Dataset Information

Evaluating False Transfer Rates from the Match-Between-Runs algorithm with a two-proteome model

ABSTRACT: Stochasticity between independent LC-MS/MS runs is a challenging problem in the field of proteomics resulting in significant missing values (i.e., abundance measurements) among observed peptides. To address this issue, several approaches have been developed including computational methods such as MaxQuant’s Match-Between-Runs (MBR) algorithm. Often dozens of runs are all considered at once by MBR, transferring identifications from any one run to any of the others. To evaluate the error associated with these transfer events, we created a two-sample/two-proteome approach. In this way, samples containing no yeast lysates were assessed for false identification transfers from samples containing yeast. Overall, transfers from any of 20 runs with yeast were assessed to any of 20 runs without yeast were measured. While MBR increased the total number of spectral identifications by ~40%, we also found that 44% of all identified yeast proteins had identifications transferred to at least one sample without yeast. However, of these only 2.7% remained in the final dataset after applying the MaxQuant LFQ algorithm. We conclude that false transfers by MBR are plentiful, but likely have only a small impact on the final dataset due to downstream removal.

INSTRUMENT(S): Orbitrap Fusion Lumos

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

SUBMITTER: Joao Paulo

LAB HEAD: Steven P. Gygi

PROVIDER: PXD014415 | Pride | 2019-09-25

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	H_v_HY_MBR_disabled_LFQ_disabeled.zip	Other
	H_v_HY_MBR_enabled_LFQ_disabeled.zip	Other
	H_v_HY_MBR_enabled_LFQ_enabled.zip	Other
	a11849_human_90min_hrMS2.raw	Raw
	a11850_human_90min_hrMS2.raw	Raw

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Publications

Evaluating False Transfer Rates from the Match-between-Runs Algorithm with a Two-Proteome Model.

Lim Matthew Y MY Paulo João A JA Gygi Steven P SP

Journal of proteome research 20191002 11

Stochasticity between independent LC-MS/MS runs is a challenging problem in the field of proteomics, resulting in significant missing values (i.e., abundance measurements) among observed peptides. To address this issue, several approaches have been developed including computational methods such as MaxQuant's match-between-runs (MBR) algorithm. Often dozens of runs are all considered at once by MBR, transferring identifications from any one run to any of the others. To evaluate the error associat ...[more]

PMID: 31547658

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