PXD047854 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | timsTOF HT improves protein identification and quantitative reproducibility for deep unbiased plasma protein biomarker discovery (Loading curve 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 Proteographâ„¢ (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 | 2024-01-18 |
AnnouncementXML | Submission_2024-01-18_05:07:05.467.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 | acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | timsTOF; timsTOF Pro 2 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-12-15 03:45:57 | ID requested | |
⏵ 1 | 2024-01-18 05:07:05 | announced | |
Publication List
Keyword List
submitter keyword: Plasma, Liquid Chromatography, Mass spectrometry, timsTOF, Proteomics, Biomarkers |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD047854
- Label: PRIDE project
- Name: timsTOF HT improves protein identification and quantitative reproducibility for deep unbiased plasma protein biomarker discovery (Loading curve dataset)