LipostarMSI is a software for mass spectrometry imaging (MSI) lipidomics that supports both untargeted and targeted data analysis, distributed as desktop application.
The workflow supported by LipostarMSI covers all the steps required for MSI data analysis: raw data processing, histological coregistration, manual drawing or importing of regions annotated by pathologists, image visualization, a variety of univariate and multivariate image and spectral analysis tools, co-localization analysis, and automated lipids, metabolites and drug metabolites annotation, including MS/MS-based identification.
- LipostarMSI_Appendix
- Tutorial_Lip_MSI_01 – Getting started with LipostarMSI
- Tutorial_Lip_MSI_02 – MSI file preview
- Tutorial_Lip_MSI_03 – First steps into LipostarMSI: from data import to ROI analysis and lipid identification
- Tutorial_Lip_MSI_04 – Multiple dataset analysis
- Tutorial_Lip_MSI_05 – Import annotations
- Tutorial_Lip_MSI_06 – The Lipostar DB manager and Lipid Builder
- Tutorial_Lip_MSI_07 – Background subtraction
- Tutorial_Lip_MSI_08 – Drug Metabolites Automatic Identification
- Tutorial_Lip_MSI_09 – Quantification
Pharma – Data Analysis – Imaging
Articles:
- Lipostar MSI: Comprehensive, Vendor-Neutral Software for Visualization, Data Analysis, and Automated Molecular Identification in Mass Spectrometry Imaging
- January 2020. Tortorella S, Tiberi P, Bowman AP, Claes BSR, Ščupáková K, Heeren RMA, Ellis SR, Cruciani G
Videos:
- Ion Mobility MSI: Açdding A New Dimension To Spatial Metabolomics
- Practical Applications for Drug Discovery 2020 Webinar. Sara Tortorella, Jens Soltwisch
- Spatial Localization And Identification Of Drug And Metabolites
- Practical Applications for Drug Discovery 2020 Webinar. Sara Tortorella, Giulia Coliva
Life Sciences – Imaging Metabolites
Articles:
- Mass spectrometry imaging of phosphatidylcholine metabolism in lungs administered with therapeutic surfactants and isotopic tracers
- January 2021. Shane R. Ellis, Emily Hall, Madhuriben Panchal, Bryn Flinders, Jens Madsen, Grielof Koster, Ron.M.A. Heeren, Howard W. Clark, Anthony D. Postle
- Comprehensive, Vendor-Neutral Software for Visualization, Data Analysis, and Automated Molecular Identification in Mass Spectrometry Imaging
- January 2020. Tortorella S, Tiberi P, Bowman AP, Claes BSR, Ščupáková K, Heeren RMA, Ellis SR, Cruciani G.
Videos:
- Comprehensive, Vendor-Neutral, High-Throughput Imaging Mass Spectrometry Data Analysis
- Practical Applications for Drug Discovery 2020 Webinar. Sara Tortorella
- Oniro: for HTS rapifleX data analysis
- Pyxis suite: for multi-purpose MSI, including ion mobility MSI
- Lipostar: for LC-MS lipidomics
- MARS: for LC-MS metabolomics
- Action: for affinity measurement
Can LipostarMSI handle data from various MSI vendor native data formats?
Yes, LipostarMSI can process almost all MSI vendor native data formats.
What file types does LipostarMSI read for different instruments?
For Bruker instruments (e.g. timsTOF), it can read the native Bruker folder (e.g., containing the .d folder, .mis file). For all Waters instruments, it reads the native .raw
For other instruments, it either has internal converters or reads the .imzml + .ibd formats.
Can I import multiple .imzML files at once?
Yes, you can import as many .imzML files as you want simultaneously, as long as their respective .ibd files are in the same folder.
How do I define processing and peak picking settings?
Click on “Settings” and then “MSI processing settings” to define your own processing and peak picking settings. You can choose among some defaults settings or create a new one.
How can I define a method for lipid identification?
In the “Settings” menu, select “Lipid identification methods” to create a new method or import an existing one from .csv file. In Tutorial 3 we provide an example of .csv identification method file.
Does LipostarMSI include a module to enrich MSI data with LC-MS/MS data?
Yes, LipostarMSI includes a module to enrich MSI data with LC-MS/MS data from different vendors and methods. This enriched data can then be used in the identification module to increase annotation confidence.
How can I create a list of m/z values to be visualized?
In the “Preferred lists” tab, click the add icon, give the list a name, and then add new m/z values in the m/z values window.
How do I import a previously created preferred list?
Click the import icon in the “Preferred lists” tab to import a .txt file containing a list of m/z values.
Which type of segmentation analyses are available in LipostarMSI?
In the “Imaging” module, you can choose among K-means segmentation, bisecting K-means segmentation, UMAP (HDBSCAN) segmentation.
Can I perform univariate statistical analysis?
Yes, you can perform univariate statistical analysis in LipostarMSI. After having defined your ROIs, go to the “Data Analysis” module, click the settings icon and select “ANOVA/Fold change analysis”.
How corrected p-value is calculated for the ANOVA/Fold change analysis?
Corr p-values are “adjusted or corrected” p-values based on Benjamini-Hochberg procedure
What exactly appears in the Data Analysis Matrix when I import the ROI into the ROI analysis module?
The Data analysis table represents a matrix in which lines are the ROIs and columns are peaks defined by m/z value. The values in the table are the Log base 2 values of the peak intensity and the number of MS/MS fragments associated with the peak, separated by a “/” symbol. Note that the peak intensity is the average peak intensity within your ROI and it also depends on the normalization you may have selected when importing your ROI.
Where can I find the standard log file in LipostarMSI?
The standard log file can be useful for troubleshooting. You can find it in Help -> About -> Open application folder. You can send this .log file to us to help with troubleshooting.
