PXD048271-1

PXD048271 is an original dataset announced via ProteomeXchange.

Title	Wideband PRM: Highly Accurate and Sensitive Method for High-Throughput Targeted Proteomics
Description	Targeted mass spectrometry (MS) approaches, which are powerful methods for uniquely and confidently quantifying a specific panel of proteins in complex biological samples, play a crucial role in validation and clinical translation of protein biomarkers discovered by global proteomic profiling. Common targeted MS methods, such as multiple reaction monitoring (MRM) and parallel-reaction monitoring (PRM), employ specific mass spectrometric technologies to quantify protein levels by comparing the transitions of specific endogenous (Endo) peptides with those of stable isotope labeled (SIL) peptide counterparts. These methods utilizing amino acid analyzed (AAA) SIL peptides warrants sensitive and precise measurements required for targeted MS assays. Compared to MRM, PRM provides higher experimental throughput by simultaneously acquiring all transitions of the target peptides and thereby compensate for different ion suppression among transitions of a target peptide. However, PRM still suffers different ion suppressions between Endo and SIL peptides due to poor spray stability as the Endo and SIL peptides were monitored at different liquid chromatography (LC) retention times. Here we introduce a new targeted MS method, termed as wideband PRM (WBPRM), designed for high-throughput targeted MS approach. WBPRM employs a wide isolation window for simultaneous fragmentations of both Endo and SIL peptides along with multiplexed single ion monitoring (SIM) scans for enhanced MS sensitivity of target peptides. Compared to PRM, WBPRM was demonstrated to provide increased sensitivity, precision, and accuracy of quantitative measurements of target peptides with increased throughput, allowing more target peptide measurements in a short experiment time. Its adaptability to a MS method provided by the manufacture makes it a facile method to implement for MS based assays, particularly in complex biological samples, where the needs for higher accuracy, sensitivity and efficiency are paramount.
HostingRepository	PRIDE
AnnounceDate	2024-08-14
AnnouncementXML	Submission_2024-08-14_10:21:34.093.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dowoon Nam
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; 6x(13)C labeled residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-05 01:46:27	ID requested
⏵ 1	2024-08-14 10:21:34	announced
2	2024-10-22 06:54:58	announced	2024-10-22: Updated project metadata.

10.1021/acs.analchem.4c00518;

Nam D, Ji M, Kang C, Kim H, Yang H, Bok KH, Bae J, Hong J, Lee SW, Wideband PRM: Highly Accurate and Sensitive Method for High-Throughput Targeted Proteomics. Anal Chem, 96(25):10219-10227(2024) [pubmed]

submitter keyword: PRM,targeted proteomics, parallel reaction monitoring, absolute quantification

Sang-Won Lee
contact affiliation	Department of Chemistry and Center for ProteoGenome Research, Korea University, Seoul 02841, Republic of Korea
contact email	sw_lee@korea.ac.kr
lab head
Dowoon Nam
contact affiliation	Korea University
contact email	dowoon0517@korea.ac.kr
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/2024/08/PXD048271

PRIDE project URI

• PRIDE
  1. PXD048271
     1. Label: PRIDE project
     2. Name: Wideband PRM: Highly Accurate and Sensitive Method for High-Throughput Targeted Proteomics