scholarly journals Generation of a Collision Cross Section Library for Multi-Dimensional Plant Metabolomics Using UHPLC-Trapped Ion Mobility-MS/MS

Metabolites ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 13 ◽  
Author(s):  
Mark Schroeder ◽  
Sven W. Meyer ◽  
Heino M. Heyman ◽  
Aiko Barsch ◽  
Lloyd W. Sumner

The utility of metabolomics is well documented; however, its full scientific promise has not yet been realized due to multiple technical challenges. These grand challenges include accurate chemical identification of all observable metabolites and the limiting depth-of-coverage of current metabolomics methods. Here, we report a combinatorial solution to aid in both grand challenges using UHPLC-trapped ion mobility spectrometry coupled to tandem mass spectrometry (UHPLC-TIMS-TOF-MS). TIMS offers additional depth-of-coverage through increased peak capacities realized with the multi-dimensional UHPLC-TIMS separations. Metabolite identification confidence is simultaneously enhanced by incorporating orthogonal collision cross section (CCS) data matching. To facilitate metabolite identifications, we created a CCS library of 146 plant natural products. This library was generated using TIMS with N2 drift gas to record the TIMSCCSN2 of plant natural products with a high degree of reproducibility; i.e., average RSD = 0.10%. The robustness of TIMSCCSN2 data matching was tested using authentic standards spiked into complex plant extracts, and the precision of CCS measurements were determined to be independent of matrix affects. The utility of the UHPLC-TIMS-TOF-MS/MS in metabolomics was then demonstrated using extracts from the model legume Medicago truncatula and metabolites were confidently identified based on retention time, accurate mass, molecular formula, and CCS.

2018 ◽  
Author(s):  
Valerie Gabelica ◽  
Alexandre A. Shvartsburg ◽  
Carlos Afonso ◽  
Perdita E. Barran ◽  
Justin L. P. Benesch ◽  
...  

Here we present a guide on ion mobility mass spectrometry experiments, which covers both linear and nonlinear methods: what is measured, how the measurements are done, and how to report the results, including the uncertainties on mobility and collision cross section values. The guide aims to clarify some possibly confusing concepts, and the reporting recommendations should help researchers, authors and reviewers to contribute comprehensive reports, so that the ion mobility data can be reused more confidently. Starting from the concept of the definition of the measurand, we emphasize that (i) mobility values (K0) depend intrinsically on ion structure, the nature of the bath gas, temperature, and E/N, (ii) ion mobility does not measure surfaces directly, but collision cross section (CCS) values are derived from mobility values using a physical model, (iii) methods relying on calibration are empirical (and thus may provide method-dependent results) only if the gas nature, temperature or E/N cannot match those of the primary method. Our analysis highlights the urgency of a community effort towards establishing primary standards and reference materials for ion mobility, and provides recommendations to do so. <br><br><br>


The Analyst ◽  
2018 ◽  
Vol 143 (4) ◽  
pp. 949-955 ◽  
Author(s):  
Li Li ◽  
Kristin R. McKenna ◽  
Zhao Li ◽  
Mahipal Yadav ◽  
Ramanarayanan Krishnamurthy ◽  
...  

Identifying small sugar isomers can be challenging by ion mobility-mass spectrometry (IM-MS) alone due to their small collision cross section differences.


2020 ◽  
Vol 92 (22) ◽  
pp. 14976-14982
Author(s):  
Ailin Li ◽  
Christopher R. Conant ◽  
Xueyun Zheng ◽  
Kent J. Bloodsworth ◽  
Daniel J. Orton ◽  
...  

2012 ◽  
Vol 65 (5) ◽  
pp. 504 ◽  
Author(s):  
Antonio N. Calabrese ◽  
Lauren A. Speechley ◽  
Tara L. Pukala

This study demonstrates the ability of travelling wave ion mobility-mass spectrometry to measure collision cross-sections of ions in the negative mode, using a calibration based approach. Here, negative mode ion mobility-mass spectrometry was utilised to understand structural transitions of calmodulin upon Ca2+ binding and complexation with model peptides melittin and the plasma membrane Ca2+ pump C20W peptide. Coexisting calmodulin conformers were distinguished on the basis of their mass and cross-section, and identified as relatively folded and unfolded populations, with good agreement in collision cross-section to known calmodulin geometries. Titration of calcium tartrate to physiologically relevant Ca2+ levels provided evidence for intermediately metalated species during the transition from apo- to holo-calmodulin, with collision cross-section measurements indicating that higher Ca2+ occupancy is correlated with more compact structures. The binding of two representative peptides which exemplify canonical compact (melittin) and extended (C20W) peptide-calmodulin binding models has also been interrogated by ion mobility mass spectrometry. Peptide binding to calmodulin involves intermediates with metalation states from 1–4 Ca2+, which demonstrate relatively collapsed structures, suggesting neither the existence of holo-calmodulin or a pre-folded calmodulin conformation is a prerequisite for binding target peptides or proteins. The biological importance of the different metal unsaturated calmodulin complexes, if any, is yet to be understood.


2016 ◽  
Vol 924 ◽  
pp. 68-76 ◽  
Author(s):  
Gerard Bryan Gonzales ◽  
Guy Smagghe ◽  
Sofie Coelus ◽  
Dieter Adriaenssens ◽  
Karel De Winter ◽  
...  

Author(s):  
Hiroshi Tsugawa ◽  
Kazutaka Ikeda ◽  
Mikiko Takahashi ◽  
Aya Satoh ◽  
Yoshifumi Mori ◽  
...  

To the EditorWe formulated mass spectral fragmentations of lipids across 117 lipid subclasses and included ion mobility tandem mass spectrometry (MS/MS) to provide a comprehensive lipidome atlas with retention time, collision cross section, and MS/MS information. The all-in-one solution from import of raw MS data to export of a common output format (mztab-M) was packaged in MS-DIAL 4 (http://prime.psc.riken.jp/) providing an enhanced standardized untargeted lipidomics procedure following lipidomics standards initiative (LSI) semi-quantitative definitions and shorthand notation system of lipid structures with a 1–2% estimated false discovery rate, which will contribute to harmonizing lipidomics data across laboratories to accelerate lipids research.


2020 ◽  
Vol 68 (39) ◽  
pp. 10937-10943
Author(s):  
Laura Righetti ◽  
Nicola Dreolin ◽  
Alberto Celma ◽  
Mike McCullagh ◽  
Gitte Barknowitz ◽  
...  

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