Identification of spliced peptides in pancreatic islets uncovers errors leading to false assignments

ABSTRACT: Spliced peptides have been identified in the class I major histocompatibility complex (MHC) peptidomes of several tumors and have emerged as novel autoantigens that can stimulate highly specific T cells. A special class of spliced peptides, hybrid insulin peptides (HIPs), bound to histocompatibility class II molecules are potential autoantigens in the development and progression of type 1 diabetes (T1D). Recently, our laboratory demonstrated that HIPs are formed during insulin granule degradation in crinosomes isolated from nonobese diabetic (NOD) mice. In our current work, we have expanded this study to examine crinosomes from two other nondiabetic mouse strains, B6 and B6.g7, to prove that HIP formation is a consequence of normal insulin granule degradation and is independent of T1D. During the course of this work, we discovered that modified peptides comprise a significant source of false positive HIP assignments in our bioinformatics pipeline and posited that similar factors could explain the high percentage of spliced peptides in recent mass spectrometry-based studies of various tumor immunopeptidomes. Therefore, we re-analyzed data files from two recent studies that reported a large percentage of spliced peptides and demonstrated that both analyses contain many spectra erroneously assigned to spliced peptide sequences.

INSTRUMENT(S): Orbitrap Fusion Lumos, TripleTOF 5600, Q Exactive HF

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Cell Culture, Pancreatic Islet Beta Cell, Fibroblast

SUBMITTER: Cheryl Lichti  

LAB HEAD: Cheryl Lichti

PROVIDER: PXD019819 | Pride | 2021-02-11

REPOSITORIES: Pride