PXD008094

PXD008094 is an original dataset announced via ProteomeXchange.

Title	A Selected Reaction Monitoring Approach for Validating Candidate Biomarkers
Description	We here describe a Selected Reaction Monitoring (SRM)-based approach for the discovery and validation of peptide biomarkers for cancer. The first stage of this approach is the direct identification of candidate peptides through comparison of proteolytic peptides derived from the plasma of cancer patients or healthy individuals. Several hundred candidate peptides were identified through this method, providing challenges for choosing and validating the small number of peptides that might prove diagnostically useful. To accomplish this validation, we used two-dimensional chromatography coupled with Selected Reaction Monitoring of candidate peptides. We applied this approach, called SAFE-SRM (for Sequential Analysis of Fractionated Eluates by Selected Reaction Monitoring) to plasma from cancer patients and discovered two peptides encoded by the PPIA (peptidyl-prolyl cis-trans isomerase A) gene whose abundance was increased in the plasma of ovarian cancer patients. At optimal thresholds, elevated levels of at least one of these two peptides was detected in 43 (68.3%) of 63 women with ovarian cancer but in none of 50 healthy controls. In addition to providing a potentially new biomarker for ovarian cancer, this approach is generally applicable to the discovery of proteins and peptides characteristic of various disease states.
HostingRepository	PRIDE
AnnounceDate	2017-12-11
AnnouncementXML	Submission_2017-12-11_00:33:30.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	QING WANG
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iTRAQ4plex-116 reporter+balance reagent acylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2017-11-01 02:10:32	ID requested
⏵ 1	2017-12-11 00:33:31	announced

Wang Q, Zhang M, Tomita T, Vogelstein JT, Zhou S, Papadopoulos N, Kinzler KW, Vogelstein B, Selected reaction monitoring approach for validating peptide biomarkers. Proc Natl Acad Sci U S A, 114(51):13519-13524(2017) [pubmed]

curator keyword: Biomedical

submitter keyword: Clinical Proteomics, Quantitative Proteomics, Targeted Detecton, Diagnostics

Qing Wang
contact affiliation	Johns Hopkins University School of Medicine
contact email	qing@jhmi.edu
lab head
QING WANG
contact affiliation	Ludwig Center and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center
contact email	qing@jhmi.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD008094
     1. Label: PRIDE project
     2. Name: A Selected Reaction Monitoring Approach for Validating Candidate Biomarkers