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Clinprotools v3

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ClinProTools v3.0 is a software package developed by Bruker for the analysis and processing of mass spectrometry data. The core function of ClinProTools is to provide a comprehensive set of tools for the visualization, preprocessing, and statistical analysis of mass spectrometry data, enabling researchers to extract meaningful insights from their data.

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Lab products found in correlation

Flexanalysis v 3, by Bruker (7 mentions) Fleximaging software v4, by Bruker (5 mentions) Prism 7, by GraphPad (2 mentions) Flexcontrol software, by Bruker (2 mentions) Maldi biotyper compass explorer v4, by Bruker (2 mentions) Autoxecute flex control software, by Bruker (2 mentions) Flexcontrol v3, by Bruker (1 mentions) Biotools 3, by Bruker (1 mentions) Flexanalysis software, by Bruker (1 mentions) Mascot server, by Matrix Science (1 mentions) Microflex lt maldi tof mass spectrometer, by Bruker (1 mentions)

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ClinProTools (21 citations)

11 protocols using clinprotools v3

1

MALDI-TOF MS Profiling for Antibiotic Resistance

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The MS spectrum of each spot was analysed by the MALDI Biotyper V.3.1.66 with the most updated spectra library, V.7.0 (7,311 spectra). High-quality spectra were captured using the flexControl V.3.4 software (Bruker Daltonics). These spectra were then imported into the ClinProTools V.3.0 software (Bruker Daltonics) for recognition of mass spectra patterns between groups and preprocessed using the default parameters. Spectra were smoothed with 10 cycles of the Savitzky/Golay algorithm for 10 cycles with a width of 2 m/z. Baseline subtraction was performed with the Top Hat algorithm. Peak picking was performed on the average spectrum from each group, with a signal to noise threshold of 5. Peak selection was performed using the P-value T-test/ANOVA sort mode.
Group selection was based on the presence or absence of drug-resistance genotypes, except for C. difficile in which hypervirulent ribotypes determination was considered.
Flores-Treviño S., Garza-González E., Mendoza-Olazarán S., Morfín-Otero R., Camacho-Ortiz A., Rodríguez-Noriega E., Martínez-Meléndez A, & Bocanegra-Ibarias P. (2019). Screening of biomarkers of drug resistance or virulence in ESCAPE pathogens by MALDI-TOF mass spectrometry. Scientific Reports, 9, 18945.
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2

MALDI Data Analysis Pipeline for Lipid Profiling

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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).
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.
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3

MALDI Lipid Profiling of Ischemia-Reperfusion

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Matrix-assisted laser desorption/ionization data were processed using FlexAnalysis v3.4 (Bruker Daltonics, Billerica, MA, USA) and visualized with FlexImaging software v4.0 (Bruker Daltonics, Billerica, MA, USA). Results were analyzed using ClinProTools v3.0 (Bruker Daltonics, Billerica, MA, USA). Lipids were identified by their m/z values using the literature and LIPID MAPS (http://www.lipidmaps.org/tools/index.html) and confirmed by tandem mass spectrometry (MS/MS) in the LIFT-TOF/TOF mode22 (link). Intergroup comparisons were displayed using data bar plots (Microsoft Excel 2016 Conditional Formatting; Microsoft Corporation, Redmond, WA, USA) 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, USA). For the heatmap, lipid profiles based on average intensities of expressed lipid ions and those associated with different durations of ischemia–reperfusion were compared in GeneCluster 3.023 (link). Hierarchical clustering was applied, and the dendrogram was displayed using Java TreeView23 (link)-25 (link, link). Intergroup differences were compared by one-way analysis of variance (ANOVA) and the Tukey post hoc repeated measures test. χ2 tests assessed proportional alterations in lipid subtypes after different durations of I/R (GraphPad Prism 7, La Jolla, CA, USA).
de la Monte S.M., Gallucci G.M., Lin A., Tong M., Chen X, & Stonestreet B.S. (2020). Critical Shifts in Cerebral White Matter Lipid Profiles After Ischemic–Reperfusion Brain Injury in Fetal Sheep as Demonstrated by the Positive Ion Mode MALDI-Mass Spectrometry. Cell Medicine, 12, 2155179019897002.
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4

Lipid Imaging and Quantification by MALDI-IMS

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MALDI-IMS data normalization to total ion count and visualization was performed with FlexImaging v4.0 software. Imaging spectra were processed by ClinProTools v3.0 (Bruker Daltonics). Each spectrum was baseline corrected, recalibrated, and a peak picking procedure was applied for further statistical analysis. Lipid identification was achieved by comparing mass-to-charge (m/z) values of precursor and product ions obtained by tandem mass spectrometry (MS/MS) analysis with those cataloged in the LIP-IDMAPS database. When MS/MS was inconclusive for lipid structure assignments, identification was made based on previously published reports. The average intensity of lipid ions per ROI was used in R-generated heatmaps and data barplots (version 3.2) to compare time course and recovery responses of ethanol relative to control samples. Barplots were generated in R using the ggplot2 module to visualize the mean percent changes in lipid ion expression. Heatmap hierarchical clustering analysis and data barplots were generated as reported (Nunez et al., 2016 ). Principal component analysis (PCA) generated by ClinProTools was used to compare lipid ion expression patterns among groups.
Yalcin E.B., McLean T., Tong M, & de la Monte S.M. (2017). Progressive white matter atrophy with altered lipid profiles is partially reversed by short-term abstinence in an experimental model of alcohol-related neurodegeneration. Alcohol (Fayetteville, N.Y.), 65, 51-62.
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5

MALDI-Based Lipidomic Analysis of AUD

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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 normalized to total ion count and analyzed using ClinProTools v3.0 (Bruker Daltonics, Billerica, MA). Principal component analysis (PCA) was used to generate 2-D and 3-D plots and compare the AUD and control groups with respect to their overall patterns of lipid ion expression. Inter-group comparisons of the mean ion expression levels were made using T-tests and applying a 5% false discovery rate. Effects of AUD were displayed with R-generated data bar plots (Version 3.2; ggplot2 module) that were scaled by calculating the mean percentage changes in lipid ion levels associated with AUD, focusing on m/z’s between 600 and 1200 Daltons. Overall effects of AUD on different subclasses of lipids were evaluated by Chi-square analysis. P-values less than 0.05 were considered statistically significant.
de la Monte S.M., Kay J., Yalcin E.B., Kril J.J., Sheedy D, & Sutherland G.T. (2017). Imaging mass spectrometry of frontal white matter lipid changes in human alcoholics. Alcohol (Fayetteville, N.Y.), 67, 51-63.
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6

MALDI Mass Spectrometry Lipid Profiling

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MALDI data were processed using Flex Analysis v3.4 (Bruker Daltonics, Billerica, MA) and visualized with Flex Imaging software v4.0 (Bruker Daltonics, Billerica, MA). Results were normalized to total ion count and analyzed statistically using ClinProTools v3.0 (Bruker Daltonics, Billerica, MA). Lipids were identified by comparing the precursor and product ion m/z values with those catalogued in the LIPID MAPS prediction tool database (http://www.lipidmaps.org/tools/index.html). Their identities were confirmed by tandem mass spectrometry (MS/MS) in the LIFT-TOF/TOF mode. Heatmaps were constructed using Version 3.2.2 of R software [37 (link)]. To scale the data, row means were subtracted from each cell. The resulting values were further divided by the standard deviation to obtain a z-score of each cell, yielding a mean of 0 and Standard Deviation (S.D.) of 1. The data were plotted using a cosmetically modified heat map library function in R with a 6-color palette. A hierarchical clustering algorithm using the Euclidean distance function was applied to the overall table to generate a lipid ions dendrogram.
Krotow A., Yalcin E.B., Kay J, & de la Monte S.M. (2016). Comparative Analysis of Lipid Extracts and Imaging Mass Spectrometry for Evaluating Cerebral White Matter Biochemical Pathology in an Experimental Second-Hand Cigarette Smoke Exposure Model. Mass spectrometry & purification techniques, 2(1), 113.
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7

MALDI Mass Spectrometry Lipid Profiling

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MALDI data were processed using Flex Analysis v3.4 (Bruker Daltonics, Billerica, MA) and visualized with Flex Imaging software v4.0 (Bruker Daltonics, Billerica, MA). Results were normalized to total ion count and analyzed statistically using ClinProTools v3.0 (Bruker Daltonics, Billerica, MA). Lipids were identified by comparing the precursor and product ion m/z values with those catalogued in the LIPID MAPS prediction tool database (http://www.lipidmaps.org/tools/index.html). Their identities were confirmed by tandem mass spectrometry (MS/MS) in the LIFT-TOF/TOF mode. Heatmaps were constructed using Version 3.2.2 of R software [37 (link)]. To scale the data, row means were subtracted from each cell. The resulting values were further divided by the standard deviation to obtain a z-score of each cell, yielding a mean of 0 and Standard Deviation (S.D.) of 1. The data were plotted using a cosmetically modified heat map library function in R with a 6-color palette. A hierarchical clustering algorithm using the Euclidean distance function was applied to the overall table to generate a lipid ions dendrogram.
Krotow A., Yalcin E.B., Kay J, & de la Monte S.M. (2016). Comparative Analysis of Lipid Extracts and Imaging Mass Spectrometry for Evaluating Cerebral White Matter Biochemical Pathology in an Experimental Second-Hand Cigarette Smoke Exposure Model. Mass spectrometry & purification techniques, 2(1), 113.
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8

MALDI-TOF MS Analysis of Biofilm Profiles

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The mass spectra obtained from each isolate after MALDI-TOF MS analysis were processed using flexAnalysis software (Bruker Daltonics) in which top-hat baseline subtraction, spectra smoothing (with the Savitzky/Golay algorithm for 10 cycles with 2 m/z width), and normalization (the average spectrum of each group was subjected to peak picking, with a signal to noise threshold of 5) were performed, and they were then imported into the ClinProTools V.3.0 software (Bruker Daltonics) for recognition of mass spectra patterns between groups. Peak selection was performed using the P-value T-test/ANOVA sort mode. Group selection was based on the biofilm production and the presence of biofilm-associated genes.
MS spectra were exported to the Biotools 3.2 software (Bruker Daltonics) in which peptide/protein assignment was performed by the Mascot Server (Matrix Science, Boston, USA) and run against the SwissProt database.
Montoya-Hinojosa E., Bocanegra-Ibarias P., Garza-González E., Alonso-Ambriz Ó.M., Salazar-Mata G.A., Villarreal-Treviño L., Pérez-Alba E., Camacho-Ortiz A., Morfín-Otero R., Rodríguez-Noriega E, & Flores-Treviño S. (2020). Discrimination of biofilm-producing Stenotrophomonas maltophilia clinical strains by matrix-assisted laser desorption ionization–time of flight. PLoS ONE, 15(12), e0244751.
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9

MALDI-TOF Mosquito Leg Profiling

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The spectral profiles obtained from the mosquito legs were visualised using a Microflex LT MALDI-TOF mass spectrometer with FlexControl software (version 3.3; Bruker Daltonics). The spectra were acquired in a positive linear mode at a laser frequency of 50 Hz. The accelerating voltage was 20 kV, and the extraction delay time was 200 ns. Each spectrum corresponded to the ions obtained from the 240 laser shots performed in six regions at the same location and acquired automatically using the AutoXecute Flex Control software (version 2.4; Bruker Daltonics). The MS profiles were visualised using the FlexAnalysis v3.4 software, MALDI Biotyper Compass Explorer v4.1.70 (Bruker Daltonics), and ClinProTools v3.0 software (Bruker Daltonics) was used for data processing.
Huynh L.N., Diarra A.Z., Nguyen H.S., Tran L.B., Do V.N., Ly T.D., Ho V.H., Nguyen X.Q, & Parola P. (2022). MALDI-TOF mass spectrometry identification of mosquitoes collected in Vietnam. Parasites & Vectors, 15, 39.
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10

MALDI-TOF Mass Spectrometry of Bed Bug Profiles

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The spectral profiles obtained from the bed bugs’ heads (adults) and cephalothoraxes (immature stage) were obtained using a Microflex LT MALDITOF mass spectrometer with FlexControl software (version 3.3, Bruker Daltonics). The spectra were acquired in a positive linear mode at a laser frequency of 50 Hz. The accelerating voltage was 20 kV, and the extraction delay time was 200 ns. Each spectrum corresponded to the ions obtained from the 240 laser shots performed in six regions at the same location and acquired automatically using the AutoXecute Flex Control software (version 2.4; Bruker Daltonics). The MS profiles were visualised using the FlexAnalysis v3.4 software, MALDI Biotyper Compass Explorer v4.1.70 (Bruker Daltonics), and ClinProTools v3.0 software (Bruker Daltonics) was used for data processing49 (link).
Hasnaoui B., Bérenger J.M., Delaunay P., Diarra A.Z., Ndiaye E.H., M’madi S.A., Masotti N., Sevestre J, & Parola P. (2023). Survey of bed bug infestations in homeless shelters in southern France. Scientific Reports, 13, 12557.
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