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:

• Precision value rounding
• Spectra filtering (m/z and intensity)
  • Targeted (target file, m/z tolerance and ppm tolerance)
  • Range (minimum and maximum m/z)
• Spectrum data filtering
  • Spectrum type (profile / centroid)
  • MS level
  • Polarity (positive / negative)
  • Exclude spectra (m/z and intensity)

Installation

ExfilMS has been tested on Windows, macOS and Linux.

CLI

[!IMPORTANT]
Prerequisite: Node.js®

$ npm install -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]

• Unable to parse mzML data that has a file size GREATER THAN 2GB.
• Large MS data may cause Node environment to terminate abruptly due to memory limit exhaustion.
• Slow output write speed due to build architecture difference (i.e, Intel vs AMD vs ARM) when running ExfilMS with Docker.
• Unable to output extracted files when running ExfilMS in interactive mode with Docker.

Citations

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

License

Please refer to our license information here.

Changelog

1.0.0 (2024-03-21)

Bug Fixes

• .tmp file path (67ef706)
• eslint config (d57ee15)
• JSON parse string value (f28ef76)
• removed unused dependencies (b222ae0)
• rounding of min and maxMZ from targetFile (4e345bb)
• testDirectory path issue (a708106)

Features

• added config for vitest UI (5e9b656)
• changed function name (4506988)
• enable Docker build (fdee34c)