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FBMN with Progenesis QI

Introduction

The Feature-Based Molecular Networking (FBMN) is a computational method that bridges popular mass spectrometry data processing tools for LC-MS/MS and molecular networking analysis on GNPS. The tools supported are: MZmine2, OpenMS, MS-DIAL, MetaboScape, XCMS, and Progenesis QI.

The main documentation for FBMN can be accessed here.

Below we describe how to use MetaboScape with the FBMN workflow on GNPS.

Using Progenesis QI and the Feature-Based Molecular Networking

Progenesis QI is a proprietary LC-MS feature detection and alignment software developed by Nonlinear Dynamics (Waters, http://www.nonlinear.com/progenesis/qi/ that is compatible with various proprietary and open mass spectrometry format.

Progenesis QI can perform feature detection, alignment and annotation of non-targeted LC-MS/MS data acquired either in data-dependent analysis (DDA) or MSE data independent analysis (DIA), and can also uses the ion mobility spectrometry (IMS) dimension. Feature-based molecular networking can be performed on any of these data types processed with Progenesis QI by exporting the feature quantification table (.TXT file format) and MS/MS spectral summary (.MGF file format) and uploading these files on GNPS for FBMN analysis.

Running Progenesis QI

Please refer to the official documentation for Progenesis QI at: http://www.nonlinear.com/progenesis/qi/

Running a FBMN with Progenesis QI files

FBMN with Progenesis QI can be performed either using the [Superquick FBMN start page] (http://dorresteinappshub.ucsd.edu:5050/featurebasednetworking) or the standard interface of the FBMN workflow (you need to be logged in GNPS first).

Upload your Progenesis QI exported files (feature quantification table and MS/MS spectral summary) to GNPS and select the "Progenesis QI" option in the "Feature Quantification Table Source".

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Refer to the main FBMN documentation. for more information.

Page contributors

Ming Wang (UCSD) and Louis Felix Nothias (UCSD).

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