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6 protocols using q exactive orbitrap lc ms ms system

1

Extracellular Vesicle Proteome Analysis

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OE-MSC-Exos were lysed in STD buffer and centrifuged at 1000 × g for 10 min to collect the supernatants. Proteins were identified using a Q Exactive Orbitrap LC-MS/MS system (Thermo Fisher Scientific, MA, USA).
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2

Differential Peptide Analysis of Preterm and Term hUC-MSC Secretomes

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The peptides from preterm and term hUC-MSC CM were reduced with 10 mM DL-dithiothreitol (DTT; Promega, WI, USA) for 1 h at 56 °C and alkylated with 55 mM iodoacetamide (Promega) for 1 h in the dark at RT. Thereafter, precooled acetone was added, and the peptides were precipitated over 3 h at − 20 °C. After centrifuging for 20 min at 20,000×g and 4 °C, the precipitate was dissolved in 300 μl of the following buffer: 50% triethylamine borane (Sigma) and 0.1% SDS (Sigma). Next, the peptide solution was desalted using a Strata-X C18 column (Phenomenex, Torrance, CA, USA) and dried and labeled with TMT reagent (TMT 6-plex Label Reagent; Thermo Fisher Scientific) for 1 h [36 (link)]. Next, the preterm and term samples were mixed at a 1:1 ratio on the basis of the total peptide amount. Analysis of labeled peptides was performed on a Q Exactive Orbitrap LC-MS/MS system (Thermo Fisher Scientific). Qualitative and relative quantitative analyses of the detected peptides were performed using the SWISSPROT_human database and Mascot software (version 2.3.01). Peptides with absolute fold change ≥ 1.5 and P value < 0.05 were considered differentially expressed.
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3

Phosphoproteomic Analysis of Rat Samples

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Lyophilized samples were dissolved in lithium dodecyl sulfate (LDS) buffer, incubated at 95 °C for 10 min, sonicated and loaded onto a one-dimensional polyacrylamide gel (1DE) system. Trypsin digestion of proteins to peptides occurred after 1DE staining with Coomassie blue and excision of the protein bands. Peptides were extracted from the gels using trifluoroacetic acid (TFA) 0,1% + ACN (50:50), and the resulting supernatant dried in SpeedVac, ressuspended in TFA 0.1% and stored at −20 °C. Proteolytic samples were injected in the Q Exactive-Orbitrap LC-MS/MS System (Thermo Scientific) and MS/MS spectra data acquisition followed by phosphoprotein identification50 (link)51 (link)52 (link), using proteome discovery software (Thermo Scientific). Semi-quantitative analysis of the data was carried out using the International Protein Index (IPI) database for protein search and Rattus novergicus as the organism model. A false discovery rate of 1% was applied. A single phosphopeptide identification was set to be sufficient for phosphoprotein identification. Further data analysis was done similar to the black-and-white method used before50 (link)52 (link). Phosphoproteins resulting from each of the experiments were analyzed as described below.
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4

Comprehensive Antioxidant and Polyphenol Analysis

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The antioxidant activities ABTS+ (2,2′-azinobis-(3-ethylbenzothiazoline-6-sulfonate), DPPH (2,2-diphenyl-1-picrylhydrazyl), and FRAP (ferric reduction antioxidant potency) were determined by UV-VIS spectrophotometry (Shimadzu, Japan) according to the protocols described by Formisano et al. (2021) (link). Results were expressed as mmol Trolox equivalents kg–1 dw. Phenolic Concentration Determination
One hundred milligrams of freeze-dried basil were used to quantify and determine polyphenols using a UHPLC system (Thermo Fisher Scientific, Waltham, MA, USA) equipped with a thermo-stated column (T=25°C, 100 × 2.1 mm, Kinetex 1.7 µm biphenyl, Phenomenex, Torrance, CA, USA) and a quaternary pump (Ultimate 3000, Dionex, Sunnyvale, CA, USA). Mass spectrometry analysis was facilitated by a Q Exactive Orbitrap LC-MS/MS system (Thermo Fisher Scientific, Waltham, MA, USA). Phenolic compound sampling was performed according to the protocol detailed by Pannico et al. (2020) (link). The accuracy and calibration of the instruments used were set and checked using a mixture of reference standards (Thermo Fisher Scientific, Waltham, MA, USA). Data processing and analysis were performed using Xcalibur software, version 3.0.63 (Thermo Fisher Scientific, Waltham, MA, USA), and the results were expressed as µg g–1 dw.
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5

Spectroscopic Analysis of Compounds

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The optical rotation was measured in MeOH by an Autopol IV polarimeter (Rudolph Research Analytical, Hackettstown, NJ, United States). UV spectra were obtained by a UH5300 UV–VIS double beam spectrophotometer (Hitachi Co., Tokyo, Japan). 1D and 2D NMR spectra were obtained by a Bruker AVANCE IIITM 500 and 600 MHz spectrometers (Bruker, Ettlingen, Germany) in methanol-d4, DMSO-d6 using TMS as internal standard. HR-ESI-MS data was obtained on a Thermo Scientific Q Exactive Orbitrap LC-MS/MS System (Thermo Scientific, Waltham, MA, United States). An Ultimate 3000 HPLC system (Dionex Co., Sunnyvale, CA, United States) with an UltiMate 3000 pump and UltiMate 3000 variable wavelength detector was employed to carry out semi-preparative HPLC, with a Nacalai Tesque 5C18-MS-II column (250 × 10 mm, 5 μm). Silica gel (200–300 mesh and 300–400 mesh) for open column chromatography (CC) was purchased from Qingdao Haiyang Chemical Group Co., Ltd. (Qingdao, China). The organic solvents were purchased from Sinopharm Chemical Reagent Co., Ltd. (Shanghai, China). Reagents used for α-glucosidase inhibitory assay (α-glucosidase, 4-nitrophenyl-α-D-glucopyranoside, and acarbose) were purchased from Shanghai Yuanye Biology Co., Ltd. (Shanghai, China), and the absorbance was measured by a full-wavelength microplate reader (Thermo Fisher Scientific Shier Technology Co., Ltd.).
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6

Proteomic Profiling of Exosome Samples

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Exosome samples (250 μg) were lysed in STD buffer (4% SDS, 100 mM Tris/Hcl, and 1 mM dithiothreitol, pH 7.6) and centrifugated at 1000 g for 10 min to collect the supernatants. Proteins were identified using Q Exactive Orbitrap LC-MS/MS system (ThermoFisher Scientific).
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