MALDI Data Analysis Pipeline for Lipid Profiling

MALDI data were processed using FlexAnalysis v3.4 (Bruker Daltonics, Billerica, MA) and visualized with FlexImaging software v4.0 (Bruker Daltonics, Billerica, MA). Results were analyzed using ClinProTools v3.0 (Bruker Daltonics, Billerica, MA). Lipids were identified using LIPID MAPS (http://www.lipidmaps.org/tools/index.html) and confirmed by tandem mass spectrometry (MS/MS) in the LIFT-TOF/TOF mode.^{15 (link)} The multiplot function from the R software scatter package (Version 3.2.2) was used to align plots across experimental groups. Intergroup comparisons were displayed using data bar plots (Microsoft Excel 2016 Conditional Formatting) and a heatmap. For the data bar plots, intergroup differences were analyzed using T tests with a 5% false discovery rate (Graphpad Prism 7, La Jolla, CA). For the heatmap, lipid profiles were analyzed using Cluster 3.0.^{16 (link)} Hierarchical clustering was applied, and the dendrogram was displayed using Java TreeView.^{16 (link)–18} Intergroup differences were compared by 1-way analysis of variance (ANOVA) and the post hoc Tukey repeated measures test. χ² tests assessed proportional alterations in lipid subtypes after different durations of I/R (Graphpad Prism 7, La Jolla, CA).

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Gallucci G.M., Tong M., Chen X., Stonestreet B.S., Lin A, & de la Monte S.M. (2019). Rapid Alterations in Cerebral White Matter Lipid Profiles After Ischemic-Reperfusion Brain Injury in Fetal Sheep as Demonstrated by MALDI-Mass Spectrometry. Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society, 22(4), 344-355.

Publication 2019

FlexAnalysis v3.4 FlexImaging software v4.0 ClinProTools v3.0 Graphpad Prism 7

Lipid Maldi Maps Prism Tandem mass spectrometry

Corresponding Organization : Women & Infants Hospital of Rhode Island

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Variable analysis

independent variables

Duration of I/R (ischemia/reperfusion)

dependent variables

Lipid profiles
Proportional alterations in lipid subtypes

control variables

Experimental conditions kept constant to ensure valid results

controls

Positive controls: Not specified
Negative controls: Not specified

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