PXD012035-1

PXD012035 is an original dataset announced via ProteomeXchange.

Title	Isotopologue multi-point calibration for proteomics biomarker quantification in clinical practice
Description	Targeted proteomics has become the method of choice for biomarker validation in human biopsies due to its capacity to measure a set of peptides in multiple samples with high sensitivity, reproducibility, accuracy and precision. However, for targeted proteomics technologies to be transferred to clinical routine there is the need to reduce its complexity and make its procedures simpler, increase its throughput and improve its analytical performance. Biomarker peptide quantification with high accuracy and precision is one of the steps that still remains a challenge in clinical routine, mainly due to the difficulty to account for matrix effects (i.e. signal variation due to biological patient variability) and to establish a valid range of quantification for each analyte in each individual sample. Research-grade proteomics laboratories perform targeted peptide quantification with stable isotopically-labelled peptides (one per analyte), which are added to the samples and used as internal standards. This strategy, known as single-point calibration, enables to confidently assign the endogenous peptide and infer its quantity by direct comparison to the internal standard. This approach however assumes that both the endogenous and the internal standard peptides are within the linear range of quantification, which is not always granted as the linear dependency between peptide areas and concentrations only occurs in a limited sample-dependent range of concentrations. Although standard peptide abundances are adjusted to endogenous levels in low-throughput projects, this is not feasible when dealing with large cohorts of patients in clinical routine that exhibit a high variability of peptide abundances and different matrix effects. External multi-point standard curves in their different forms (calibrated, reverse) have been used to alleviate part of these limitations, but the requirement of a representative blank matrix and the fact that they do not account for matrix effects in individual samples nor establish a valid range of quantification for each individual sample limit their application. Here we present the Isotopologue Multiple-point Calibration (ImCal) quantification strategy, which uses a mix of isotopologue peptides to generate internal multiple-point calibration curves for each individual sample and to accurately quantify biomarker peptides in clinical applications without the need of expert supervision. ImCal relies on the use of five different isotopically-labelled peptides of different nominal mass―ranging from 10 to 39 Da mass shifts—mixed at different concentrations to be used as internal calibration curve for each endogenous peptide of interest
HostingRepository	PanoramaPublic
AnnounceDate	2019-03-23
AnnouncementXML	Submission_2019-03-23_11:42:15.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Cristina Chiva
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	Carbamidomethyl; Label:13C(6)15N(2); Label:13C(6)15N(1); Label:13C(6)15N(4); Label:13C(5)15N(1); Label:13C(9)15N(1)
Instrument	QTRAP 5500

Revision	Datetime	Status	ChangeLog Entry
0	2018-12-12 09:54:39	ID requested
⏵ 1	2019-03-23 11:42:16	announced

Chiva C, Pastor O, Trilla-Fuertes L, G, á, mez-Pozo A, Fresno Vara J Á, Sabid, ó E, Isotopologue Multipoint Calibration for Proteomics Biomarker Quantification in Clinical Practice. Anal Chem, 91(8):4934-4938(2019) [pubmed]

submitter keyword: targeted proteomics, SRM, clinical proteomics, HER2, isotopologues, internal calibration

Eduard Sabidó
contact affiliation	Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
contact email	eduard.sabido@crg.cat
lab head
Cristina Chiva
contact affiliation	Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
contact email	cristina.chiva@upf.edu
dataset submitter

Panorama Public dataset URI