Software Development for LC/MS-Based Glycoproteomic Analysis

Screenshot shows the results after loading the mass spectrometry raw data file and an analysis file from the OpenMS pipeline into the glyXtoolMSEvaluator. On the lower left side all features classified as glycopeptide features are shown. For the selected feature the extracted ion chromatogram of the precursor and its isotopic pattern are visualized, together with its consensus fragment spectrum on the lower right side. Within the spectrum, the oxonium ions found by the GlycospectrumFilter tool are marked in red. The identifications tab shows all identifications for the selected feature, suggested by the GlycopeptideMatcher tool. By selecting an identification, the fragment spectrum is updated with the y- and b- ion series of the peptide sequence and other glycopeptide fragments calculated by the PeptideFragmentSearch tool. — Screenshot shows the results after loading the mass spectrometry raw data file and an analysis file from the OpenMS pipeline into the *glyXtool^MSEvaluator*. On the lower left side all features classified as glycopeptide features are shown. For the selected feature the extracted ion chromatogram of the precursor and its isotopic pattern are visualized, together with its consensus fragment spectrum on the lower right side. Within the spectrum, the oxonium ions found by the *GlycospectrumFilter* tool are marked in red. The identifications tab shows all identifications for the selected feature, suggested by the *GlycopeptideMatcher* tool. By selecting an identification, the fragment spectrum is updated with the y- and b- ion series of the peptide sequence and other glycopeptide fragments calculated by the *PeptideFragmentSearch* tool.

Screenshot shows the results after loading the mass spectrometry raw data file and an analysis file from the OpenMS pipeline into the *glyXtool^MSEvaluator*. On the lower left side all features classified as glycopeptide features are shown. For the selected feature the extracted ion chromatogram of the precursor and its isotopic pattern are visualized, together with its consensus fragment spectrum on the lower right side. Within the spectrum, the oxonium ions found by the *GlycospectrumFilter* tool are marked in red. The identifications tab shows all identifications for the selected feature, suggested by the *GlycopeptideMatcher* tool. By selecting an identification, the fragment spectrum is updated with the y- and b- ion series of the peptide sequence and other glycopeptide fragments calculated by the *PeptideFragmentSearch* tool.

The open-source python software suite glyXtool^MS facilitates the semi-automated analysis of N- and O-glycopeptide mass spectrometry fragmentation data. The software adds new analysis tools for the pipeline engine of OpenMS, which was developed for proteomics experiments. These include a filter to discriminate between glycopeptide and peptide spectra, glycopeptide identification via precursor matching to glycan compositions and in-silico generated peptide sequences, fragment ion annotation as well as scoring tools. The analysis results can be visualized within the glyXtool^MS Evaluator, which also enables further manual analysis, inspection and verification. glyXtool^MS is freely available online on https://github.com/glyXera/glyXtoolMS licensed under the GPL-3.0 open-source license.

Publications

Pioch, M.; Hoffmann, M.; Pralow, A.; Reichl, U.; Rapp, E.: GlyXtool^MS: An Open-Source Pipeline for Semiautomated Analysis of Glycopeptide Mass Spectrometry Data. Analytical Chemistry 90 (20), pp. 11908 - 11916 (2018)

MPG.PuRe

DOI

post-print