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UPS1-yeast standard analysis - Technical Brief Calibration Plot for Proteomics (CP4P): A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments

ABSTRACT: Label-free quantification of various concentrations of Universal Proteomic Standard (UPS1, Sigma-Aldrich) spiked in yeast extract.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human) Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Yohann Couté

LAB HEAD: Christophe Bruley

PROVIDER: PXD002370 | Pride | 2015-11-27

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	C-25fmol-R1_QEx2_000090.raw	Raw
	C-25fmol-R2_QEx2_000099.raw	Raw
	C-25fmol-R3_QEx2_000116.raw	Raw
	D-10fmol-R1_QEx2_000089.raw	Raw
	D-10fmol-R2_QEx2_000098.raw	Raw

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Publications

Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments.

Giai Gianetto Quentin Q Combes Florence F Ramus Claire C Bruley Christophe C Couté Yohann Y Burger Thomas T

Proteomics 20160101 1

In MS-based quantitative proteomics, the FDR control (i.e. the limitation of the number of proteins that are wrongly claimed as differentially abundant between several conditions) is a major postanalysis step. It is classically achieved thanks to a specific statistical procedure that computes the adjusted p-values of the putative differentially abundant proteins. Unfortunately, such adjustment is conservative only if the p-values are well-calibrated; the false discovery control being spuriously ...[more]

PMID: 26572953

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yeast-UPS1 standard LC-MS/MS dataset

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S. cerevisiae DDA orbitrap-based benchmark datasets. C4PR_LIV

Project description:In this study, label free peptide intensities from a well quantitatively characterised yeast cell lysate were acquired on two orbitrap mass spectrometers (LTQ-Velos and Q Exactive HF). Additionally, samples containing Universal Proteomics Standard and the Proteomics Dynamic range Standard (http://www.sigmaaldrich.com/life-science/proteomics/mass-spectrometry/ups1-and-ups2-proteomic.html) in a yeast background were also acquired. The absolute abundances of over 340 proteins present in that yeast lysate (determined in a parallel SRM-based study) were then used in order to determine the flyability (or detectability) of thousands of peptides. The flyability scores, termed the ‘F-factors’, reflect how well a peptide ionises in a complex chromatographically separated sample. Specifically, F-factors are calculated by normalising peptide precursor ion intensity by the absolute abundance of its parent protein. Based on the analysis of the six datasets deposited here (reflecting different gradients and instrument platforms) the study found that physicochemical properties including peptide length, charge and hydrophobicity are predictors of peptide detectability. Furthermore, it was established that hydrophobicity has a non-linear relationship with detectability and that coelution with competing ions significantly affects peptide detectability. The analysis based on the data deposited here suggests that F-factors have great utility for understanding peptide detectability and gas-phase ion chemistry in complex chromatographically-separated peptide mixtures. The concept of F-factors will also undoubtedly assist in better surrogate selection in targeted mass spectrometry studies and allow more accurate calibration of peptide ion signal in label-free workflows.

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Benchmarking DIA data analysis workflows

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