IIN with XCMS-CAMERA

Introduction

The use of XCMS and CAMERA to generate IIN relies on two custom utility functions (getFeatureAnnotations and getEdgelist) to extract and export MS1 based feature and edge annotations (i.e. grouping of features to adduct/isotope groups of the same compound). In addition, the utility function formatSpectraForGNPS is also used to export MS2 spectra.

Development

These custom functions are available in the GitHub repository https://github.com/jorainer/xcms-gnps-tools.

Representative R-markdown documents and python scripts are available on http://ccms-ucsd.github.io/GNPSDocumentation/fbmn-iin-xcms.

XCMS3 GitHub repository: https://github.com/sneumann/xcms This work builds on the efforts of our many colleagues, please cite their work:

Citations

For IIN: Schmid et al. In preparation.

For FBMN: Nothias, L.F. et al Feature-based Molecular Networking in the GNPS Analysis Environment bioRxiv 812404 (2019).

For GNPS: Wang, M. et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat. Biotechnol. 34, 828–837 (2016).

For XCMS 1) Tautenhahn R, Boettcher C, Neumann S. Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008).

For XCMS 2) Smith, C.A., Want, E.J., O'Maille, G., Abagyan,R., Siuzdak, G. XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification. Analytical Chemistry, 78, 779–787 (2006).

For CAMERA 1): Kuhl, C., Tautenhahn, R., Böttcher, C., Larson, T. R. & Neumann, S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Anal. Chem. 84, 283–289 (2012)

For CAMERA 2): Treutler, H. & Neumann, S. Prediction, Detection, and Validation of Isotope Clusters in Mass Spectrometry Data. Metabolites 6, (2016)

Running the FBMN IIN workflow with XCMS-CAMERA

Step 1: Process your non-targeted LC-MS/MS data with XCMS-CAMERA following the FBMN documentation guidelines.

Step 2: Export the Supplementary Annotations/Pairs:

The use of XCMS and CAMERA to generate IIN relies on two custom utility functions:

getFeatureAnnotations: extracts and exports MS1 based feature annotation. It contains the adduct/isotope annotations generated by CAMERA.

getEdgelist: extracts and exports the Supplementary Pairs file that contains related pairs (i.e. from peak shape correlation analysis, etc) .

Note that the utility function formatSpectraForGNPS of the FBMN must also be used to export MS2 spectra as MGF.

Step 3: Run a FBMN job and add the Supplementary Pairs file following the main IIN documentation See an example of job with IIN job with XCMS-CAMERA

See our tutorial below for detailed example.

Tutorials

See our FBMN IIN tutorial with XCMS using a subset of the American Gut Project samples on this repository DorresteinLaboratory/XCMS3_FeatureBasedMN/.

TO DO NOTES

  • Cytoscape documentation (import of the supplementary feature annotation file, mapping of the feature annotation).

Contributors

This integration was made possible by Johannes Rainer (Eurac Research) and Mar Garcia-Aloy (Eurac Research). This page was created by Louis Felix Nothias (UCSD).