KNIME Workflows for CSC Data

The KNIME platform is the foundation upon which our data analysis workflows are built. KNIME is freely available for download and among the most broadly utilized platforms for analytical workflows. 

To facilitate the use of our tools and approaches in other laboratories, the KNIME workflows we use to process and interrogate our mass spectrometry data are provided below. In addition to the workflow file, an accompanying instructional protocol is also available for download.

cSCIFTING

This workflow begins with an Excel file containing MS database search results. The cScIFTING workflow filters for cell surface N-glycoproteins (de-glycosylated peptides), and generates output suitable for further processing in SurfaceGenie and deposition into the VISUN data repository. Other complementary information includes complete protein annotation (e.g., gene symbol, protein name, GO terms, localization information, and links to relevant websites) and an analysis of the specificity achieved during the CSC experiment (i.e. specific vs. non-specific binders).

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cScIFTING Workflow - KNIME file

cScIFTING Workflow User Guide

GlycoLA

This workflow begins with an Excel file containing MS database search results. GlycoLA filters for cell surface N-glycoproteins (de-glycosylated peptides) and provides the specific position (amino acid residue) in the protein where the N-glycan was localized at the time of the experiment. This information is useful for comparison to established repositories (e.g. UniProt) to determine if unique glycosites have been identified.

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GlycoLA Workflow - KNIME file

GlycoLA Workflow User Guide

CSCombiner

This workflow combines results from individual experiments (e.g. multiple biological replicates of a single cell type, multiple cell types or experiments) into a single merged data file. The CSCombiner uses the output from the cScIFTING workflow and generates an Excel file output suitable for publication and .CSV outputs that are directly compatible with SurfaceGenie, UpSetR, and Protter.

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CSCombiner Workflow - KNIME file

CSCombiner Workflow User Guide