AutoCCS

Automated Collision Cross Section calculation software for ion mobility-mass spectrometry

Main features

AutoCCS supports the following platforms and methods:

• Platforms
  • Drift tube-based ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) instrument (Stow,S.M. et al., 2017), PMID 28763190
  • Traveling wave based-IMS MS (TWIMS-MS) such as Structures for Lossless Ion Manipulations (SLIM)-based IMS-MS (Wojcik,R. et al., 2019), PMID 31450886
• Methods
  • Stepped field method (Stow,S.M. et al., 2017), PMID 28763190
  • Single field method (Kurulugama,R.T. et al., 2015), PMID 26178817
  • Traveling wave-based method
• Calibration functions for single field and traveling wave-based methods
  • Linear function
  • Polynomial functions (e.g. quadratic or cubic functions)
  • Linearized power function (Ruotolo,B.T. et al., 2008), PMID 18600219

How to install AutoCCS

Use conda environment (Recommended)

Please install conda and create an environment from an environment.yml file. More details about managing the conda environment can be found on the Managing environments.

conda env create -f environment.yml

And then activate the new conda environment autoccs.

conda activate autoccs

Use pip

Install Python 3.7 (or newer) [link] and use pip as follows to install dependencies.

pip install -r requirements.txt

Tutorial with demo data

In this tutorial, we demonstrated the CCS determination using AutoCCS for the Agilent tune-mix samples in three different platforms: stepped-field DTIMS-MS, single-field RapidFire-DTIMS-MS, SLIM-based IMS.

Demo dataset is publicly available at MassIVE (Accession: MSV000085979)

For readability purposes, the input parameters are split over multiple lines. When using the command line, all parameters must be included as a single line.

Stepped-Field DTIMS-MS

python -u autoCCS.py
  --target_list_file data/SteppedField-DTIMS/TargetList.csv
  --config_file data/SteppedField-DTIMS/autoCCS_config.xml
  --framemeta_files "data/SteppedField-DTIMS/ImsMetadata/*.txt"
  --feature_files "data/SteppedField-DTIMS/Features_csv/*.csv"
  --output_dir data/SteppedField-DTIMS/Results/
  --threshold_n_fields 5
  --mode multi &> "data/SteppedField-DTIMS/LogFiles/multi.log"

Single-Field RapidFire-DTIMS-MS

python autoCCS.py
  --config_file data/SingleField-RapidFire-DTIMS/autoCCS_config.xml
  --framemeta_files "data/SingleField-RapidFire-DTIMS/ImsMetadata/*.txt"
  --feature_files "data/SingleField-RapidFire-DTIMS/Features_csv/*.csv"
  --calibrant_file data/SingleField-RapidFire-DTIMS/TuneMix-CCS.txt
  --output_dir data/SingleField-RapidFire-DTIMS/Results/
  --tunemix_sample_type AgilentTuneMix
  --sample_meta data/SingleField-RapidFire-DTIMS/Datasets.csv
  --colname_for_sample_type SampleType
  --colname_for_filename RawFileName
  --colname_for_ionization IonPolarity
  --degree 1
  --single_mode batch
  --mode single &> data/SingleField-RapidFire-DTIMS/LogFiles/single.log

SLIM-based IMS-MS

python -u autoCCS.py
  --config_file data/SLIM-IMS/autoCCS_config.xml
  --feature_files "data/SLIM-IMS/Features_csv/*.csv"
  --output_dir data/SLIM-IMS/Results/
  --mode single
  --calibrant_file data/SLIM-IMS/TuneMix-CCS_POS.txt
  --sample_meta data/SLIM-IMS/Datasets.csv
  --tunemix_sample_type AgilentTuneMix
  --colname_for_sample_type SampleType
  --colname_for_filename RawFileName
  --colname_for_ionization IonPolarity
  --single_mode batch
  --degree 2
  --calib_method poly
  --ppm 150 &> data/SLIM-IMS/LogFiles/slim.log

Users are allowed to apply high-order polynomial functions: quadratic (--degree 2), cubic (--degree 3), quartic (--degree 4), and so on.

  --degree 3 # for cubic

Also, it allows users to apply non-linear regression based on the linearized power function.

  --calib_method power

Citation

JY Lee, A Bilbao, CR Conant, KJ Bloodsworth, DJ Orton, M Zhou, … & TO Metz (2021). AutoCCS: Automated collision cross section calculation software for ion mobility spectrometry-mass spectrometry. Bioinformatics. DOI: 10.1093/bioinformatics/btab429, PMID 28763190

Contacts

Written by Joon-Yong Lee for the Department of Energy (PNNL, Richland, WA)\
Copyright 2020, Battelle Memorial Institute. All Rights Reserved.\
E-mail: proteomics@pnnl.gov\
Website: https://github.com/PNNL-Comp-Mass-Spec/AutoCCS or https://www.pnnl.gov/integrative-omics

License

AutoCCS is licensed under the BSD 2-Clause License; License