exfilms

Introduction

ExfilMS is a cross-platform, command line interface (CLI) tool to extract mass spectrometry (MS) data from mzML formatted files, with spectrum 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

   • Spectrum type (profile / centroid)
   • MS level
   • Polarity (positive / negative)
   • Exclude spectra (m/z and intensity)

Supported MS Platforms

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

Instrument Vendor	MS Platform	Status
Bruker	EVOQ TQ-MS	Not Working
ImpactII QToF-MS	Working
solariX MRMS	Working
timsTOFPro TIMS-ToF-MS	Not Working
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 arguments

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

# Interactive

$ exfilms -x

Docker

# Using command line arguments

$ 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 ....

# Interactive

$ 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 Docker command. For example,

-v "/path/on/the/local/machine/":/tmpPath

Once the volume mapping is done, you would use /tmpPath as the input data where required, instead of the actual path on the local machine. For the successful execution of ExfilMS, you are REQUIRED to provide the following:

• -v "/path/to/input/directory/":/inputDirectory
• -v "/path/to/output/directory/":/outputDirectory
• -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 format by ProteoWizard).

2. Unable to parse mzML data that has a file size GREATER THAN 2GB.

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

4. Slow output write speed due to build architecture difference (i.e, Intel vs AMD vs ARM) when running ExfilMS with Docker.

Citations

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

Nambiar, V. (2024). ExfilMS. GitHub. https://github.com/vmalnathnambiar/exfilms

License

Please refer to our license information here.

Changelog

1.1.0 (2024-03-28)

Features

• chromatogram extraction: fix and update isolation window target extraction (1439919), closes #3