peakSegmentation: Determine fraction of evidence which causes segmentation,...

In PTXQC: Quality Report Generation for MaxQuant and mzTab Results

Determine fraction of evidence which causes segmentation, i.e. sibling peaks at different RTs confirmed either by genuine or transferred MS/MS.

Description

Sometimes, MQ splits a feature into 2 or more if the chromatograpic conditions are not optimal and there is a drop in RT intensity. If both features contain successful MS/MS scans, we will find the same peptide twice (with slightly different RT) in the same charge state. This constitutes a natively split peak and is rare (95

Usage

peakSegmentation(df_evd_all)

Arguments

df_evd_all

A data.frame of evidences containing the above columns

Details

If Match-between-runs is used and the RT alignment is not perfect, then a peptide might be inferred at a wrong RT position, even though this Raw file already contains MS/MS evidence of this peptide. Usually the number of peak duplicates rises drastically (e.g. only 75 In most cases, the RT is too far off to be a split peak. It's rather a lucky hit with accidentally the same mass-to-charge, and thus the intensity is random. To find by how much these peak pairs differ in RT, use idTransferCheck() and inMatchWindow().

Required columns are 'is.transferred', 'fc.raw.file', 'modified.sequence', 'charge', 'type'.

Note that this function must be given MS/MS identifications of type "MULTI-MSMS" and "MSMS-MATCH". It will stop() otherwise.

Value

A data.frame with one row per Raw file and three columns: 1) 2) 3)

PTXQC documentation built on May 29, 2024, 9:26 a.m.