Dataset Information

Data files for manuscript "Acidic methanol treatment facilitates MALDI-mass spectrometry imaging of energy metabolism"

ABSTRACT: The MALDI mass spectrometry image files for mouse brain sections under various wash condition in negative mode with NEDC matrix and positive mode with THAP matrix: no wash control, wash with 5 mL chloroform, 5 mL MeOH, and 5mL MeOH + 0.05%FA (Fig 1c, Fig S7, Table S7). The files were converted from Bruker .d files to reduce file size and can be opened using IsoScope (https://github.com/xxing9703/Isoscope) under MATLAB environment. Spatial resolution is 50 um.

INSTRUMENT(S): solariX

ORGANISM(S): Mus Musculus (ncbitaxon:10090)

SUBMITTER: Wenyun Lu Shawn M. Davidson

PROVIDER: MSV000092611 | MassIVE | Mon Aug 07 08:03:00 BST 2023

REPOSITORIES: MassIVE

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Publications

Acidic Methanol Treatment Facilitates Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry Imaging of Energy Metabolism.

Lu Wenyun W Park Noel R NR TeSlaa Tara T Jankowski Connor S R CSR Samarah Laith L McReynolds Melanie M Xing Xi X Schembri Jessica J Woolf Morgan T MT Rabinowitz Joshua D JD Davidson Shawn M SM

Analytical chemistry 20230927 40

Detection of small molecule metabolites (SMM), particularly those involved in energy metabolism using MALDI-mass spectrometry imaging (MSI), is challenging due to factors including ion suppression from other analytes present (e.g., proteins and lipids). One potential solution to enhance SMM detection is to remove analytes that cause ion suppression from tissue sections before matrix deposition through solvent washes. Here, we systematically investigated solvent treatment conditions to improve SM ...[more]

PMID: 37756255

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Project description:Experimental Design Type of experiment: In order to evaluate the influence of subinhibitory concentrations of the macrolide antibiotic Azithromycin (AZM) on the global Pseudomonas aeruginosa gene expression, we performed a comparative gene expression analysis of AZM-treated versus untreated P. aeruginosa PAO1 cultures. Experimental factors: P. aeruginosa PAO1 cultures with and without addition of 2 µg/ ml AZM were grown until early stationary phase. Total RNA was extracted when the cultures reached an OD600 of 2.8. The transcriptomes of the untreated cultures were taken as reference values. Both of the AFFYMETRIX Chips of AZM-treated PAO1 (GSM45590, GSM45591) were compared with each of the two chips of the untreated PAO1 (GSM45588, GSM45589). Hybridization procedures and parameters: Hybridization of the probes was carried out according to the manufacturer’s “Expression Analysis Protocol (p. 25: Modified Fluidic Protocol for P. aeruginosa cDNA Assay)”, see http://www.affymetrix.com: Hybridization for 16 h at 50°C and 60 rpm. - Post Hyb Wash 1: 10 cycles of 2 mixes/cycle with Wash Buffer A at 25°C - Post Hyb Wash 2: 4 cycles of 15 mixes/cycle with Wash Buffer B at 50°C - Stain: Stain the probe array for 10 minutes in Streptavidin Solution Mix at 25°C - Post Stain Wash: 10 cycles of 4 mixes/cycle with Wash Buffer A at 30°C - 2nd Stain Wash: Stain the probe array for 10 minutes in antibody solution at 25°C - 3rd Stain Wash: Stain the probe array for 10 minutes in SAPE solution at 25°C - Final Wash: 15 cycles of 4 mixes/cycle with Wash Buffer A at 30°C. The holding temperature is 25°C. Measurement of data and specifications: Data transformation and selection procedures: · The entire signals were scaled to 150 (4% capped median); scaling factors of the arrays were within 3.4 fold of each other, as the % genes called present were in the range of 23.7% and 38.1% for three arrays (GSM455889, GSM45589, GSM45591) and 74,4% for one array (GSM45590). The background levels (Average Background) were similar for all arrays (in a range of 47.20 and 55.64). The Q scores were comparable (in a range of 2.38 and 2.81). The Average Signals of the four arrays were similar (between 187.8 and 228.7). · Scanning hardware: AFFYMETRIX Scanner; software: AFFYMETRIX MAS 5 (Statistical Algorithms Reference Guide, http://www.affymetrix.com/support/technical/technotes/statistical_reference_guide.pdf), MICRO DB 3 and DMT 3 · Image analysis software: AFFYMETRIX MAS 5 Data selection: · Threshold of Signal Log ratio: -1/1; change is I (increased), MI (marginally increased), D (decreased), MD (marginally decreased); change p-value >0.999 or <0.001; only genes that are present (Detection=P) in at least one of the compared chipsets. · Only following genes were considered: Minimal threshold of regulation ±2 fold; minimal change p-values of 0.999 and 0.001, respectively; minimal difference of signal intensities of 200. · The final gene expression data table used by the authors to make their conclusions after data selection and transformation will be published as supplementary data. Keywords: other

Dataset Information

Data files for manuscript "Acidic methanol treatment facilitates MALDI-mass spectrometry imaging of energy metabolism"

Publications

Acidic Methanol Treatment Facilitates Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry Imaging of Energy Metabolism.

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