Academic Journal
AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry–mass spectrometry
| العنوان: | AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry–mass spectrometry |
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| المؤلفون: | Lee, Joon-Yong, Bilbao, Aivett, Conant, Christopher R, Bloodsworth, Kent J, Orton, Daniel J, Zhou, Mowei, Wilson, Jesse W, Zheng, Xueyun, Webb, Ian K, Li, Ailin, Hixson, Kim K, Fjeldsted, John C, Ibrahim, Yehia M, Payne, Samuel H, Jansson, Christer, Smith, Richard D, Metz, Thomas O |
| المساهمون: | Valencia, Alfonso, Genomic Science Program, Office of Biological and Environmental Research, National Institutes of Health, National Institute of Environmental Health Sciences, National Institute of General Medical Sciences, US Department of Energy Advanced Research Projects Agency, Pacific Northwest National Laboratory |
| المصدر: | Bioinformatics ; volume 37, issue 22, page 4193-4201 ; ISSN 1367-4803 1367-4811 |
| بيانات النشر: | Oxford University Press (OUP) |
| سنة النشر: | 2021 |
| الوصف: | Motivation Ion mobility spectrometry (IMS) separations are increasingly used in conjunction with mass spectrometry (MS) for separation and characterization of ionized molecular species. Information obtained from IMS measurements includes the ion’s collision cross section (CCS), which reflects its size and structure and constitutes a descriptor for distinguishing similar species in mixtures that cannot be separated using conventional approaches. Incorporating CCS into MS-based workflows can improve the specificity and confidence of molecular identification. At present, there is no automated, open-source pipeline for determining CCS of analyte ions in both targeted and untargeted fashion, and intensive user-assisted processing with vendor software and manual evaluation is often required. Results We present AutoCCS, an open-source software to rapidly determine CCS values from IMS-MS measurements. We conducted various IMS experiments in different formats to demonstrate the flexibility of AutoCCS for automated CCS calculation: (i) stepped-field methods for drift tube-based IMS (DTIMS), (ii) single-field methods for DTIMS (supporting two calibration methods: a standard and a new enhanced method) and (iii) linear calibration for Bruker timsTOF and non-linear calibration methods for traveling wave based-IMS in Waters Synapt and Structures for Lossless Ion Manipulations. We demonstrated that AutoCCS offers an accurate and reproducible determination of CCS for both standard and unknown analyte ions in various IMS-MS platforms, IMS-field methods, ionization modes and collision gases, without requiring manual processing. Availability and implementation https://github.com/PNNL-Comp-Mass-Spec/AutoCCS. Supplementary information Supplementary data are available at Bioinformatics online. Demo datasets are publicly available at MassIVE (Dataset ID: MSV000085979). |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| DOI: | 10.1093/bioinformatics/btab429 |
| DOI: | 10.1093/bioinformatics/btab429/38843745/btab429.pdf |
| الاتاحة: | https://doi.org/10.1093/bioinformatics/btab429 http://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btab429/38843745/btab429.pdf https://academic.oup.com/bioinformatics/article-pdf/37/22/4193/50335241/btab429.pdf |
| Rights: | https://creativecommons.org/licenses/by/4.0/ |
| رقم الانضمام: | edsbas.45CA90D4 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1093/bioinformatics/btab429 |
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