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Bouwmeester R, Richardson K, Denny R, Wilson ID, Degroeve S, Martens L, Vissers JPC. Predicting ion mobility collision cross sections and assessing prediction variation by combining conventional and data driven modeling. Talanta 2024; 274:125970. [PMID: 38621320 DOI: 10.1016/j.talanta.2024.125970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/01/2024] [Accepted: 03/20/2024] [Indexed: 04/17/2024]
Abstract
The use of collision cross section (CCS) values derived from ion mobility studies is proving to be an increasingly important tool in the characterization and identification of molecules detected in complex mixtures. Here, a novel machine learning (ML) based method for predicting CCS integrating both molecular modeling (MM) and ML methodologies has been devised and shown to be able to accurately predict CCS values for singly charged small molecular weight molecules from a broad range of chemical classes. The model performed favorably compared to existing models, improving compound identifications for isobaric analytes in terms of ranking and assigning identification probability values to the annotation. Furthermore, charge localization was seen to be correlated with CCS prediction accuracy and with gas-phase proton affinity demonstrating the potential to provide a proxy for prediction error based on chemical structural properties. The presented approach and findings represent a further step towards accurate prediction and application of computationally generated CCS values.
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Affiliation(s)
- Robbin Bouwmeester
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
| | | | | | - Ian D Wilson
- Computational & Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, United Kingdom
| | - Sven Degroeve
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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George AC, Schmitz I, Rouvière F, Alves S, Colsch B, Heinisch S, Afonso C, Fenaille F, Loutelier-Bourhis C. Interplatform comparison between three ion mobility techniques for human plasma lipid collision cross sections. Anal Chim Acta 2024; 1304:342535. [PMID: 38637036 DOI: 10.1016/j.aca.2024.342535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
The implementation of ion mobility spectrometry (IMS) in liquid chromatography-high-resolution mass spectrometry (LC-HRMS) workflows has become a valuable tool for improving compound annotation in metabolomics analyses by increasing peak capacity and by adding a new molecular descriptor, the collision cross section (CCS). Although some studies reported high repeatability and reproducibility of CCS determination and only few studies reported good interplatform agreement for small molecules, standardized protocols are still missing due to the lack of reference CCS values and reference materials. We present a comparison of CCS values of approximatively one hundred lipid species either commercially available or extracted from human plasma. We used three different commercial ion mobility technologies from different laboratories, drift tube IMS (DTIMS), travelling wave IMS (TWIMS) and trapped IMS (TIMS), to evaluate both instrument repeatability and interlaboratory reproducibility. We showed that CCS discrepancies of 0.3% (average) could occur depending on the data processing software tools. Moreover, eleven CCS calibrants were evaluated yielding mean RSD below 2% for eight calibrants, ESI Low concentration tuning mix (Tune Mix) showing the lowest RSD (< 0.5%) in both ion modes. Tune Mix calibrated CCS from the three different IMS instruments proved to be well correlated and highly reproducible (R2 > 0.995 and mean RSD ≤ 1%). More than 90% of the lipid CCS had deviations of less than 1%, demonstrating high comparability between techniques, and the possibility to use the CCS as molecular descriptor. We highlighted the need of standardized procedures for calibration, data acquisition, and data processing. This work demonstrates that using harmonized analytical conditions are required for interplatform reproducibility for CCS determination of human plasma lipids.
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Affiliation(s)
- Anaïs C George
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000, Rouen, France
| | - Isabelle Schmitz
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000, Rouen, France
| | - Florent Rouvière
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280 CNRS, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Sandra Alves
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), Paris, France
| | - Benoit Colsch
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191, Gif sur Yvette, France
| | - Sabine Heinisch
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280 CNRS, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Carlos Afonso
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000, Rouen, France
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191, Gif sur Yvette, France
| | - Corinne Loutelier-Bourhis
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000, Rouen, France.
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George AC, Schmitz I, Colsch B, Afonso C, Fenaille F, Loutelier-Bourhis C. Impact of Source Conditions on Collision Cross Section Determination by Trapped Ion Mobility Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:696-704. [PMID: 38430122 DOI: 10.1021/jasms.3c00361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Collision cross section (CCS) values determined in ion mobility-mass spectrometry (IM-MS) are increasingly employed as additional descriptors in metabolomics studies. CCS values must therefore be reproducible and the causes of deviations must be carefully known and controlled. Here, we analyzed lipid standards by trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) to evaluate the effects of solvent and flow rate in flow injection analysis (FIA), as well as electrospray source parameters including nebulizer gas pressure, drying gas flow rate, and temperature, on the ion mobility and CCS values. The stability of ion mobility experiments was studied over 10 h, which established the need for a delay-time of 20 min to stabilize source parameters (mostly pressure and temperature). Modifications of electrospray source parameters induced shifts of ion mobility peaks and even the occurrence of an additional peak in the ion mobility spectra. This behavior could be essentially explained by ion-solvent cluster formation. Changes in source parameters were also found to impact CCS value measurements, resulting in deviations up to 0.8%. However, internal calibration with the Tune Mix calibrant reduced the CCS deviations to 0.1%. Thus, optimization of source parameters is essential to achieve a good desolvation of lipid ions and avoid misinterpretation of peaks in ion mobility spectra due to solvent effects. This work highlights the importance of internal calibration to ensure interoperable CCS values, usable in metabolomics annotation.
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Affiliation(s)
- Anaïs C George
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000 Rouen, France
| | - Isabelle Schmitz
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000 Rouen, France
| | - Benoit Colsch
- Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, Université Paris-Saclay, CEA, INRAE, F-91191 Gif sur Yvette, France
| | - Carlos Afonso
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000 Rouen, France
| | - François Fenaille
- Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, Université Paris-Saclay, CEA, INRAE, F-91191 Gif sur Yvette, France
| | - Corinne Loutelier-Bourhis
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000 Rouen, France
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Jariyasopit N, Limjiasahapong S, Kurilung A, Sartyoungkul S, Wisanpitayakorn P, Nuntasaen N, Kuhakarn C, Reutrakul V, Kittakoop P, Sirivatanauksorn Y, Khoomrung S. Traveling Wave Ion Mobility-Derived Collision Cross Section Database for Plant Specialized Metabolites: An Application to Ventilago harmandiana Pierre. J Proteome Res 2022; 21:2481-2492. [PMID: 36154058 PMCID: PMC9552781 DOI: 10.1021/acs.jproteome.2c00413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Indexed: 11/29/2022]
Abstract
The combination of ion mobility mass spectrometry (IM-MS) and chromatography is a valuable tool for identifying compounds in natural products. In this study, using an ultra-performance liquid chromatography system coupled to a high-resolution quadrupole/traveling wave ion mobility spectrometry/time-of-flight MS (UPLC-TWIMS-QTOF), we have established and validated a comprehensive TWCCSN2 and MS database for 112 plant specialized metabolites. The database included 15 compounds that were isolated and purified in-house and are not commercially available. We obtained accurate m/z, retention times, fragment ions, and TWIMS-derived CCS (TWCCSN2) values for 207 adducts (ESI+ and ESI-). The database included novel 158 TWCCSN2 values from 79 specialized metabolites. In the presence of plant matrix, the CCS measurement was reproducible and robust. Finally, we demonstrated the application of the database to extend the metabolite coverage of Ventilago harmandiana Pierre. In addition to pyranonaphthoquinones, a group of known specialized metabolites in V. harmandiana, we identified flavonoids, xanthone, naphthofuran, and protocatechuic acid for the first time through targeted analysis. Interestingly, further investigation using IM-MS of unknown features suggested the presence of organonitrogen compounds and lipid and lipid-like molecules, which is also reported for the first time. Data are available on the MassIVE (https://massive.ucsd.edu, data set identifier MSV000090213).
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Affiliation(s)
- Narumol Jariyasopit
- Metabolomics
and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj
Metabolomics and Phenomics Center, Faculty
of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Suphitcha Limjiasahapong
- Siriraj
Metabolomics and Phenomics Center, Faculty
of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Alongkorn Kurilung
- Metabolomics
and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Sitanan Sartyoungkul
- Metabolomics
and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Pattipong Wisanpitayakorn
- Metabolomics
and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj
Metabolomics and Phenomics Center, Faculty
of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Narong Nuntasaen
- Center
of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok 10400 Thailand
| | - Chutima Kuhakarn
- Center
of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok 10400 Thailand
| | - Vichai Reutrakul
- Center
of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok 10400 Thailand
| | - Prasat Kittakoop
- Chulabhorn
Graduate Institute, Program in Chemical Sciences, Chulabhorn Royal Academy, Laksi,
Bangkok 10210, Thailand
- Chulabhorn
Research Institute, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand
| | - Yongyut Sirivatanauksorn
- Siriraj
Metabolomics and Phenomics Center, Faculty
of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Sakda Khoomrung
- Metabolomics
and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj
Metabolomics and Phenomics Center, Faculty
of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Center
of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok 10400 Thailand
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