Introduction

ExfilMS is a cross-platform, command line interface (CLI) tool that allows you to easily extract mass spectrometry (MS) data from mzML formatted files, with filtering capabilities.

Features

1. MS data extraction (spectrum and chromatogram)

2. Precision value rounding

3. Spectra filtering (m/z and intensity)

   • Targeted (target file, m/z tolerance and ppm tolerance)
   • Range (minimum and maximum m/z)

4. Spectrum data filtering

   • Type (profile / centroid)
   • MS level (i.e., 1, 2, ..., n)
   • Polarity (positive / negative)
   • Exclude spectra (m/z and intensity)

Supported MS Platforms

Data extraction and spectrum filtration have been tested on data files acquired on the following MS platforms:

Instrument Vendor	MS Platform	Status / Description
Bruker	EVOQ TQ-MS	Untested (Conversion not supported by ProteoWizard)
	ImpactII QToF-MS	Working
	solariX MRMS	Working
	timsTOFPro TIMS-ToF-MS	Not Working (File size > 2GB)
Waters	XEVOTQXS TQ-MS	Working
	XEVOG2XSQTOF DESI-MS	Working
	XEVOG2XSQTOF REIMS	Working
SCIEX	QTRAP6500+ TQ-MS	Working

Installation

ExfilMS has been tested on Windows, macOS and Linux.

CLI

Important

Prerequisite: Node.js®

$ npm i -g exfilms

Docker

Important

Prerequisite: Docker

# Clone repository

$ git clone https://github.com/vmalnathnambiar/exfilms.git

# Navigate into repository

$ cd exfilms

# Build Docker image

$ docker build -t exfilms .

Usage

CLI

# Using command line flags

$ exfilms -i "/path/to/input/directory/containing/mzML/data/files/" ...

# Running interactive mode

$ exfilms -x

Docker

# Using command line flags

$ docker run --rm -it -v "/path/to/input/directory/":/inputDirectory -v "/path/to/output/directory/":/outputDirectory -v "/path/to/log/directory/":/logDirectory exfilms -i /inputDirectory -o /outputDirectory -l /logDirectory ....

# Running interactive mode

$ docker run --rm -it -v "/path/to/input/directory/":/inputDirectory -v "/path/to/output/directory/":/outputDirectory -v "/path/to/log/directory/":/logDirectory exfilms -x

Note

Running ExfilMS using Docker requires the use of volume mapping in the executed Docker command using -v "/path/on/the/local/machine/":/mappedPath. Once the volume mapping is done, you would then use the appropriate mapped path as the input where required.

For the successful execution of ExfilMS, you are required to map the following paths:

• Input directory (-v "/path/to/input/directory/":/inputDirectory)
• Output directory (-v "/path/to/output/directory/":/outputDirectory)
• Log directory (-v "/path/to/log/directory/":/logDirectory)

For more guidance on how to use ExfilMS, please refer to our available guides below:

• Data Conversion to mzML using ProteoWizard
• How to ExfilMS: The Complete Guide
• How to Create a Target File

Limitations

Warning

1. Unable to extract MS data from Bruker EVOQ instruments (Unsupported file formats by ProteoWizard).

2. Unable to parse mzML data with a file size > 2GB.

3. Large MS data may cause Node environment to terminate abruptly due to memory limit exhaustion.

4. May have slow output write speed due to build architecture difference.

5. Unable to perform chromatogram filtering (work in progress).

Citations

If you use ExfilMS in your work, please cite it using the following:

Nambiar, V., & Nambiar, S. (2024). ExfilMS (Version 1.3.0) [Computer software]. https://doi.org/10.5281/zenodo.10976761

License

Please refer to our license information here.