Project description:ddMS2 run of mouse lung tissue and plasma extract using C8 column in 7.5-minute gradient and positive polarity mode in Q Exactive plus.
Project description:apply C8 column and 7.5 minutes run to feces, small intestine and large intestine samples from mice under negative polarity mode in ddMS2.
Project description:ddMS2 in positive polarity for swab recovery of chemicals from desk top after sampling different concentrations using PRM in Q Exactive Plus.
Project description:This study provides an untargeted lipidomics investigation of ATG7-deficient (cKO) mouse renal proximal tubule cells compared to wild-type (WT) controls to evaluate lipidomic alterations associated with autophagy deficiency. Lipids were extracted from cell culture wells using a single-phase isopropanol:methanol (1:1) extraction protocol at -80 °C, followed by protein precipitation and reconstitution in methanol:isopropanol (1:1). High-resolution LC-MS/MS data acquisition was performed on a Thermo Vanquish Horizon tandem LC system coupled to a Thermo Scientific Exploris 480 mass spectrometer equipped with a Heating Electrospray Ionization (HESI) source. Chromatographic separation was achieved via reverse-phase liquid chromatography using a Waters Premier BEH C18 column (50 mm × 2.1 mm, 1.7 µm) operating at 60 °C with a 7.5-minute segmented gradient. Data were acquired in Data-Dependent Acquisition (DDA) mode (Top 5) in both positive and negative ESI polarities in separate analytical runs across an m/z range of 150–2000. Raw mass spectrometry data files (.raw) were processed using Thermo Compound Discoverer (version 3.3). Structural lipid identification was performed by matching experimental spectra against the LipidBlast spectral library in compliance with Lipid Standards Initiative (LSI) guidelines, using strict accurate mass, retention time, and fragmentation criteria. Peak areas were median-normalized, log-transformed, and statistically evaluated to identify significantly altered lipid species between WT and ATG7-deficient cell groups.
Project description:The presented approach is a combination of analytical flow rate chromatography with ion mobility separation of peptide ions, data-independent acquisition, and raw data processing using the DIA-NN software suite, to conduct fast, low-cost proteomic experiments that only require moderate sample amounts. The present dataset contains a series of benchmarks. Specifically, a dilution series of a K562 digest standard acquired using 5-minute and 3-minute chromatographic gradients, as well as a mixed-species human–E.coli benchmark for quantitative performance. We further demonstrate the application of the proposed approach to the analysis of plasma proteomes of COVID-19 patients, using a 3-minute gradient acquisition on a dual-column liquid chromatography system at a throughput of 398 samples/day.