Dataset Information

Proteome-wide evaluation of two common protein quantification methods

ABSTRACT: Proteomics experiments commonly aim to estimate and detect differential abundance across all expressed proteins. Within this experimental design, some of the most challenging measurements are small fold changes for lower abundance proteins. While bottom-up proteomics methods are approaching comprehensive coverage of even complex eukaryotic proteomes, failing to reliably quantify lower abundance proteins can limit the precision and reach of experiments to much less than the identified -let alone total- proteome. Here we test the ability of two common methods, a tandem mass tagging (TMT) method and a label- free quantitation method (LFQ), to achieve comprehensive quantitative coverage by benchmarking their capacity to measure 3 different levels of change (3-, 2-, and 1.5-fold) across an entire dataset. Both methods achieved comparably accurate estimates for all three fold-changes. However, the TMT method detected changes that reached statistical significance three times more often due to higher precision and fewer missing values. These findings highlight the importance of refining proteome quantitation methods to bring the number of usefully quantified proteins into closer agreement with the number of total quantified proteins.

INSTRUMENT(S): Orbitrap Fusion Lumos

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

SUBMITTER: Joao Paulo

LAB HEAD: Steven P. Gygi

PROVIDER: PXD007683 | Pride | 2018-04-05

REPOSITORIES: pride

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Proteome-Wide Evaluation of Two Common Protein Quantification Methods.

O'Connell Jeremy D JD Paulo Joao A JA O'Brien Jonathon J JJ Gygi Steven P SP

Journal of proteome research 20180419 5

Proteomics experiments commonly aim to estimate and detect differential abundance across all expressed proteins. Within this experimental design, some of the most challenging measurements are small fold changes for lower abundance proteins. While bottom-up proteomics methods are approaching comprehensive coverage of even complex eukaryotic proteomes, failing to reliably quantify lower abundance proteins can limit the precision and reach of experiments to much less than the identified-let alone t ...[more]

PMID: 29635916

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