pgb_liv\php_ms\Search\Parameters\MsgfPlusSearchParameters::setFragmentationMethodId

(0: as written in the spectrum or CID if no info (Default), 1: CID, 2: ETD, 3: HCD, 4: Merge spectra from the same precursor)

Fragmentation method identifier (used to determine the scoring model). If the identifier is 0 and fragmentation method is written in the spectrum file (e.g. mzML files), MS-GF+ will recognize the fragmentation method and use a relevant scoring model. If the identifier is 0 and there is no fragmentation method information in the spectrum (e.g. mgf files), CID model will be used by default. If the identifier is non-zero and the spectrum has fragmentation method information, only the spectra that match with the identifier will be processed. If the identifier is non-zero and the spectrum has no fragmentation method information, MS-GF+ will process all spectra assuming the specified fragmentation method. If the identifier is 4, MS/MS spectra from the same precursor ion (e.g. CID/ETD pairs, CID/HCD/ETD triplets) will be merged and the "merged" spectrum will be used for searching instead of individual spectra. See Kim et al., MCP 2010 for details.