Four datasets are presented to demonstrate the capabilities of the MSroi graphical user-friendly interface. In all cases, raw data files acquired by the vendor software have been converted to commonly used standard open-source data formats (i.e. netCDF, mzXML or imzML). 1. LIPSTAN dataset The LIPSTAN dataset consists of a single LC-MS file in which the analysis of a sample of the EQUISPLASH® standards mixture (Avanti Polar Lipids distributed by Merck) is performed. This mixture contains 13 deuterated lipid internal standards (15:0-18:1(d7) PC, 18:1(d7) Lyso PC, 15:0-18:1(d7) PE, 18:1(d7) Lyso PE, 15:0-18:1(d7) PG sodium salt, 15:0-18:1(d7) PI ammonium salt, 15:0-18:1(d7) PS sodium salt, 15:0-18:1(d7)-15:0 TAG, 15:0-18:1(d7) DAG, 18:1(d7) MAG, 18:1(d7) Chol Ester, d18:1-18:1(d9) SM and C15 Ceramide-d7) at a concentration of 100 µg·mL-1 each. The LC-MS chromatographic method employed a Waters Acquity UPLC system connected to a Waters LCT Premier orthogonal accelerated time of flight mass spectrometer (Waters), operated in both positive and negative electrospray ionisation mode. Full scan spectra were acquired from 100 to 1500 Da. The analytical column was a Waters Acquity UPLC BEH HILIC (100 x 2.1 mm, 1.7 mm of particle size). The two mobile phases were phase A: ACN/H2O 95:5 (v/v) with 10 mM ammonium acetate (adjusted at pH = 8 with NH3); and phase B: ACN/H20 50:50 (v/v) with 10 mM ammonium acetate. Elution gradient was as follows (percentages of A and B, respectively): 0 min (99.9, 0.1), 10 min (80, 20), 11 min (2, 98), 13 min (2, 98), 14 min (99.9, 0.1) and 20 min (99.9, 0.1). This dataset consists of a single netCDF file of the positive ionisation mode named “lipstan.cdf” converted from the raw data using the Waters Databridge tool. 2. LIPJEG3 dataset The LIPJEG3 dataset was generated in a previous study from our research group [https://doi.org/10.1007/s11356-014-3172-5]. Samples correspond to a lipidomic study of human placental choriocarcinoma cells (JEG-3) exposed to DMSO (controls) and a non-lethal dose of the chemical endocrine disruptor TBT (exposed) for 24 h. After lipids extraction, three samples of each group (control and exposed samples) were measured. Details related to the chromatographic conditions can be found in reference [https://doi.org/10.1007/s11356-014-3172-5]. The LIPJEG3 dataset contains six netCDF files corresponding to the three control samples and to the three exposed samples converted from the raw data using the Waters Databridge tool. 3. LCLC dataset The LCLC dataset is composed of data from a single run of an LC×LC-MS analysis. This dataset contains a single mzXML file named “lclc.mzXML” converted from the raw vendor data using the MSconvertGUI tool of the Proteowizard suite. Due to the large size of the LC×LC-MS data, a signal prefilter (threshold peak filter of absolute intensity higher than 100) was applied to reduce the number of m/z values kept for each retention time. In this example, a mixture of nine lipids (17:0 MG, 17:0 Lyso PA, 17:1 Lyso PE, 17:1 Lyso PG, 17:1 Lyso PS, 17:0 Lyso PC, 1,3-17:0 D5 DG, 17:0 cholesteryl ester, 16:0 D31-18:1 PE, 16:0 D31-18:1 PG, 16:0 D31-18:1 PC, 16:0 D31-18:1 PS and 1,2,3-17:0 TG) was analyzed to evaluate the distribution of these compounds into the two-dimensional chromatographic space. 4. PBCMSI dataset The PBCMSI dataset is built up by a single MS image of the tissue surface of a tumour from primary breast carcinoma in mouse. The experimental details can be found in a previous study by Bedia [https://doi.org/10.1007/s00216-020-02595-8]. The MSI acquisition was performed using an Autoflex III MALDI-TOF/TOF instrument (Bruker) equipped with a Smartbeam laser operated at 200 Hz laser repetition rate at the “large focus” setting. MS was acquired in the negative mode in the 400-1200 m/z range, in which the detected molecules were mostly lipids. The pixel size was set to 150 mm, and the final size of the image was 1591 pixels (43 x 37). This dataset is composed of two files: an imzML (metadata file) named “pbcmsi.imzML” containing the data structure, and an ibd (imaging binary file) “pbcmsi.ibd” containing the mass spectral data. The conversion from the raw data to the imzML files using the export tool of the Bruker SCILS software.

The research leading to these results has received funding from the Spanish Ministry of Science and Innovation (MCI, Grant CTQ2017-82598-P). The authors also want to grant support from the Catalan Agency for Management of University and Research Grants (AGAUR, Grant 2017SGR753) and the Spanish MCI (Severo Ochoa Project CEX2018-000794-S). MPC acknowledges a predoctoral FPU 16/02640 scholarship from Spanish Ministry of Education and Vocational Training (MEFP). DRS acknowledges support from a Thought Leader Award from Agilent Technologies.