Trapped ion mobility spectrometry (TIMS) adds an additional separation dimension to mass spectrometry (MS) imaging, however, the lack of fragmentation spectra (MS2) impedes confident compound annotation in spatial metabolomics. Here, we describe spatial ion mobility-scheduled exhaustive fragmentation (SIMSEF), a dataset-dependent acquisition strategy that augments TIMS-MS imaging datasets with MS2 spectra. The fragmentation experiments are systematically distributed across the sample and scheduled for multiple collision energies per precursor ion. Extendable data processing and evaluation workflows are implemented into the open source software MZmine. The workflow and annotation capabilities are demonstrated on rat brain tissue thin sections, measured by matrix-assisted laser desorption/ionisation (MALDI)-TIMS-MS, where SIMSEF enables on-tissue compound annotation through spectral library matching and rule-based lipid annotation within MZmine and maps the (un)known chemical space by molecular networking. The SIMSEF algorithm and data analysis pipelines are open source and modular to provide a community resource.

Bruker Daltonics GmbH and Co KG Bremen Germany

Clinic for Diagnostic Imaging Diagnostic Imaging Research Unit University of Zurich Zürich Switzerland

Collaborative Mass Spectrometry Innovation Center University of California San Diego La Jolla CA USA

Institute of Inorganic and Analytical Chemistry University of Münster Münster Germany

Institute of Neuropathology University Hospital Münster Münster Germany

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague Czech Republic

Zobrazit více v PubMed

Taylor MJ, Lukowski JK, Anderton CR. Spatially resolved mass spectrometry at the single cell: recent innovations in proteomics and metabolomics. J. Am. Soc. Mass Spectrom. 2021;32:872–894. doi: 10.1021/jasms.0c00439. PubMed DOI PMC

Niehaus M, Soltwisch J, Belov ME, Dreisewerd K. Transmission-mode MALDI-2 mass spectrometry imaging of cells and tissues at subcellular resolution. Nat. Methods. 2019;16:925–931. doi: 10.1038/s41592-019-0536-2. PubMed DOI

Soltwisch J, et al. MALDI-2 on a trapped ion mobility quadrupole time-of-flight instrument for rapid mass spectrometry imaging and ion mobility separation of complex lipid profiles. Anal. Chem. 2020;92:8697–8703. doi: 10.1021/acs.analchem.0c01747. PubMed DOI

Müller MA, Kompauer M, Strupat K, Heiles S, Spengler B. Implementation of a high-repetition-rate laser in an AP-SMALDI MSI system for enhanced measurement performance. J. Am. Soc. Mass Spectrom. 2021;32:465–472. doi: 10.1021/jasms.0c00368. PubMed DOI

Körber A, Keelor JD, Claes BSR, Heeren RMA, Anthony IGM. Fast mass microscopy: mass spectrometry imaging of a gigapixel image in 34 min. Anal. Chem. 2022;94:14652–14658. doi: 10.1021/acs.analchem.2c02870. PubMed DOI PMC

Bednařík A, et al. MALDI MS imaging at acquisition rates exceeding 100 pixels per second. J. Am. Soc. Mass Spectrom. 2019;30:289–298. doi: 10.1007/s13361-018-2078-8. PubMed DOI

Miki A, et al. MALDI-TOF and MALDI-FTICR imaging mass spectrometry of methamphetamine incorporated into hair. J. Mass Spectrom. 2011;46:411–416. doi: 10.1002/jms.1908. PubMed DOI

Sommella E, et al. MALDI mass spectrometry imaging highlights specific metabolome and lipidome profiles in salivary gland tumor tissues. Metabolites. 2022;12:530. doi: 10.3390/metabo12060530. PubMed DOI PMC

Wang M, et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat. Biotechnol. 2016;34:828–837. doi: 10.1038/nbt.3597. PubMed DOI PMC

Nothias L-F, et al. Feature-based molecular networking in the GNPS analysis environment. Nat. Methods. 2020;17:905–908. doi: 10.1038/s41592-020-0933-6. PubMed DOI PMC

Dührkop K, et al. Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra. Nat. Biotechnol. 2021;39:462–471. doi: 10.1038/s41587-020-0740-8. PubMed DOI

Ludwig M, et al. Database-independent molecular formula annotation using Gibbs sampling through ZODIAC. Nat. Mach. Intell. 2020;2:629–641. doi: 10.1038/s42256-020-00234-6. DOI

Dührkop K, et al. SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information. Nat. Methods. 2019;16:299–302. doi: 10.1038/s41592-019-0344-8. PubMed DOI

Landgraf RR, Prieto Conaway MC, Garrett TJ, Stacpoole PW, Yost RA. Imaging of lipids in spinal cord using intermediate pressure matrix-assisted laser desorption-linear ion trap/Orbitrap MS. Anal. Chem. 2009;81:8488–8495. doi: 10.1021/ac901387u. PubMed DOI PMC

Perdian DC, Lee YJ. Imaging MS methodology for more chemical information in less data acquisition time utilizing a hybrid linear ion trap-orbitrap mass spectrometer. Anal. Chem. 2010;82:9393–9400. doi: 10.1021/ac102017q. PubMed DOI

OuYang C, Chen B, Li L. High throughput in situ DDA analysis of neuropeptides by coupling novel multiplex mass spectrometric imaging (MSI) with gas-phase fractionation. J. Am. Soc. Mass Spectrom. 2015;26:1992–2001. doi: 10.1007/s13361-015-1265-0. PubMed DOI PMC

Hansen RL, Lee YJ. Overlapping MALDI-mass spectrometry imaging for in-parallel MS and MS/MS data acquisition without sacrificing spatial resolution. J. Am. Soc. Mass Spectrom. 2017;28:1910–1918. doi: 10.1007/s13361-017-1699-7. PubMed DOI

Ellis SR, et al. Automated, parallel mass spectrometry imaging and structural identification of lipids. Nat. Methods. 2018;15:515–518. doi: 10.1038/s41592-018-0010-6. PubMed DOI

Trim PJ, et al. Matrix-assisted laser desorption/ionization-ion mobility separation-mass spectrometry imaging of vinblastine in whole body tissue sections. Anal. Chem. 2008;80:8628–8634. doi: 10.1021/ac8015467. PubMed DOI

Lanekoff I, et al. High-speed tandem mass spectrometric in situ imaging by nanospray desorption electrospray ionization mass spectrometry. Anal. Chem. 2013;85:9596–9603. doi: 10.1021/ac401760s. PubMed DOI PMC

Skowronek P, et al. Rapid and in-depth coverage of the (phospho-)proteome with deep libraries and optimal window design for dia-PASEF. Mol. Cell. Proteom. 2022;21:100279. doi: 10.1016/j.mcpro.2022.100279. PubMed DOI PMC

Meier F, Park MA, Mann M. Trapped ion mobility spectrometry and parallel accumulation-serial fragmentation in proteomics. Mol. Cell. Proteom. 2021;20:100138. doi: 10.1016/j.mcpro.2021.100138. PubMed DOI PMC

Helmer PO, Behrens A, Rudt E, Karst U, Hayen H. Hydroperoxylated vs dihydroxylated lipids: differentiation of isomeric cardiolipin oxidation products by multidimensional separation techniques. Anal. Chem. 2020;92:12010–12016. doi: 10.1021/acs.analchem.0c02605. PubMed DOI

Drakopoulou SK, Damalas DE, Baessmann C, Thomaidis NS. Trapped ion mobility incorporated in LC-HRMS workflows as an integral analytical platform of high sensitivity: targeted and untargeted 4D-metabolomics in extra virgin olive oil. J. Agric. Food Chem. 2021;69:15728–15737. doi: 10.1021/acs.jafc.1c04789. PubMed DOI

Fernandez-Lima FA, Kaplan DA, Park MA. Note: integration of trapped ion mobility spectrometry with mass spectrometry. Rev. Sci. Instrum. 2011;82:126106. doi: 10.1063/1.3665933. PubMed DOI PMC

Fernandez-Lima, F., Kaplan, D. A., Suetering, J. & Park, M. A. Gas-phase separation using a trapped ion mobility spectrometer. Int. J. Ion Mobil. Spectrom. 14, 93–98 (2011). PubMed PMC

Meier F, et al. Online parallel accumulation–serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer *. Mol. Cell. Proteom. 2018;17:2534–2545. doi: 10.1074/mcp.TIR118.000900. PubMed DOI PMC

Meier F, et al. Parallel accumulation-serial fragmentation (PASEF): multiplying sequencing speed and sensitivity by synchronized scans in a trapped ion mobility device. J. Proteome Res. 2015;14:5378–5387. doi: 10.1021/acs.jproteome.5b00932. PubMed DOI

Meier F, et al. diaPASEF: parallel accumulation-serial fragmentation combined with data-independent acquisition. Nat. Methods. 2020;17:1229–1236. doi: 10.1038/s41592-020-00998-0. PubMed DOI

Lesur A, et al. Highly multiplexed targeted proteomics acquisition on a TIMS-QTOF. Anal. Chem. 2021;93:1383–1392. doi: 10.1021/acs.analchem.0c03180. PubMed DOI

Distler, U. et al. midiaPASEF maximizes information content in data-independent acquisition proteomics. bioRxiv, 10.1101/2023.01.30.526204 (2023).

Szyrwiel, L., Sinn, L., Ralser, M. & Demichev, V. Slice-PASEF: fragmenting all ions for maximum sensitivity in proteomics. bioRxiv, 10.1101/2022.10.31.514544 (2022).

Skowronek P, et al. Synchro-PASEF allows precursor-specific fragment ion extraction and interference removal in data-independent acquisition. Mol. Cell. Proteom. 2022;22:100489. doi: 10.1016/j.mcpro.2022.100489. PubMed DOI PMC

Wolf C, et al. Mobility-resolved broadband dissociation and parallel reaction monitoring for laser desorption/ionization-mass spectrometry—Tattoo pigment identification supported by trapped ion mobility spectrometry. Anal. Chim. Acta. 2023;1242:340796. doi: 10.1016/j.aca.2023.340796. PubMed DOI

Eiersbrock FB, Orthen JM, Soltwisch J. Validation of MALDI-MS imaging data of selected membrane lipids in murine brain with and without laser postionization by quantitative nano-HPLC-MS using laser microdissection. Anal. Bioanal. Chem. 2020;412:6875–6886. doi: 10.1007/s00216-020-02818-y. PubMed DOI PMC

Burnum KE, et al. Spatial and temporal alterations of phospholipids determined by mass spectrometry during mouse embryo implantation. J. Lipid Res. 2009;50:2290–2298. doi: 10.1194/jlr.M900100-JLR200. PubMed DOI PMC

Hankin JA, Murphy RC. Relationship between MALDI IMS intensity and measured quantity of selected phospholipids in rat brain sections. Anal. Chem. 2010;82:8476–8484. doi: 10.1021/ac101079v. PubMed DOI PMC

Helmer PO, et al. Complementing matrix-assisted laser desorption ionization-mass spectrometry imaging with chromatography data for improved assignment of isobaric and isomeric phospholipids utilizing trapped ion mobility-mass spectrometry. Anal. Chem. 2021;93:2135–2143. doi: 10.1021/acs.analchem.0c03942. PubMed DOI

Schmid R, et al. Integrative analysis of multimodal mass spectrometry data in MZmine 3. Nat. Biotechnol. 2023;41:447–449. doi: 10.1038/s41587-023-01690-2. PubMed DOI PMC

Pulfer M, Murphy RC. Electrospray mass spectrometry of phospholipids. Mass Spectrom. Rev. 2003;22:332–364. doi: 10.1002/mas.10061. PubMed DOI

Korf A, Jeck V, Schmid R, Helmer PO, Hayen H. Lipid species annotation at double bond position level with custom databases by extension of the MZmine 2 open-source software package. Anal. Chem. 2019;91:5098–5105. doi: 10.1021/acs.analchem.8b05493. PubMed DOI

Liebisch G, et al. Update on LIPID MAPS classification, nomenclature, and shorthand notation for MS-derived lipid structures. J. Lipid Res. 2020;61:1539–1555. doi: 10.1194/jlr.S120001025. PubMed DOI PMC

Groessl M, Graf S, Knochenmuss R. High resolution ion mobility-mass spectrometry for separation and identification of isomeric lipids. Analyst. 2015;140:6904–6911. doi: 10.1039/C5AN00838G. PubMed DOI

Zhou Z, Tu J, Xiong X, Shen X, Zhu Z-J. LipidCCS: prediction of collision cross-section values for lipids with high precision to support ion mobility-mass spectrometry-based lipidomics. Anal. Chem. 2017;89:9559–9566. doi: 10.1021/acs.analchem.7b02625. PubMed DOI

Zheng X, et al. A structural examination and collision cross section database for over 500 metabolites and xenobiotics using drift tube ion mobility spectrometry. Chem. Sci. 2017;8:7724–7736. doi: 10.1039/C7SC03464D. PubMed DOI PMC

Wang J, et al. MALDI-TOF MS imaging of metabolites with a N-(1-naphthyl) ethylenediamine dihydrochloride matrix and its application to colorectal cancer liver metastasis. Anal. Chem. 2015;87:422–430. doi: 10.1021/ac504294s. PubMed DOI

Heuckeroth, S. SteffenHeu/simsef_py: SIMSEF v1.0.0. Zenodo10.5281/ZENODO.8009939 (2023).

Xi Y, et al. SMART: a data reporting standard for mass spectrometry imaging. J. Mass Spectrom. 2023;58:e4904. doi: 10.1002/jms.4904. PubMed DOI PMC