Formalin fixed and paraffin embedded (FFPE) AC, SqCC, LCC, SCLC (n=10, 9, 10, 9, respectively) and tumor adjacent normal tissue sections (n=8, 8, 8, 9, respectively) were analyzed.
Samples were analyzed using a Maxis II QTOF instrument equipped with a CaptiveSpray nanoBooster ion source coupled to a Dionex UltiMate 3000 RSLCnano system (Bruker Daltonics GmbH, Bremen, Germany). Peptides were separated on an Acquity M Class BEH130 C18 analytical column (1.7 um, 75 um x 250 mmu) using gradient elution (isocratic hold at 4% for 11 min, then elevating B solvent content to 25% in 75 min, and to 40% in 15 min) following trapping on an Acclaim PepMap100 C18 (5 um, 100 um x 20 mmu) trap column. Solvent A consisted of 0.1% FA in water, Solvent B was 0.1% FA in ACN, and the sample loading buffer was 0.1% TFA + 0.01% HFBA in water.
For MS analysis, DDA measurements were performed. The cycle time was set at 2.5 s, with a dynamic MS/MS exclusion of the same precursor ion for 2 min, or if its intensity is at least 3 times larger than previously. Preferred charge states were set between + 2 and + 5. MS spectra were acquired at 3 Hz in the 150 to 2200 m/z range, while MS/MS spectra were at 4 or 16 Hz depending on the intensity of the precursor. Internal calibration was performed by infusing sodium formate and raw data were recalibrated using the Compass DataAnalysis software 4.3.
[doi:10.25345/C5FB4WQ6K]
[dataset license: CC0 1.0 Universal (CC0 1.0)]
Keywords: lung cancer ; lung tissue ; cancer ; proteomics ; mass spectrometry ; HPLC-MS
Principal Investigators: (in alphabetical order) |
Lilla Turiak, MS Proteomics Research Group, Research Centre for Natural Sciences, Eotvos Lorand Research Network, Hungary |
Submitting User: | rozmarakiraly |
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