PXD047839

PXD047839 is an original dataset announced via ProteomeXchange.

Title	timsTOF HT improves protein identification and quantitative reproducibility for deep unbiased plasma protein biomarker discovery (Cancer cohort dataset)
Description	Mass spectrometry (MS) has emerged as a valuable tool for plasma proteome profiling and disease biomarker discovery. However, wide range of plasma protein concentrations along with technical and biological variabilities, continue to present significant challenges for deep and reproducible protein quantitation across large patient cohorts. Here we demonstrate the qualitative and quantitative performance gain of the timsTOF HT over the timsTOF Pro 2 mass spectrometer in the analysis of neat (unfractionated) and Proteograph™ (PG)-processed plasma across a wide range of peptide loading masses and liquid chromatography (LC) gradients. We observed up to a 76% increase in total plasma peptide precursors identified and a >2-fold boost in quantifiable plasma peptide precursors (CV<20%) with timsTOF HT compared to timsTOF Pro 2. In an exploratory study of 20 late-stage cancer and 20 control sampleswe observed a ~50% increase in total and statistically significant plasma peptide precursors (q<0.05) with timsTOF HT compared to Pro 2. Our data demonstrated the superior performance of timsTOF HT in identifying and quantifying differences between biologically diverse samples, which can improve disease biomarker discovery in large cohort studies. Moreover, researchers can leverage datasets from this study to optimize their LCMS workflows for plasma protein profiling and biomarker discovery. See the details in a paper, entitled "timsTOF HT improves protein identification and quantitative reproducibility for deep unbiased plasma protein biomarker discovery".
HostingRepository	PRIDE
AnnounceDate	2024-01-17
AnnouncementXML	Submission_2024-01-16_21:39:35.960.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joon-Yong Lee
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF; timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-14 14:20:17	ID requested
⏵ 1	2024-01-16 21:39:36	announced

10.1021/ACS.JPROTEOME.3C00646;

submitter keyword: Plasma, Liquid Chromatography, Mass spectrometry, timsTOF, Proteomics, Biomarkers

Bruce Wilcox
contact affiliation	PrognomiQ Inc.
contact email	bruce.wilcox@prognomiq.com
lab head
Joon-Yong Lee
contact affiliation	PrognomiQ Inc.
contact email	joon-yong.lee@prognomiq.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD047839
     1. Label: PRIDE project
     2. Name: timsTOF HT improves protein identification and quantitative reproducibility for deep unbiased plasma protein biomarker discovery (Cancer cohort dataset)