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PXD014815 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleMatrix-matched calibration curves
DescriptionMass spectrometry is a powerful tool for quantifying protein abundance in complex samples. Advances in sample preparation and the development of data independent acquisition (DIA) mass spectrometry approaches have increased the number of peptides and proteins measured per sample. However, methods to assess quantitative figures of merit (e.g. lower limit of quantification, LLOQ) are not easily extended to multiplex assays with hundreds or thousands of analytes. Here we present a series of experiments demonstrating how to assess whether a peptide measurement is quantitative by mass spectrometry. In a study of the yeast proteome, only 52% of detected proteins (41% of detected peptides) have a peptide that is above the LLOQ in the reference material. A similar trend was observed in human cerebrospinal fluid, suggesting that this observation is not sample-specific. Our results demonstrate that increasing the number of detected peptides and proteins in an unbiased proteomics experiment does not necessarily result in increased numbers of peptides or proteins that can be measured quantitatively. Furthermore, our method provides an approach to determining useful figures of merit for hundreds to thousands of proteins in the same experiment.
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterLindsay Pino
SpeciesList scientific name: Homo sapiens; NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae; NCBI TaxID: 4932;
ModificationListCarbamidomethyl; Label:13C(6)15N(2); Label:13C(6)15N(4)
InstrumentQ Exactive HF; Orbitrap Fusion Lumos; TSQ Quantiva
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-07-29 09:13:58ID requested
12019-07-29 09:17:37announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: loq, calibration curve, matrix matched
Contact List
Michael MacCoss
contact affiliationUniversity of Washington
contact emailmaccoss@uw.edu
lab head
Lindsay Pino
contact affiliationUniversity of Washington
contact emaillpino@uw.edu
dataset submitter
Full Dataset Link List
Panorama Public dataset URI