a multi-step matching algorithm. Compared to regular and/or modified peptide ion matching, our triple-ion strategy significantly increased the median interpretable fraction of the glycation product MS/MS spectra. For reference, we apply our approach for Amadori product characterization and identify all established diagnostic ions automatically. We further show how this method effectively applies the open search concept and allows for optimized elucidation of unknown structures by presenting two hitherto undescribed peptide glycation modifications with a delta mass of 102.0311 and 268.1768 Da. We characterize their fragmentation signature by integration with isotopically labeled glycation products, which provides high validity for non-targeted structure identification.

Discovery of Glycation Products: Unraveling the Unknown Glycation Space Using a Mass Spectral Library from In Vitro Model Systems

“…As indicated in Figure C, the most shared modifications found across various model systems are 162.053 Da followed by 144.042, 126.032, and 180.064 Da, corresponding to ARP (C 6 H 10 O 5 , 162.0528 Da), its dehydration products ARP – H 2 O (C 6 H 8 O 4 , 144.0423 Da), ARP – 2H 2 O (C 6 H 6 O 3 , 126.0317 Da), and Glc addition (C 6 H 12 O 6 , 180.0634 Da). Similar glycation modifications were observed with high abundance in peptide-Glc model systems . This aligns with general MR reaction pathway that starts with the formation and degradation of the ARP .…”

“…Similar glycation modifications were observed with high abundance in peptide-Glc model systems. 51 This aligns with general MR reaction pathway that starts with the formation and degradation of the ARP. 12 The modification at 42.0109 Da could be attributed to acetylation (C 2 H 2 O, 42.0106 Da).…”