IIN with XCMS-CAMERA¶
The use of XCMS and CAMERA to generate IIN relies on two custom utility functions (
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.
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:
For IIMN: Schmid R., Petras D., Nothias LF, et al. Ion Identity Molecular Networking for mass spectrometry-based metabolomics in the GNPS Environment. Nat. Comm. 12, 3832 (2021).
For FBMN: Nothias, L.-F., Petras, D., Schmid, R. et al. Feature-based molecular networking in the GNPS analysis environment. Nat. Methods 17, 905–908 (2020).
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
For visualizing results in Cytoscape. Please refer to the main FBMNxIIN documentation.
See our tutorial below for detailed example.
See our FBMN IIN tutorial with XCMS using a subset of the American Gut Project samples on this repository DorresteinLaboratory/XCMS3_FeatureBasedMN/.
This integration was made possible by Johannes Rainer (Eurac Research) and Mar Garcia-Aloy (Eurac Research).