Optimum collision energies for proteomics: The impact of ion mobility separation.

Autor: Nagy K; MS Proteomics Research Group, Research Centre for Natural Sciences, Budapest, H-1117, Hungary.; Hevesy György PhD School of Chemistry, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary., Gellén G; MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary., Papp D; Hevesy György PhD School of Chemistry, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary.; MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary., Schlosser G; MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary., Révész Á; MS Proteomics Research Group, Research Centre for Natural Sciences, Budapest, H-1117, Hungary.
Jazyk: angličtina
Zdroj: Journal of mass spectrometry : JMS [J Mass Spectrom] 2023 Sep; Vol. 58 (9), pp. e4957. Date of Electronic Publication: 2023 Jul 06.
DOI: 10.1002/jms.4957
Abstrakt: Ion mobility spectrometry (IMS) is a widespread separation technique used in various research fields. It can be coupled to liquid chromatography-mass spectrometry (LC-MS/MS) methods providing an additional separation dimension. During IMS, ions are subjected to multiple collisions with buffer gas, which may cause significant ion heating. The present project addresses this phenomenon from the bottom-up proteomics point of view. We performed LC-MS/MS measurements on a cyclic ion mobility mass spectrometer with varied collision energy (CE) settings both with and without IMS. We investigated the CE dependence of identification score, using Byonic search engine, for more than 1000 tryptic peptides from HeLa digest standard. We determined the optimal CE values-giving the highest identification score-for both setups (i.e., with and without IMS). Results show that lower CE is advantageous when IMS separation is applied, by 6.3 V on average. This value belongs to the one-cycle separation configuration, and multiple cycles may supposedly have even larger impact. The effect of IMS is also reflected in the trends of optimal CE values versus m/z functions. The parameters suggested by the manufacturer were found to be almost optimal for the setup without IMS; on the other hand, they are obviously too high with IMS. Practical consideration on setting up a mass spectrometric platform hyphenated to IMS is also presented. Furthermore, the two CID (collision induced dissociation) fragmentation cells of the instrument-located before and after the IMS cell-were also compared, and we found that CE adjustment is needed when the trap cell is used for activation instead of the transfer cell. Data have been deposited in the MassIVE repository (MSV000090944).
(© 2023 The Authors. Journal of Mass Spectrometry published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
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