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Update workflow to support xcms version > 4 #19

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49 changes: 36 additions & 13 deletions README.md
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Original file line number Diff line number Diff line change
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## Introduction

The Feature-Based Molecular Networking (FBMN) workflow is a computational method that bridges popular mass spectrometry data processing tools for LC-MS/MS and molecular networking analysis on [GNPS](http://gnps.ucsd.edu). The tools supported are: MZmine2, OpenMS, MS-DIAL, MetaboScape, XCMS, and the mzTab-M format.

The main documentation for Feature-Based Molecular Networking with XCMS can be accessed [here](https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-xcms3/). See our preprint Nothias, L.F. et al [bioRxiv 812404 (2019)](https://www.biorxiv.org/content/10.1101/812404v1).

This repository contains example scripts in Python and R showing how `XCMS` version >= 3 (XCMS3) can be used for the
FBMN workflow in GNPS using a subset of samples of the American Gut Project ([MSV000082678](https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=de2d18fd91804785bce8c225cc94a444)) and soil bacteria ([MSV000079204](https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=d74ca92d9dec4e2883f28506c670e3ca)).
The Feature-Based Molecular Networking (FBMN) workflow is a computational method
that bridges popular mass spectrometry data processing tools for LC-MS/MS and
molecular networking analysis on [GNPS](http://gnps.ucsd.edu). The tools
supported are: MZmine2, OpenMS, MS-DIAL, MetaboScape, XCMS, and the mzTab-M
format.

The main documentation for Feature-Based Molecular Networking with XCMS can be
accessed
[here](https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-xcms3/). See
also the publication [Nothias, L.F. et al Nat Methods 2020
Sep;17(9):905-908](https://doi.org/10.1038/s41592-020-0933-6).

This repository contains example scripts in Python and R showing how
[*xcms*](https://bioconductor.org/packages/xcms) (version >= 4) can be used for
the FBMN workflow in GNPS using a subset of samples of the American Gut Project
([MSV000082678](https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=de2d18fd91804785bce8c225cc94a444))
and soil bacteria
([MSV000079204](https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=d74ca92d9dec4e2883f28506c670e3ca)).

Note: this is an updated version of the workflow to use the newer result objects
and more efficient mass spectrometry (MS) data infrastructure introduced with
*xcms* version 4. For the version with *xcms* < 4 see
[here](https://github.com/DorresteinLaboratory/XCMS3_FeatureBasedMN/tree/1e6f0f36cd9a24eb2ad2b126ad45083fcbde0a72).

### Installation of the XCMS-GNPS workflow for FBMN

Install the latest version of XCMS3 (version >= 3.4) from Bioconductor in R
with:
Install R version >= 4.5. Install the latest version of *xcms* from Bioconductor
in R with:

```
install("BiocManager")
BiocManager::install("xcms")
```
For more information, also refer to the [xcms Bioconductor package](https://www.bioconductor.org/packages/release/bioc/html/xcms.html).

For more information, also refer to the [xcms Bioconductor
package](https://www.bioconductor.org/packages/release/bioc/html/xcms.html).

For utility functions specific to this workflow refer to the Github repository:
[https://github.com/jorainer/xcms-gnps-tools](https://github.com/jorainer/xcms-gnps-tools).
Expand All @@ -25,7 +44,8 @@ For utility functions specific to this workflow refer to the Github repository:

This work builds on the efforts of our many colleagues, please cite their work:

Nothias, L.F. et al [Feature-based Molecular Networking in the GNPS Analysis Environment](https://www.biorxiv.org/content/10.1101/812404v1) bioRxiv 812404 (2019).
[Nothias, L.F. et al Nat Methods 2020
Sep;17(9):905-908](https://doi.org/10.1038/s41592-020-0933-6)

[https://github.com/sneumann/xcms](https://github.com/sneumann/xcms)

Expand All @@ -38,9 +58,12 @@ mass spectrometry data for metabolite profiling using nonlinear peak alignment,

### Running Feature Based Molecular Networking on GNPS

The main documentation for Feature-Based Molecular Networking with GNPS can be accessed [here](https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking/).
The main documentation for Feature-Based Molecular Networking with GNPS can be
accessed
[here](https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking/).

### Contributions

The XCMS-GNPS integration was developed by Johannes Rainer and Michael Witting, in coordination with Louis-Félix Nothias and Daniel Petras.
This tutorial was prepared by Madeleine Ernst and Ricardo da Silva.
The XCMS-GNPS integration was developed by Johannes Rainer and Michael Witting,
in coordination with Louis-Félix Nothias and Daniel Petras. This tutorial was
prepared by Madeleine Ernst and Ricardo da Silva.
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