Proteome Informatics Group > Java Proteomic Library

JPL-MSMatch 1.0 Documentation


Here is the documentation about how we make comparisons of MS spectra.

First, some definitions:

Pairwise spectral comparison
A comparison between 2 MS spectra considering peaks'mzs [and intensities].
MS peaks'match
A match is a pair of similar peaks between spectra to compare.
Error mz tolerance
Expression of the maximum tolerated variation of mz when comparing 2 peaks.
Pairwise spectral alignment
A pairwise alignment is an arrangement of two spectra highlighting their similarity. Each match is represented by a vertical bar.
Alignment Conflicts
Conflicts appear when one peak is involved in more than one match giving many possible alignments between spectra. Resolution of conflicts may be done afterwards.
Alignment Scoring
Total matches [and mismatches] in an alignment are used to compute a score (many different scoring system).

Match Model

Match Algorithm

Alignment types

There are 2 types of alignments, the one involving peak list pairs and binned peak list pairs.

Binned peak list alignment is the simpler one as they share the same number of intervals. Their alignment is global without gaps. They could be represented as histogramms.

Peak list alignment are kind of global alignment with gaps.

They can both be represented in dot-matrices.

Mass matcher