An open-source software suite for processing glycomics and glycoproteomics mass spectral data

Analytical methods for liquid chromatography-mass spectrometry (LC-MS) of glycans and glycopepeptides are mature and available to biomedical scientists with access to mass spectrometry instruments. The primary barrier to the adoption of such methods by non-glycoscientists is the lack of tools for processing the raw LCMS data, evaluating the results, and results visualizations that present those findings in a systematic fashion. Academic research groups have defined algorithmic approaches for interpretation mass spectra in the glycoscience domain. Despite this effort, there remains a paucity of practical, user accessible tools for processing glycan and glycopeptide mass spectral data. The first problem is that public domain and commercial proteomics workflows make peptide-specific assumptions that exclude released glycans and glycosylated peptides. The second is that available glycoscience mass spectral analysis tools, do not address the full scope of data processing needed for high throughput LC-MS data sets. Thus, users with access to mass spectrometry through local proteomics core facilities do not have access to adequate software tools for processing the liquid-chromatography-mass spectrometry (LC-MS) datasets. The result is a serious bottleneck for dissemination and use of glycoscience LC-MS methods in biomedicine. We have developed three software programs for glycoscience mass spectrometry that we now propose to engineer and disseminate as accessible solutions for biomedical scientists. GlycReSoft processes glycan profiling and integrated omics of glycoproteins. GAGfinder is a second generation algorithm for sequencing glycosaminoglycans from electron activated dissociation (ExD) tandem mass spectra. GlycoDeNovo determines branched glycan topologies and linkage configurations from ExD tandem mass spectra. We propose to engineer and disseminate open source pipelines for processing glycan and glycopeptide LC-MS data. This will include all modules necessary to process vendor-independent mass spectrometry data, perform LC-MS profiling, tandem mass spectrometry assignments and generate publication quality graphical outputs. We will deliver software that builds on available data standards and MS processing libraries. The software will use modern glycan representation standards and communicate with the international glycan structure repository and namespace (GlyTouCan). Users will have the option of running the software as a desktop application, through a server, or as a GRITS Toolbox plugin. The software tools will be available open source through a Github repository. In Aim 1, we will develop our GlycReSoft program and related tools into a complete solution for glycomics and glycoproteomics LC-MS data analysis. In Aim 2, we will develop GAGfinder software into a complete solution for sequencing glycosaminoglycans from ExD tandem mass spectra. In Aim 3, we will develop a pipeline based on our GlycoDeNovo software for sequencing N- and Oglycans.