Raw data from the manuscript entitled Lipidomic profile of meningiomas harboring different NF2 mutation status
Joanna Bogusiewicz1, Ivana Stanimirova2, Magdalena Gaca-Tabaszewska1, Paulina Szeliska1, Krystyna Soszyńska3, Anna Majdańska3, Agata Ryfa3, Alicja Bartoszewska-Kubiak3, Jacek Furtak4,5, Marcin Birski5, Marek Harat4,5, Barbara Bojko1
1 Department of Pharmacodynamics and Molecular Pharmacology, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-089 Bydgoszcz, Poland
2 Institute of Chemistry, University of Silesia in Katowice, 40-006 Katowice, Poland
3 Laboratory of Clinical Genetics and Molecular Pathology, Department of Pathology, 10th Military Research Hospital and Polyclinic, Bydgoszcz, Poland, 85-681 Bydgoszcz, Poland
4 Medical Faculty, Bydgoszcz University of Science and Technology, 85-796 Bydgoszcz, Poland
5 Department of Neurosurgery, 10th Military Research Hospital and Polyclinic, 85-681 Bydgoszcz, Poland
Data collection: May 2016 - January 2023
1. Chemicals and Materials
Isopropanol, methanol, water, acetonitrile, ammonium acetate and acetic acid used in this research were liquid chromatography-mass spectrometry (LC-MS) grade and were purchased from Merck (Warsaw, Poland). External calibrant Pierce LTQ Velos ESI Positive Ion Calibration Solution was obtained from Thermo Scientific (San Jose, CA, USA), and fibers coated with an octadecyl (C18) were kindly provided by Supelco (Bellefonte, PA, USA).
2. Biological Material
Brain tumors were obtained during neurosurgical procedures in the 10th Military Research Hospital and Polyclinic in Bydgoszcz. The study was approved by the Bioethical Committee in Bydgoszcz (KB 628/2015).
3. Histological Data and Genetic Test Results
Tumor specimens were formalin-fixed and paraffin-embedded. All samples were classified by histopathological examination and graded according to WHO 2016 guidelines. The NF2 mutation was carried out using the multiplex ligation-dependent probe amplification (MLPA) method and followed the manufacturer's protocol.
4. Chemical Biopsy (Solid-Phase Microextraction) Protocol
SPME probes with 7mm C18 sorbent were used to sample the excised brain tumors. The exact protocol was described elsewhere (Bogusiewicz et al. 2022). Briefly, the sorbent was preconditioned in a methanol-water solution, 1:1,v/v. Then, the probe was inserted into the brain tumor for 30 minutes. Subsequently, the probe was removed from the sample, washed, and stored at -30°C until instrumental analysis. Finally, the analytes were desorbed in 150μl of isopropanol: methanol (1:1 v/v) using silanized inserts during 1h desorption under agitation at 850 rpm. Extraction blanks were also prepared (probes underwent all of SPME protocol steps, omitting extraction).
5. Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS) Analysis
LC-HRMS (Q Exactive Focus, Thermo Scientific, Bremen, Germany) was used for instrumental analysis.
The HILIC (HILIC) parameters were as follows: phase A—5 mM ammonium acetate in water; phase B—acetonitrile; gradient—0–2 min at 96% B, gradual decrease of B until 80% B at 15.0 min, and 15.1–21.0 min at 96% B; SeQuantZIC-cHILIC (Merck, Poznań, Poland) 3 µm 100 × 2.1 mm column; mobile phase flow rate—0.4 mL/min; oven temperature—40 °C; and injection volume—10 μL. HILIC-HRMS analysis was conducted in positive (HILIC_pos) and negative (HILIC_neg) ion modes. The MS parameters were given elsewhere (Bogusiewicz et al. 2020).
The RPLC (RPLC) mobile phase was A: methanol: water, 40:60 with 10 mM ammonium acetate and 1 mM acetic acid, and B: isopropanol: methanol, 90:10 with 10 mM ammonium acetate and 1 mM acetic acid. Mobile phases were pumped with the flow rate: 0.2 mL/min, and the gradient was as follows: 0 min – 20% B; 1.0 min – 20% B; 1.5 min – 50% B; 7.5 min – 70% B; 13.0 min – 95% B; 17.0 min – 95% B; 17.1 min – 23.0 min – 20 % B. XSelect C18 Column (Waters, Warsaw, Poland), 3.5 μm, 2.1 mm x 75 mm. The oven temperature was set at 55 °C and the injection volume at 10 μL. RPLC-HRMS analysis was conducted in positive (RPLC_pos) and negative (RPLC_neg) ion modes. The MS parameters were given elsewhere (Bogusiewicz et al. 2020).
Samples were run in full scan mode with a confirmation of inclusion list (dda_MS). The inclusion list was prepared based on the preliminary analysis of the pooled quality control sample run in full scan with discovery fragmentation (dia_MS). Identification was based on LipidSearch 4.1.30 (Thermo Fisher Scientific, San Jose, CA, USA) library search with mass accuracy of <3ppm was searched. The MS parameters were given elsewhere (Bogusiewicz et al. 2020).
The MS was externally calibrated every 72 h and mass accuracy was below 2ppm. Tumor samples in the sequence were randomized, and pooled quality controls (QC) were analyzed every 10–12 injections.
Bogusiewicz et al, 2020; DOI: 10.3791/61260-v
