PXD049979-1
PXD049979 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Proteome Profiling - Quality and Quantifiability using the Orbitrap Astral MS (IBD) |
| Description | Biomarker development has two key challenges; the high rate of false positives in discovery and the slow validation phase. To address these challenges we have developed and rigorously tested the Targeted Evaluation and Assessment of Quality (TEAQ) software package. This innovative tool for identifying and selecting precursors, peptides, and proteins that meet the stringent criteria of targeted assays, thus overcoming the limitations faced in the current biomarker development landscape. We implemented the TEAQ to evaluate the performance of the Orbitrap Astral MS using Data-Independent Acquisition Mass Spectrometry (DIA-MS) on plasma samples. This assessment focused on crucial parameters such as proteome linearity, specificity, repeatability, reproducibility, and others essential for substituting dedicated targeted techniques in the more rigorous discovery phase of biomarker development. Through the application of TEAQ on a clinical cohort comprising individuals with inflammation bowel disease (n=493) and an 11-point loading curve, our software successfully identified the signature precursors of quantifiable proteins. A signature peptide or precursor, as per our definition, is a unique peptide or precursor sequence specific to the target protein, exhibiting no miss-cleavages, a linearity R2 value exceeding 0.8, and a coefficient of variation (CV) below 20%. Furthermore, deviations should be less than 20% at low limited quantification concentrations. In instances where multiple peptides or precursors originate from the same protein, it is imperative that all peptides demonstrate a correlation coefficient within the same proteins (>0.7) in the study. Our data set has been made available to as a resource for targeted assay development. This comprehensive approach ensures the reliability and accuracy of our biomarker identification process, paving the way for advancements in clinical practice. |
| HostingRepository | MassIVE |
| AnnounceDate | 2024-10-19 |
| AnnouncementXML | Submission_2024-10-19_21:32:36.989.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Manasa Vegesna |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | Carbamidomethyl |
| Instrument | Orbitrap Astral |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-02-20 19:40:00 | ID requested | |
| ⏵ 1 | 2024-10-19 21:32:37 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: Biomarker Identification, DIA, Orbitrap Astral, Quality Control, Proteome Profiling, IBD |
Contact List
| Jennifer Van Eyk | |
|---|---|
| contact affiliation | Cedars Sinai Medical Center |
| contact email | jennifer.vaneyk@cshs.org |
| lab head | |
| Manasa Vegesna | |
| contact affiliation | Cedars-Sinai Medical Center |
| contact email | manasa.vegesna@cshs.org |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| 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://massive.ucsd.edu/v07/MSV000094137/ |
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