PXD019819

PXD019819 is an original dataset announced via ProteomeXchange.

Title	Identification of spliced peptides in pancreatic islets uncovers errors leading to false assignments
Description	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.
HostingRepository	PRIDE
AnnounceDate	2021-02-11
AnnouncementXML	Submission_2021-02-11_01:50:34.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD019819
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Cheryl Lichti
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	dehydrated residue; monohydroxylated residue; acetylated residue; monosodium salt; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF; Orbitrap Fusion Lumos; TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-16 16:34:30	ID requested
⏵ 1	2021-02-11 01:50:35	announced

Lichti CF, Identification of spliced peptides in pancreatic islets uncovers errors leading to false assignments. Proteomics, 21(7-8):e2000176(2021) [pubmed]

submitter keyword: MHC-I peptidome, crinosomes

Cheryl Lichti
contact affiliation	Washington University
contact email	clichti@wustl.edu
lab head
Cheryl Lichti
contact affiliation	Washington University
contact email	clichti@wustl.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD019819
     1. Label: PRIDE project
     2. Name: Identification of spliced peptides in pancreatic islets uncovers errors leading to false assignments