M/Z: 731.545

The Bathymodiolus puteoserpentis specimen used for high resolution AP-MALDI-MSI was collected during the RV Meteor M126 cruise in 2016 at the Logatchev hydrothermal vent field on the Mid-Atlantic Ridge. The specimen was retrieved with the MARUM-Quest remotely operated vehicle (ROV) at the Irina II vent site at 3038 m depth, 14°45’11.01”N and 44°58’43.98”W, and placed in an insulated container to prevent temperature changes during recovery. Gills were dissected from the mussel as soon as brought on board after ROV retrieval, submerged in precooled 2% w/v carboxymethyl cellulose gel (CMC, Mw ~ 700,000, Sigma-Aldrich Chemie GmbH) and snap-frozen in liquid N2. Samples were stored at -80 °C until use.
The CMC-embedded gills were cross-sectioned at 10 µm thickness with a cryostat (Leica CM3050 S, Leica Biosystems Nussloch GmbH) at a chamber temperature of -35 °C and object holder at -22 °C. Individual sections were thaw-mounted onto coated Polysine slides (Thermo Scientific) and subsequently frozen in the cryostat chamber. Slides with tissue sections were stored in slide containers with silica granules, to prevent air moisture condensation on the tissue upon removal from the freezer. Before AP-MALDI matrix application, the sample was warmed to room temperature under a dry atmosphere in a sealed slide container (LockMailer microscope slide jar, Sigma-Aldrich, Steinheim, Germany), filled with silica granules (Carl Roth GmbH) to avoid condensation on the cold glass slide. The sample glass slide was marked with white paint around the tissue for orientation during image acquisition as previously described[1]. Additionally, optical images of the tissue section were acquired with a digital microscope (VHX-5000 Series, Keyence, Neu-Isenburg, Germany) prior to matrix application. To apply the matrix, we used an ultrafine pneumatic sprayer system with N2 gas (SMALDIPrep, TransMIT GmbH, Giessen, Germany)[2], to deliver 100 μl of a 30 mg/ml solution of 2,5-dihydroxybenzoic acid (DHB; 98% 574 purity, Sigma-Aldrich, Steinheim, Germany) dissolved in acetone/water (1:1 v/v) containing 0.1% trifluoroacetic acid (TFA). To locate the field of view and facilitate laser focusing, a red marker was applied adjacent to the matrix-covered tissue section. Ref: [1] Kaltenpoth M, Strupat K, Svatoš A Linking metabolite production to taxonomic identity in environmental samples by (MA)LDI-FISH. ISME J. 2016 Feb;10(2):527-31. doi: 10.1038/ismej.2015.122. PMID:26172211 [2] Kompauer M, Heiles S, Spengler B. Atmospheric pressure MALDI mass spectrometry imaging of tissues and cells at 1.4-μm lateral resolution. Nat Methods. 2017 Jan;14(1):90-96. doi: 10.1038/nmeth.4071. PMID:27842060
High-resolution AP-MALDI-MSI measurements were carried out at an experimental ion source setup [1][2], coupled to a Fourier transform orbital trapping mass spectrometer (Q Exactive HF, Thermo Fisher Scientific GmbH, Bremen, Germany). The sample was rastered with 233 x 233 laser spots with a step size of 3 µm without oversampling, resulting in an imaged area of 699 x 699 µm. AP-MALDI-MSI measurements were performed in positive mode for a mass detection range of 400–1200 Da and a mass resolving power of 240,000 (at 200 m/z). After AP-MALDI-MSI, the measured sample surface was recorded using a stereomicroscope (SMZ25, Nikon, Düssedorf, Germany). Ref: [1] Kompauer M, Heiles S, Spengler B. Atmospheric pressure MALDI mass spectrometry imaging of tissues and cells at 1.4-μm lateral resolution. Nat Methods. 2017 Jan;14(1):90-96. doi: 10.1038/nmeth.4071. PMID:27842060 [2] Kompauer M, Heiles S, Spengler B. Autofocusing MALDI mass spectrometry imaging of tissue sections and 3D chemical topography of nonflat surfaces. Nat Methods. 2017 Dec;14(12):1156-1158. doi:10.1038/nmeth.4433. PMID:28945703

Fig. 2 MALDI-MSI data from the same mouse lung tissue analyzed in Fig. 1. A: Optical image of the post-MSI, H&E-stained tissue section. B–D, F–G: Ion images of (B) m/z 796.6855 ([U13C-DPPC+Na]+), (C) m/z 756.5514 ([PC32:0+Na]+), (D) m/z 765.6079 ([D9-PC32:0+Na]+), (F) m/z 754.5359 ([PC32:1+Na]+), and (G) m/z 763.5923 ([D9-PC32:1+Na]+). E, H: Ratio images of (E) [D9-PC32:0+Na]+:[PC32:0+Na]+ and (H) [D9-PC32:1+Na]+:[PC32:1+Na]+. Part-per-million (ppm) mass errors are indicated in parentheses. All images were visualized using total-ion-current normalization and using hotspot removal (high quantile = 99%). DPPC = PC16:0/16:0. U13C-DPPC, universally 13C-labeled dipalmitoyl PC; PC, phosphatidylcholine; MSI, mass spectrometry imaging; H&E, hematoxylin and eosin. Fig 1-3, Fig S1-S3, S5

Supplementary Figure S6. Ion distribution images for (a) [PC36:4+Na]+ (m/z 804.5514) and (b) [PC38:6+Na]+ (m/z 828.5515) obtained from mouse lung tissue collected 6 h after administration of D9- choline and U13C-DPPC–containing CHF5633. Parts-per-million (ppm) mass errors are indicated in parentheses. (c) Magnification of the boxed region in (a) with selected bronchiolar regions outlined in white boxes. (d) The corresponding H&E-stained tissue section with the same selected bronchiolar regions outlined in black boxes. These data demonstrate the co-localisation of the polyunsaturated lipids PC36:4 and PC38:6 with the bronchiolar regions of the lung. All MSI images were visualised using total ion current normalisation and hotspot removal (high quantile = 99%).

A more complete and holistic view on host–microbe interactions is needed to understand the physiological and cellular barriers that affect the efficacy of drug treatments and allow the discovery and development of new therapeutics. Here, we developed a multimodal imaging approach combining histopathology with mass spectrometry imaging (MSI) and same section imaging mass cytometry (IMC) to study the effects of Salmonella Typhimurium infection in the liver of a mouse model using the S. Typhimurium strains SL3261 and SL1344. This approach enables correlation of tissue morphology and specific cell phenotypes with molecular images of tissue metabolism. IMC revealed a marked increase in immune cell markers and localization in immune aggregates in infected tissues. A correlative computational method (network analysis) was deployed to find metabolic features associated with infection and revealed metabolic clusters of acetyl carnitines, as well as phosphatidylcholine and phosphatidylethanolamine plasmalogen species, which could be associated with pro-inflammatory immune cell types. By developing an IMC marker for the detection of Salmonella LPS, we were further able to identify and characterize those cell types which contained S. Typhimurium. [dataset] Nicole Strittmatter. Holistic Characterization of a Salmonella Typhimurium Infection Model Using Integrated Molecular Imaging, metabolights_dataset, V1; 2022. https://www.ebi.ac.uk/metabolights/MTBLS2671.

The human colorectal adenocarcinoma sample was excised during a surgical operation performed at the Imperial College Healthcare NHS Trust. The sample and procedures were carried out in accordance with ethical approval (14/EE/0024).