PXD008234 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Absolute Quantitation of All Plasma Proteins from SWATH Data for Biomarker Discovery |
Description | The current state of proteomics requires a choice between targeted and discovery methods. The former provides exceptional quantitation and data completeness, but only with few analytes. Discovery proteomics can identify hundreds and thousands of proteins in a sample, but with poor quantitation and data completeness. We have established and optimized a method that combines targeted and data-independent acquisition for absolute quantitation of all plasma proteins in a single sequential window acquisition of all theoretical fragment ions (SWATH) acquisition run using a panel of spike-in standards (SIS). We compared the absolute quantitation (AQ) of SWATH and high-resolution multiple-reaction monitoring (MRM-HR) acquisition methods using the 100 protein PlasmaDive SIS panel spiked into human plasma. SWATH provided equivalent quantitation and differentially abundant protein profiles as MRM-HR. Absolute quantities of the SIS peptides from the SWATH data were used to estimate the absolute quantities (eAQ) for all the proteins in the run. The eAQ values provided similar quantitation and differentially abundant protein profiles as AQ and protein group (PG) values, and the eAQ method was the only scheme where all selected proteins were verified by MRM-HR. We applied the eAQ method to a cohort of 16 non-small cell lung cancer (NSCLC) patients receiving immunotherapeutics and found that fibronectin (FN1) and proteoglycan 4 (PRG4) were useful markers for predicting patients who would stay on these agents for at least 6 months (area under the curve of 0.8438 and 0.6735, respectively). Thirteen additional plasma samples confirmed that FN1 and PRG4 are putative biomarkers (positive predictive value is 100% and 85.7%, respectively) for a prolonged (>6 months) response to immunotherapeutic agents. In conclusion, we describe an optimized method for absolute quantification of all proteins in a SWATH run, and this approach is amenable for the identification of plasma biomarkers. |
HostingRepository | PRIDE |
AnnounceDate | 2019-01-02 |
AnnouncementXML | Submission_2019-01-02_05:31:56.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Shawn Rice |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | carbamoylated residue; carboxylated residue; monohydroxylated residue; acetylated residue; deamidated residue |
Instrument | TripleTOF 5600 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2017-11-17 08:53:12 | ID requested | |
⏵ 1 | 2019-01-02 05:31:58 | announced | |
Publication List
Rice SJ, Liu X, Zhang J, Belani CP, Absolute Quantification of All Identified Plasma Proteins from SWATH Data for Biomarker Discovery. Proteomics, 19(3):e1800135(2019) [pubmed] |
Keyword List
curator keyword: Biological, Biomedical |
submitter keyword: SWATH, data-independent acquisition, absolute quantification, plasma biomarkers, lung cancer |
Contact List
Chandra P. Belani |
contact affiliation | Department of Medicine, Penn State Cancer Institute, Penn State College of Medicine, Hershey, PA. |
contact email | cbelani@pennstatehealth.psu.edu |
lab head | |
Shawn Rice |
contact affiliation | Penn State College of Medicine |
contact email | srice@pennstatehealth.psu.edu |
dataset submitter | |
Full Dataset Link List
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/2019/01/PXD008234 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD008234
- Label: PRIDE project
- Name: Absolute Quantitation of All Plasma Proteins from SWATH Data for Biomarker Discovery