Join aligner

Description

This method aligns detected peaks in different samples through a match score. This score is calculated based on the mass and retention time of each peak and ranges of tolerance stipulated in the parameters setup dialog.

Algorithm

The peak alignment algorithm uses:

1. a master list of peaks (L) against which every new sample (Sj) will be matched. When aligning peaks from multiple samples, the master list is initially set to the first sample, and subsequently it will be the combination of samples aligned thus far, with the samples as the columns and the matching peaks as the rows.

2. for every row i in L, a two-dimensional window (where the window size is selected by the user), called Alignment window (AW) defining the ranges of m/z and RT and centered around the average of m/z and RT of all the individual peaks in the row; and

3. a score function to compute the similarity of peaks between L and the new sample Sj inside the alignment window. The score function computes the similarity based on the similarities in m/z, retention time, and optionally on identification, and isotope patterns between the peaks to be matched. The score is calculated as follows:
score = ((1 - MZdifference / MZtolerance) × MZweight) + ((1 - RTdifference / RTtolerance) × RTweight)

The algorithm works as follows. It iterates through the rows of L, and for each row, it looks for peaks within the alignment window in Sj that has to be aligned with L. A score is calculated for each possible match and the pair getting the best score will be aligned.


Method parameters

Peak list name
Name of the new aligned peak list
m/z tolerance
This value sets the range, in terms of m/z, for possible peaks to be aligned. Maximum allowed m/z difference
Weight for m/z
This is the assigned weight for m/z difference at the moment of match score calculation between peak rows. In case of perfectly matching m/z values the score receives the complete weight.
Retention time tolerance type
Maximum RT difference can be defined either using absolute or relative value
Absolute RT tolerance
Maximum allowed absolute RT difference
Relative RT tolerance
Maximum allowed relative RT difference
Weight for RT
This is the assigned weight for RT difference at the moment of match score calculation between peak rows. In case of perfectly matching RT values the score receives the complete weight.
Require same charge state
If checked, only rows having same charge (taken from best MS/MS spectra) can be aligned
Require same ID
If checked, only rows having same compound identities (or no identities) can be aligned.
Compare isotope pattern
If both peaks represent an isotope pattern, add isotope pattern score to match score.
Isotope pattern score threshold level
If the score between isotope pattern is lower, discard this match.

New aligned peak list showing peaks from 3 different samples.