DIA pipeline quantifies peptides at wrong retention time

[tomvaiuw]

Hi, We are running some data through DIA-SpecLib-Quant pipeline and we find that several peptides are quantified at wrong retention time (we check the chromatograms in Skyline) as shown in this correlation:

x-axis Skyline manually curated true retention time, y-axis - retention time reported in the diann-output.tsv For example the major outlier (16min vs 20.5 min peak) - peptide LSPLGEEMR shows no peak at the 20.5 min -

I am not sure how to explain this and correct it.

Thanks, Tomas University of Washington

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