PXD037681-1

PXD037681 is an original dataset announced via ProteomeXchange.

Title	A PTM-centric Proteome Informatic Pipeline for Monitoring Post-Translational Modifications by PEIMAN2
Description	Post-translational modifications (PTMs) are under significant focus in molecular biomedicine due to their importance in signal transduction in most cellular and organismal processes. Identification of PTMs, determination of PTM location sites, discrimination between functional and inert PTMs, and quantification of their occupancies are demanding tasks, especially in the light of PTM crosstalk in each biosystem. On top of that, the study of each PTM often necessitates a particular experimental design in majority of cases. Computational approaches can identify the relevant PTMs in a biosystem and help to design follow-up experiments involving specific PTM enrichment. Here, we present a PTM-centric proteome informatic pipeline for prediction of most probable and relevant PTMs in mass spectrometry-based proteomics data and refining raw data search parameters based on the acquired knowledge. Using expression profiling, we identified cellular proteins that are differentially regulated in response to multikinase inhibitors dasatinib and staurosporine at four different concentrations. Computational enrichment analysis was employed to determine the potential PTMs of protein targets for both drugs. Finally, we conducted an additional round of database search with these predicted chemical modifications. Our pipeline helped analyze the enriched PTMs and even detected proteins that were not picked up in the initial search. Our findings support the idea of PTM-oriented searching of MS data in proteomics based on computational enrichment analysis.
HostingRepository	PRIDE
AnnounceDate	2025-05-06
AnnouncementXML	Submission_2025-05-06_09:19:00.859.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Amir Ata Saei
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2022-10-24 02:01:10	ID requested
⏵ 1	2025-05-06 09:19:01	announced

10.1002/pmic.202400238;

Nickchi P, Vadadokhau U, Mirzaie M, Baumann M, Saei AA, Jafari M, Monitoring Functional Posttranslational Modifications Using a Data-Driven Proteome Informatic Pipeline. Proteomics, 25(8):e202400238(2025) [pubmed]

submitter keyword: PTM,Proteomics, mass spectromtery

Prof. Roman A. Zubarev
contact affiliation	Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 65 Stockholm, Sweden
contact email	roman.zubarev@ki.se
lab head
Amir Ata Saei
contact affiliation	Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
contact email	amirata.saei.dibavar@ki.se
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD037681

PRIDE project URI

• PRIDE
  1. PXD037681
     1. Label: PRIDE project
     2. Name: A PTM-centric Proteome Informatic Pipeline for Monitoring Post-Translational Modifications by PEIMAN2