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

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 lysate (n = 20) were assessed for false identification transfers from samples containing yeast (n = 20). While MBR increased the total number of spectral identifications by similar to 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 data set after applying the MaxQuant LFQ algorithm. We conclude that false transfers by MBR are plentiful, but few are retained in the final data set.