PXD042546

PXD042546 is an original dataset announced via ProteomeXchange.

Title	Spectral Library Search for Improved TMTpro Labelled Peptide Assignment in Human Plasma Proteomics
Description	Clinical biomarker discovery is often based on the analysis of human plasma samples. However, the high dynamic range and complexity of plasma pose significant challenges to mass spectrometry-based proteomics. Current methods for improving protein identifications require laborious pre-analytical sample preparation. In this study, we developed and evaluated a TMTpro-specific spectral library for improved protein identification in human plasma proteomics. The library was constructed by LC-MS/MS analysis of highly fractionated TMTpro-tagged human plasma, human cell lysates, and relevant arterial tissues. The library was curated using several quality filters to ensure reliable peptide identifications. Our results show that spectral library searching using the TMTpro spectral library improves the identification of proteins in plasma samples compared to conventional sequence database searching.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:12:30.768.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hans Christian Beck
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-05-30 09:53:22	ID requested
1	2023-10-24 15:42:00	announced
⏵ 2	2023-11-14 09:12:39	announced	2023-11-14: Updated project metadata.

Palstr, ø, m NB, Campbell AJ, Lindegaard CA, Cakar S, Matthiesen R, Beck HC, Spectral library search for improved TMTpro labelled peptide assignment in human plasma proteomics. Proteomics, 24(6):e2300236(2024) [pubmed]

submitter keyword: peptide identification

plasma proteomics

spectral library search

TMTpro

Hans Christian Beck
contact affiliation	Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
contact email	hans.christian.beck@rsyd.dk
lab head
Hans Christian Beck
contact affiliation	Odense University Hospital, Odense, Denmark
contact email	hans.christian.beck@rsyd.dk
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/2023/10/PXD042546

PRIDE project URI

• PRIDE
  1. PXD042546
     1. Label: PRIDE project
     2. Name: Spectral Library Search for Improved TMTpro Labelled Peptide Assignment in Human Plasma Proteomics