The input is a data frame containing feature evidence with corrected retention times, e.g. a 'calibrated.retention.time' column.
A data.frame with columns 'type', 'calibrated.retention.time', 'modified.sequence', 'charge', 'raw.file'
Note that this function must be given MS/MS identifications of type "MULTI-MSMS" and "MSMS-MATCH". It will stop() otherwise.
We compare for each peptide sequence (and charge) the RT difference within groups of genuine and mixed pairs. For every comparison made, we report the RT difference. If alignment worked perfectly, the differences are very small (<1 min), for the mixed group, i.e. the pairs are accidentally split 3D peaks. Alignment performance has no influence on the genuine-only groups.
Note: We found early MaxQuant versions (e.g. 220.127.116.11) to have an empty 'modified.sequence' column for 'MULTI-MATCH' entries. The sequence which SHOULD be present is equal to the immediate upper row. This is what we use to guess the sequence. However, this relies on the data.frame not being subsetted before (we can sort using the 'id' column)!
A data.frame containing the RT diff for each ID-group found in a Raw file (bg = genuine).
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