Page IDMapper: The parameter handling of this tool has been reworked. For greater consistency with other tools, the parameters rt_delta and mz_delta have been renamed to rt_tolerance and mz_tolerance. The possible values of the mz_reference parameter have also been renamed. The default value of mz_tolerance has been increased from 1 ppm to a more realistic 20 ppm.
Most importantly, the use_centroids parameter from previous versions has been split into two parameters, feature:use_centroid_rt and feature:use_centroid_mz. In OpenMS 1.6, peptide identifications would be matched only against monoisotopic mass traces of features if mz_reference was PeptideMass; otherwise, all mass traces would be used. This implicit behaviour has been abandoned, you can now explicitly control it with the feature:use_centroid_mz parameter. feature:use_centroid_mz does not take into account m/z deviations in the monoisotopic mass trace, but this can be compensated by increasing mz_tolerance. The new implementation should work correctly even if the monoisotopic mass trace itself was not detected.
Class PeptideHit: Use SpectrumMatch instead. PeptideHit may be removed in a future OpenMS version.
Class PeptideIdentification: Use SpectrumIdentification instead. PeptideIdentification may be removed in a future OpenMS version.
Member SpectrumLookup::extractScanNumber (const String &native_id, const boost::regex &scan_regexp, bool no_error=false): Use SpectrumNativeIDParser::extractScanNumber() instead for better discoverability.
Member SpectrumLookup::extractScanNumber (const String &native_id, const String &native_id_type_accession): Use SpectrumNativeIDParser::extractScanNumber() instead for better discoverability.
Member SpectrumLookup::getRegExFromNativeID (const String &native_id): Use SpectrumNativeIDParser::getRegExFromNativeID() instead for better discoverability.
Member SpectrumLookup::isNativeID (const String &id): Use SpectrumNativeIDParser::isNativeID() instead for better discoverability.