exfilms

Introduction

ExfilMS is a cross-platform, command line interface (CLI) tool to 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 (Untested on wiff2 scan files acquired using the new SCIEX OS acquisition software - Conversion not supported by ProteoWizard)

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 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 and SCIEX wiff2 scan files (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 (i.e, Intel vs AMD vs ARM) when running ExfilMS with Docker.

5. Unable to perform chromatogram filtering as of now.

Citations

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

Nambiar, V., & Nambiar, S. (2024). ExfilMS (Version 1.2.7) [Computer software]. https://doi.org/10.5281/zenodo.10976761

License

Please refer to our license information here.

Changelog

1.2.7 (2024-04-18)

Bug Fixes

• npm: update npm package version (a3a46bb)