{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T14:49:47Z","timestamp":1785941387896,"version":"3.56.0"},"reference-count":33,"publisher":"American Chemical Society (ACS)","issue":"8","license":[{"start":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T00:00:00Z","timestamp":1783641600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Matrix-assisted laser desorption\/ionization mass spectrometry imaging (MALDI MSI) enables spatial mapping of biomolecules within biological tissues, where conventional MS1-based workflows often result in ambiguous compound annotations. Data-dependent acquisition (DDA) can improve annotation specificity but is biased toward high-abundant ions and lacks reproducibility. Here, we present a novel MALDI MSI workflow integrating data-independent acquisition (DIA) to obtain both spatial and fragmentation information. In this approach, MS1 and DIA MS2 spectra are acquired alternately across the sample without prior knowledge of compound localization. Each image pixel consists of one MS1 and several DIA MS2 subpixels, providing both high spatial resolution for MS1 data and broad m\/z coverage. Using small, randomized m\/z isolation windows reduces spectral overlap and improves fragment-ion specificity. Data were processed using an extended Compound Discoverer, integrating mzCloud and LipidSearch for compound annotation. Applied to tissue of the parasitic worm Fasciola hepatica, this workflow produced detailed lipid maps and improved annotation confidence by combining precursor-mass, DIA MS2, and spatial-correlation information. Our results demonstrate that DIA offers a flexible strategy to integrate fragmentation information into MALDI MSI, expanding its capabilities for spatial metabolomics.<\/jats:p>","DOI":"10.1021\/jasms.6c00128","type":"journal-article","created":{"date-parts":[[2026,7,11]],"date-time":"2026-07-11T03:16:51Z","timestamp":1783739811000},"page":"1890-1900","source":"Crossref","is-referenced-by-count":0,"title":["Data-Independent Acquisition\nfor Improved Compound\nAnnotation in MALDI MS Imaging"],"prefix":"10.1021","volume":"37","author":[{"given":"Carmen","family":"Paschke","sequence":"first","affiliation":[{"name":"Thermo Fisher Scientific (Bremen) GmbH , ,","place":["Bremen, Germany, 28199"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kerstin","family":"Strupat","sequence":"additional","affiliation":[{"name":"Thermo Fisher Scientific (Bremen) GmbH , ,","place":["Bremen, Germany, 28199"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolin M.","family":"Morawietz","sequence":"additional","affiliation":[{"name":"Justus Liebig University , ,","place":["Giessen, Germany, 35392"]},{"name":"TransMIT GmbH , ,","place":["Giessen, Germany, 35392"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karl-Christian","family":"Schaefer","sequence":"additional","affiliation":[{"name":"TransMIT GmbH , ,","place":["Giessen, Germany, 35392"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christoph","family":"Henrich","sequence":"additional","affiliation":[{"name":"Thermo Fisher Scientific (Bremen) GmbH , ,","place":["Bremen, Germany, 28199"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0179-5653","authenticated-orcid":true,"given":"Bernhard","family":"Spengler","sequence":"additional","affiliation":[{"name":"Justus Liebig University , ,","place":["Giessen, Germany, 35392"]},{"name":"TransMIT GmbH , ,","place":["Giessen, Germany, 35392"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,7,10]]},"reference":[{"key":"2026080510101959300_cit1a","first-page":"1041","article-title":"MALDI Ion Imaging\nand Biological Ion Imaging with a new Scanning UV-Laser Microprobe","volume-title":"Proceedings of the In 42nd Annual Conference on Mass\nSpectrometry and Allied Topics","author":"Spengler","year":"1994"},{"key":"2026080510101959300_cit1b","first-page":"1044","article-title":"Development of\na new Scanning UV-Laser Microprobe for Ion Imaging and Confocal Microscop","volume-title":"Proceedings of the In 42nd Annual Conference on Mass\nSpectrometry and Allied Topics","author":"Hubert","year":"1994"},{"key":"2026080510101959300_cit2","doi-asserted-by":"publisher","first-page":"4751","DOI":"10.1021\/ac970888i","article-title":"Molecular\nImaging of Biological Samples:\nLocalization of Peptides and Proteins Using MALDI-TOF MS","volume":"69","author":"Caprioli","year":"1997","journal-title":"Anal. Chem."},{"issue":"4","key":"2026080510101959300_cit3","doi-asserted-by":"publisher","first-page":"606","DOI":"10.1002\/mas.20124","article-title":"Imaging mass spectrometry","volume":"26","author":"McDonnell","year":"2007","journal-title":"Mass\nSpectrom. Rev."},{"issue":"1","key":"2026080510101959300_cit4","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1021\/ac504543v","article-title":"Mass spectrometry\nimaging of biomolecular information","volume":"87","author":"Spengler","year":"2015","journal-title":"Anal. Chem."},{"issue":"1","key":"2026080510101959300_cit5","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1038\/nmeth.4071","article-title":"Atmospheric\npressure MALDI mass spectrometry\nimaging of tissues and cells at 1.4-\u03bcm lateral resolution","volume":"14","author":"Kompauer","year":"2017","journal-title":"Nat. Methods"},{"issue":"20","key":"2026080510101959300_cit6","doi-asserted-by":"publisher","first-page":"2299","DOI":"10.1021\/ac00171a028","article-title":"Laser desorption ionization of proteins with molecular\nmasses exceeding 10,000 Da","volume":"60","author":"Karas","year":"1988","journal-title":"Anal. Chem."},{"issue":"2","key":"2026080510101959300_cit7","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1021\/cr010375i","article-title":"The Desorption\nProcess in MALDI","volume":"103","author":"Dreisewerd","year":"2003","journal-title":"Chem. Rev."},{"issue":"5","key":"2026080510101959300_cit8","doi-asserted-by":"publisher","first-page":"1017","DOI":"10.1021\/jasms.4c00466","article-title":"Mass Spectrometry Imaging\nof Lipid and Metabolite Distributions in Cysts of Besnoitia besnoiti-Infected\nBovine Skin","volume":"36","author":"Wiedemann","year":"2025","journal-title":"J. Am. Soc. Mass Spec."},{"issue":"12","key":"2026080510101959300_cit9","doi-asserted-by":"publisher","first-page":"1897","DOI":"10.1007\/s13361-016-1469-y","article-title":"Untargeted Metabolomics\nStrategies\u2500Challenges and Emerging Directions","volume":"27","author":"Schrimpe-Rutledge","year":"2016","journal-title":"J. Am. Soc. Mass Spec."},{"issue":"1","key":"2026080510101959300_cit10","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1007\/s12566-010-0015-9","article-title":"Advances in structure\nelucidation of small molecules using mass spectrometry","volume":"2","author":"Kind","year":"2010","journal-title":"Bioanalytical Reviews"},{"issue":"5","key":"2026080510101959300_cit11","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1016\/j.jasms.2004.01.007","article-title":"De novo sequencing,\npeptide composition analysis, and composition-based sequencing: A\nnew strategy employing accurate mass determination by fourier transform\nion cyclotron resonance mass spectrometry","volume":"15","author":"Spengler","year":"2004","journal-title":"J.\nAm. Soc. Mass Spec."},{"issue":"1","key":"2026080510101959300_cit12","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1111\/tpj.12608","article-title":"Natural products in Glycyrrhiza glabra (licorice) rhizome\nimaged at the cellular level by atmospheric pressure matrix-assisted\nlaser desorption\/ionization tandem mass spectrometry imaging","volume":"80","author":"Li","year":"2014","journal-title":"Plant Journal"},{"key":"2026080510101959300_cit13","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1016\/j.ijms.2018.06.006","article-title":"Multiple\nTOF\/TOF events in a single\nlaser shot for multiplexed lipid identifications in MALDI imaging\nmass spectrometry","volume":"437","author":"Prentice","year":"2019","journal-title":"Int. J. Mass Spectrom."},{"issue":"16","key":"2026080510101959300_cit14","doi-asserted-by":"publisher","first-page":"7158","DOI":"10.1021\/ac3015142","article-title":"Evaluation of an\nAccurate Mass Approach for the Simultaneous Detection of Drug and\nMetabolite Distributions via Whole-Body Mass Spectrometric Imaging","volume":"84","author":"Shahidi-Latham","year":"2012","journal-title":"Anal. Chem."},{"issue":"9","key":"2026080510101959300_cit15","doi-asserted-by":"publisher","DOI":"10.1002\/ange.202214804","article-title":"Tandem Mass\nSpectrometry Imaging Enables High Definition for Mapping Lipids in\nTissues","volume":"135","author":"Guo","year":"2023","journal-title":"Angew. Chem., Int. E"},{"key":"2026080510101959300_cit16","doi-asserted-by":"publisher","first-page":"515","DOI":"10.1038\/s41592-018-0010-6","article-title":"Automated,\nparallel mass spectrometry imaging and structural identification of\nlipids","volume":"15","author":"Ellis","year":"2018","journal-title":"Nat. Methods"},{"issue":"1","key":"2026080510101959300_cit17","doi-asserted-by":"publisher","first-page":"7495","DOI":"10.1038\/s41467-023-43298-9","article-title":"On-tissue\ndataset-dependent MALDI-TIMS-MS2 bioimaging","volume":"14","author":"Heuckeroth","year":"2023","journal-title":"Nat. Commun."},{"issue":"6","key":"2026080510101959300_cit18","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.O111.016717","article-title":"Targeted Data\nExtraction of the MS\/MS Spectra Generated by Data-independent Acquisition:\nA New Concept for Consistentand Accurate Proteome Analysis","volume":"11","author":"Gillet","year":"2012","journal-title":"Mol. Cell. Proteomics"},{"key":"2026080510101959300_cit19","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1038\/nmeth.2767","article-title":"Drift time-specific collision energies enable deep-coverage\ndata-independent acquisition proteomics","volume":"2","author":"Distler","year":"2014","journal-title":"Nat.\nMethods"},{"key":"2026080510101959300_cit20","volume-title":"A Novel High Definition\nImaging (HDI) Informatics\nPlatform. Technical Report","author":"Waters Corporation.","year":"2011"},{"key":"2026080510101959300_cit21","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1016\/j.chroma.2018.03.002","article-title":"A non-targeted metabolomic\napproach to identify food markers to support discrimination between\norganic and conventional tomato crops","volume":"1546","author":"Marti\u0301nez Bueno","year":"2018","journal-title":"J. Chromatogr.\nA"},{"issue":"25","key":"2026080510101959300_cit22","doi-asserted-by":"publisher","first-page":"4229","DOI":"10.1016\/j.chroma.2010.04.034","article-title":"Precise and global\nidentification of phospholipid molecular\nspecies by an Orbitrap mass spectrometer and automated search engine\nLipid Search","volume":"1217","author":"Taguchi","year":"2010","journal-title":"J. Chromatogr. A"},{"issue":"4","key":"2026080510101959300_cit23","doi-asserted-by":"publisher","DOI":"10.1128\/cmr.00088-19","article-title":"Human and Animal Fascioliasis: Origins\nand Worldwide Evolving Scenario","volume":"35","author":"Mas-Coma","year":"2022","journal-title":"Clin. Microbiol.\nRev."},{"issue":"4","key":"2026080510101959300_cit24","doi-asserted-by":"publisher","first-page":"1145","DOI":"10.1007\/s00436-021-07388-1","article-title":"Spatial visualization of drug uptake and distribution\nin Fasciola hepatica using high-resolution AP-SMALDI mass spectrometry\nimaging","volume":"121","author":"Morawietz","year":"2022","journal-title":"Parasitol. Res."},{"key":"2026080510101959300_cit25","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2020.611270","article-title":"Targeting\nKinases in Fasciola hepatica:\nAnthelminthic Effects and Tissue Distribution of Selected Kinase Inhibitors","volume":"7","author":"Morawietz","year":"2020","journal-title":"Frontiers in Veterinary Science"},{"key":"2026080510101959300_cit26","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1007\/s00216-011-4990-7","article-title":"Mass spectrometry imaging\nwith high resolution in mass and space (HR2MSI) for reliable investigation\nof drug compound distributions on the cellular level","volume":"401","author":"Ro\u0308mpp","year":"2011","journal-title":"Anal. Bioanal. Chem."},{"key":"2026080510101959300_cit27","doi-asserted-by":"publisher","first-page":"W606","DOI":"10.1093\/nar\/gkm324","article-title":"LIPID MAPS\nonline tools for lipid\nresearch","volume":"35","author":"Fahy","year":"2007","journal-title":"Nucleic Acids Res."},{"issue":"5","key":"2026080510101959300_cit28","doi-asserted-by":"publisher","first-page":"32","DOI":"10.5120\/9546-3999","article-title":"Image Recognition\nusing Coefficient\nof Correlation and Structural SIMilarity Index in Uncontrolled Environment","volume":"59","author":"Kaur","year":"2012","journal-title":"International journal of computer applications"},{"issue":"16","key":"2026080510101959300_cit29","doi-asserted-by":"publisher","DOI":"10.1002\/rcm.9110","article-title":"Matrix ions\nas internal standard for high mass accuracy\nmatrix-assisted laser desorption\/ionization mass spectrometry imaging","volume":"35","author":"Treu","year":"2021","journal-title":"Rapid Commun. Mass Spectrom."},{"issue":"6","key":"2026080510101959300_cit30","doi-asserted-by":"publisher","first-page":"2339","DOI":"10.1073\/pnas.94.6.2339","article-title":"Quantitative\nanalysis of biological membrane lipids at the low picomole level by\nnano-electrospray ionization tandem mass spectrometry","volume":"94","author":"Bru\u0308gger","year":"1997","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"issue":"2","key":"2026080510101959300_cit31","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1021\/jasms.0c00368","article-title":"Implementation\nof a High-Repetition-Rate Laser in an AP-SMALDI MSI System for Enhanced\nMeasurement Performance","volume":"32","author":"Mu\u0308ller","year":"2021","journal-title":"J. Am. Soc. Mass Spec."},{"key":"2026080510101959300_cit32","article-title":"MS\nImaging with &gt; 100 pixels\/sec and HRAM: TransMIT AP-SMALDI5AF ion\nsource and Thermo Scientific Orbitrap Astral Analyzer","volume-title":"73rd Annual Conference on Mass Spectrometry and Allied\nTopics","author":"Scha\u0308fer","year":"2025"}],"container-title":["Journal of the American\nSociety for Mass Spectrometry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/jasms.6c00128","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jamsef\/article-pdf\/37\/8\/1890\/65880690\/jasms.6c00128.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jamsef\/article-pdf\/37\/8\/1890\/65880690\/jasms.6c00128.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T14:11:04Z","timestamp":1785939064000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jamsef\/article\/37\/8\/1890\/5206835\/Data-Independent-Acquisition-for-Improved-Compound"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,10]]},"references-count":33,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,7,10]]},"published-print":{"date-parts":[[2026,8,5]]}},"URL":"https:\/\/doi.org\/10.1021\/jasms.6c00128","relation":{},"ISSN":["1044-0305","1879-1123"],"issn-type":[{"value":"1044-0305","type":"print"},{"value":"1879-1123","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,10]]}}}