PXD040820

PXD040820 is an original dataset announced via ProteomeXchange.

Title	Impact of bioinformatic search parameters for peptide identification and their post-translational modifications: case study of proteolyzed gelatines from beef, pork and fish.
Description	Bioinformatic software allowing the identification of peptides by confrontation of peptide fragmentation spectra obtained by mass spectrometry against targeted databases or directly by de novo sequencing are now mandatory in peptidomics/proteomics approach. The programming of the identification software requires specifying, among other things, the mass measurement accuracy of the instrument, the digestion enzyme used with the number of missed cleavages allowed. Moreover, these software are able to identify a large number of post-translational modifications (PTMs). However, peptide- and PTM-identifications are challenging in the agrofood field due to a non-specific cleavage site of physiological- or food-grade-enzymes used and the number and location of PTMs. In this study, we show the importance of adapted software programming to obtain a better peptide- and PTM-identification rate in the agrofood field. A gelatine product and one industrial gelatine hydrolysate from three different sources (beef, pork or fish), each digested by simulated gastro-intestinal digestion, by MS-grade trypsin or both were used to perform the comparisons. Two points were illustrated i) the impact of the set-up of specific enzyme- versus no specific-enzyme use and ii) the impact of a maximum 6 PTMs allowed per peptides against routinely 3. Prior knowledge of the composition of the raw proteins is an important asset for a better identification of peptide sequences.
HostingRepository	PRIDE
AnnounceDate	2026-08-17
AnnouncementXML	Submission_2026-08-16_17:40:04.137.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Barbara Deracinois
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: NEWT:9913; scientific name: Sus scrofa domesticus (domestic pig); NCBI TaxID: NEWT:9825;
ModificationList	iodoacetamide derivatized residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-13 09:59:06	ID requested
⏵ 1	2026-08-16 17:40:05	announced

Ambli M, Deracinois B, Jenequin AS, Ravallec R, Cudennec B, Flahaut C, Impact of Bioinformatics Search Parameters for Peptides' Identification and Their Post-Translational Modifications: A Case Study of Proteolysed Gelatines from Beef, Pork, and Fish. Foods, 12(13):(2023) [pubmed]

10.3390/foods12132524;

submitter keyword: mass spectrometry, post-translational modifications.,bioinformatics, gelatine, hydroxyproline, hydrolysate

Jean Louis HILBERT
contact affiliation	UMR Transfrontaliere BioEcoAgro N° 1158, Univ. Artois, Univ. Lille, INRAe, Univ. Liege, UPJV, JUNIA, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 62300 Lens, France.
contact email	jean-louis.hilbert@univ-lille.fr
lab head
Barbara Deracinois
contact affiliation	UMRT BioEcoAgro
contact email	barbara.deracinois@univ-lille.fr
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD040820
     1. Label: PRIDE project
     2. Name: Impact of bioinformatic search parameters for peptide identification and their post-translational modifications: case study of proteolyzed gelatines from beef, pork and fish.