Identifies precursor mass traces and tries to correlate them with fragment ion mass traces in SWATH maps.

This algorithm will try to correlate the masstraces to find co-eluting traces and cluster them.

This program looks at mass traces in a precursor MS1 map and tries to correlate them with features found in the corresponding MS2 map based on their elution profile. It uses

the mass traces from the MS1 in consensusXML format [note this is an unintended use of the consesusXML format to also store intensities]
the mass traces from the MS2 (SWATH map)

It does a separate correlation analysis on the MS1 and the MS2 map, both produces a set of pseudo spectra. In a second (optional) step, the MS2 pseudo spectra are correlated with the MS1 traces and the most likely precursor is assigned to the pseudo spectrum.

It is based on the following papers: ETISEQ – an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics BMC Bioinformatics 2009, 10:244 doi:10.1186/1471-2105-10-244 ; http://www.biomedcentral.com/1471-2105/10/244 they use FFT to correlate and then use lag of at least 1 scan and pearson correlation of 0.7 to assign precursors to product ions If one fragment matches to multiple precursors, it is assigned to all of them. If it doesnt match any, it is assigned to all