PXD048271 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
Publication List
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] |
Keyword List
submitter keyword: PRM,targeted proteomics, parallel reaction monitoring, absolute quantification |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD048271
- Label: PRIDE project
- Name: Wideband PRM: Highly Accurate and Sensitive Method for High-Throughput Targeted Proteomics