Duplicate filter

Description

Three different modes:
Old average (the old filter): Keeps only the feature list row with the maximum average area. Checks for average m/z and RT.
New average: Two peaks are considered duplicates when their average m/z and retention time differences are lower than the tolerances set by the user. When two (or more) duplicates are found, a consensus row is created with the lowest row ID of all duplicates. For this consensus row, all DETECTED features are favored over ESTIMATED (gap-filled) and ESTIMATED are favored over UNKNOWN. Furthermore, if there are only ESTIMATED features in a raw data file, the highest is chosen.
Single feature: Marks rows as duplicates if they share one feature within the RT and m/z tolerance in the same raw data file. Creates a consensus row.

Notes

This filter might be very helpful to eliminate misaligned feature list rows after the gap-filling process. As the average retention time and m/z value for two duplicates should be very close after gap-filling. A more restrictive option is to mark all rows as duplicates that share one duplicate feature. To use this filter, turn off the average option.

Method parameters

Name sufix
This is the suffix to identify the new aligned peak list in Peak list frame of desktop.
Filter mode:
Old average: Compares rows with the average m/z and RT (like the old algorithm)
New average: Compares rows with the average m/z and RT. Creates a consensus row
Single feature: Compares rows on a raw data file basis. Marks rows as duplicates if two rows share a feature in a raw data file with the same RT and m/z (and identity/charge state)
M/Z tolerance
Maximum m/z difference between duplicate peaks.
RT tolerance
Maximum retention time difference between duplicate peaks.
Require same identification
If the checkbox is selected duplicate peaks must have the same identification.
Remove source peak list after fitering
It the checkbox is selected the source peak list will be remove and the filtered version remains.

Aligned, gap-filled feature list prior and after duplicate row filter (new average).