Release v0.4.3
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Joshua Klein
Dec 3, 2020, 10:46:15 PM12/3/20
to GlycReSoft
This release adds support for reading MGF files and MS2-only mzML and mzXML files to the spectrum preprocessor. These data will not benefit from precursor correction or the mass recalibration and no chromatogram information will be available, but all other features should work as expected.
This release adds two new search options. The first is the ability to permute decoy glycopeptide's peptide+Y ions which was enabled unintentionally in earlier v0.4.0 releases. This option is useful when some or all glycopeptide spectra are dominated peptide+Y ions which would otherwise be shared between targets and decoys exactly. This also makes the FDR estimation less conservative. The second is to enable more rare signature ion penalties when searching spectra which contain peaks for O-acetyl NeuAc (NeuAc and @Acetyl) and phospho-Hex (Hex and @Phospho) oxonium ions and these monosaccharide-substituent combinations are not present in the glycan composition, or vice-versa.
In addition to a myriad of small adjustments, this release vastly improves the speed of peptide+Y ion generation for multiply glycosylated peptides.
This release adds two new search options. The first is the ability to permute decoy glycopeptide's peptide+Y ions which was enabled unintentionally in earlier v0.4.0 releases. This option is useful when some or all glycopeptide spectra are dominated peptide+Y ions which would otherwise be shared between targets and decoys exactly. This also makes the FDR estimation less conservative. The second is to enable more rare signature ion penalties when searching spectra which contain peaks for O-acetyl NeuAc (NeuAc and @Acetyl) and phospho-Hex (Hex and @Phospho) oxonium ions and these monosaccharide-substituent combinations are not present in the glycan composition, or vice-versa.
In addition to a myriad of small adjustments, this release vastly improves the speed of peptide+Y ion generation for multiply glycosylated peptides.
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