Predicting fragment intensities and retention time of iTRAQ- and TMTPro-labeled peptides with Prosit-TMT.
Fragment intensity prediction
Prosit
Retention time prediction
TMTPro
iTRAQ
Journal
Proteomics
ISSN: 1615-9861
Titre abrégé: Proteomics
Pays: Germany
ID NLM: 101092707
Informations de publication
Date de publication:
10 2022
10 2022
Historique:
revised:
22
04
2022
received:
13
02
2022
accepted:
05
05
2022
pubmed:
18
5
2022
medline:
22
10
2022
entrez:
17
5
2022
Statut:
ppublish
Résumé
Isobaric labeling increases the throughput of proteomics by enabling the parallel identification and quantification of peptides and proteins. Over the past decades, a variety of isobaric tags have been developed allowing the multiplexed analysis of up to 18 samples. However, experiments utilizing such tags often exhibit reduced identification rates and thus show decreased analytical depth. Re-scoring has been shown to rescue otherwise missed identifications but was not yet systematically applied on isobarically labeled data. Because iTRAQ 4/8-plex and the recently released TMTpro 16/18-plex share similar characteristics with TMT 6/10/11-plex, we hypothesized that Prosit-TMT, trained exclusively on 6/10/11-plex labeled peptides, may be applicable to these isobaric labeling strategies as well. To investigate this, we re-analyzed nine publicly available datasets covering iTRAQ and TMTpro labeling for samples with human and mouse origin. We highlight that Prosit-TMT shows remarkably good performance when comparing experimentally acquired and predicted fragmentation spectra (R of 0.84 - 0.9) and retention times (ΔRT95% of 3% - 10% gradient time) of peptides. Furthermore, re-scoring substantially increases the number of confidently identified spectra, peptides, and proteins.
Identifiants
pubmed: 35578405
doi: 10.1002/pmic.202100257
doi:
Substances chimiques
Peptides
0
Proteins
0
Indicators and Reagents
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e2100257Informations de copyright
© 2022 The Authors. Proteomics published by Wiley-VCH GmbH.
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