Project description:To explore the protein components for scallop byssus, the soluble fractions of scallop byssus was extract. For mass spectrometric analysis, proteins were extracted from byssal adhesive plaques, and the whole protein smple was treated with trypsin and analyzed using Thermo Fisher Q Exactive Mass Spectrometer (Thermo Fisher Scientific, USA). The mass spectrometry raw data were searched against the full set of predicted proteins from the C. farreri genome and Transcriptome using Mascot v2.3.0 (Matrix Science, London, UK).
Project description:<p>18 Bacteroidetes isoaltes were analyzed for their neuroactive potentail using un-targeted and targeted metabolomics. The bacteria were grown to stationary phase, the supernatant was separated and purified using 0.22 um filter. The metabolome from the supernatant was extracted using standard Methanol extraction. The reconstituted supernatant samples were transferred into LC vials and loaded onto a sample tray in the nanoLC coupled to the Q-Exactive Plus mass spectrometer (Thermo Fisher Scientific). Chromatographic separation of metabolites was performed on a Proxeon EASY nLC II System (Thermo Fisher Scientific) equipped with a Thermo Scientific Acclaim PepMap RSLC C18 column (P/N ES800A). The Xbridge BEH Amide (2.5 μm, 2.1 x 150 mm, Waters, Milford, MA, USA) column was used for metabolite separation.</p>
Project description:M. hominis cells were grown in liquid medium supplied with arginine or thymidine as a carbon source. LC-MS analysis was performed on Ultimate 3000 Nano LC System (Thermo Fisher Scientific) coupled with Q Exactive HF benchtop Orbitrap mass spectrometer (Thermo Fisher Scientific) via a nanoelectrospray source (Thermo Fisher Scientific), an untargeted label-free bottom-up proteomic strategy was used, DDA (Data Dependent Acquisition) approach. Protein identification and label-free quantification were performed with PEAKS software.
Project description:LC-MS/MS identification of small subunit peptides of Photosystem II assembly intermediate (NRC) with/without trypsin digestion. Peptide sequence identification with HCD fragmentation using Q-Exactive plus mass spectrometer (Thermo-Fisher)
Project description:Female BVSC clone H18 mESCs were cultured in 2i+LIF culture medium (N2B27 Media, CHIR99021 [30 µM; NC9785126; Thermo Fisher], PD0325901 [10 µM; NC9753132; Thermo Fisher], ESGRO Leukemia Inhibitory Factor (LIF) [1000 U/mL, ESG1106; Sigma-Aldrich]) for 72 hr. Differentiation of ESCs to EpiLCs was performed by seeding the cells on Human Plasma Fibronectin (HPF)-coated plates [16.7 µg/mL; 33016015; Thermo Fisher] in the presence of EpiLC induction medium (N2B27 medium containing activin A [20 ng/mL; 50-398-465; Thermo Fisher]), basic fibroblast growth factor (bFGF) [12 ng/mL; 3139FB025; R&D Systems], and KnockOut Serum Replacement [KSR, 1%; Thermo Fisher]. EpiLC samples were collected 48 hours after starting differentiation. Samples were mock treated with water.
Project description:This study examined microRNA expression of cells maintained in media prepared with replete serum (EVR) or with serum depleted of extracellular vesicles (EVs) by either of two methods: standard overnight ultracentrifugation (UC-EVD) or a proprietary method used by Thermo Fisher (TF-EVD).
Project description:HEK293T cells were ectopically expressing Flag tagged p62 (p62 group) or empty vectors (Control group) for 48h, cell lysates were incubated with anti-Flag affinity gels, and co-immunoprecipitates were subjected to trypsin digestion followed by mass spectrometry analysis. Peptides were separated by the EASY-nLC system (Thermo Fisher) and analyzed by the Q Exactive mass spectrometer (Thermo Fisher). Protein analysis were performed with Thermo Proteome Discoverer 2.1 (Thermo Fisher) and searched against Uniprot Human database. Three samples per group.
Project description:HEK293T cells were ectopically expressing Flag tagged p62 (p62 group) or empty vectors (Control group) for 48h, cell lysates were incubated with anti-Flag affinity gels, and co-immunoprecipitates were subjected to trypsin digestion followed by mass spectrometry analysis. Peptides were separated by the EASY-nLC system (Thermo Fisher) and analyzed by the Q Exactive mass spectrometer (Thermo Fisher). Protein analysis were performed with Thermo Proteome Discoverer 2.1 (Thermo Fisher) and searched against Uniprot Human database. Three samples per group.
Project description:In this project, Q-Exactive HF(Thermo Fisher Scientific,San Jose,CA) was used to acquire mass spectrometry (MS) data for 7 samples in Data Independent Acquisition (DIA) mode. Quantification of peptides and proteins was performed using Spectronaut™ and MSstats software packages
Project description:<p _msttexthash='64160037318' _msthash='272'>Ultra-high-performance liquid chromatography (UHPLC) was conducted using a Vanquish UHPLC system (Thermo Fisher), coupled with a Q Exactive™ HF/Q Exactive™ HF-X mass spectrometer for liquid chromatography-mass spectrometry (LC-MS) analysis. To ensure high resolution and effective analyte retention, a Hypesil Gold chromatographic column (100 × 2.1 mm, 1.9 µm) was used to separate the samples by hydrophilic interaction chromatography (HILIC). In both positive and negative electrospray ionization (ESI) modes, the chromatographic parameters were as follows: flow rate: 0.2 mL/min, column temperature: 40℃, mobile phase A = 0.1% formic acid, B = methanol. The separated metabolites were then analyzed via mass spectrometry, with a scanning range of m/z 100–1500. The MS/MS secondary scan was performed using a data-dependent acquisition mode, and QC samples were used to correct instrument drift and signal fluctuation. Subsequently, the raw LC-MS data files were processed using Compound Discoverer 3.3 (CD3.3; Thermo Fisher Scientific) (Cooper and Yang, 2024). Initially, each metabolite was screened, and the peak area was normalized using the first QC sample. In the subsequent steps, high-resolution molecular ion peaks and characteristic fragment ions were used to predict molecular formulas, and compared with the mzCloud, mzVault, and MassList databases to achieve accurate metabolite identification and relative quantification.</p>