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)
- Traveling wave based-IMS MS (TWIMS-MS) such as Structures for Lossless Ion Manipulations (SLIM)-based IMS-MS (Wojcik,R. et al., 2019)
Methods
- Stepped field method (Stow,S.M. et al., 2017)
- Single field method (Kurulugama,R.T. et al., 2015)
- 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)

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) [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 (Dataset ID: MSV000085979)

For sake of readability, the input parameters are split over multiple lines. When using the command line, however, all parameters should 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

Lee, J-Y, Bilbao, A, Conant, CR, Bloodsworth, KJ, Orton, DJ, Zhou, M, ... & Metz, TO (2021). AutoCCS: Automated collision cross section calculation software for ion mobility spectrometry-mass spectrometry. Bioinformatics. https://doi.org/10.1093/bioinformatics/btab429

Contacts

Written by Joon-Yong Lee for the Department of Energy (PNNL, Richland, WA)
Copyright 2020, Battelle Memorial Institute. All Rights Reserved.
E-mail: joonyong.lee@pnnl.gov or proteomics@pnnl.gov
Website: https://omics.pnl.gov/ or https://panomics.pnnl.gov/

License

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