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4 protocols using dl dithiothreitol

1

Proteomic Sample Preparation Protocol

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Trypsin, endoprotease Lysine-C (LysC), whole cell yeast protein extract from Saccharomyces cerevisiae, whole cell protein extract from human K562 cells, and DL-dithiothreitol (DTT) were obtained from Promega in Madison, WI. MS-grade Pierce LysN protease (LysN) was obtained from Thermo Fisher in Rockford, IL. Bovine serum albumin (BSA), bradykinin, poly-DL-alanine, iodoacetamide (IAA), and trifluoroacetic acid (TFA) were purchased from Sigma Aldrich in St. Louis, MO. Optima grade water, acetonitrile (ACN), formic acid (FA), and acetic acid (HAc) were purchased from Fisher Scientific in Pittsburg, PA.
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2

Detailed Reagents and Materials for Protein Analysis

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Chemicals were purchased from Sigma-Aldrich Co. (St. Louis, MO, USA), unless stated otherwise. Carbo-free blocking solution was purchased from Vector Laboratory (Burlingame, CA, USA). SuperSignal West Pico Chemiluminescent Substrate was purchased from Thermo Scientific (Rockford, IL, USA). Precast gel (4–20%) and Precision Plus Protein Standard Kaleidoscope Pre-stained protein markers were purchased from Bio-Rad (Hercules, CA, USA). Percoll was purchased from Pharmacia (Piscataway, NJ, USA). NP-40 was purchased from Calbiochem EMD Millipore (Billerica, MA, USA). SimplyBlue SafeStain was purchased from Life Technologies (Carlsbad, CA, USA). The BCA assay kit was purchased from Thermo Scientific. Biotinylated glycans were obtained from Lectinity (Moscow, Russia). ACS grade methanol (MeOH), ACS grade acetonitrile (ACN), Optima LC-MS grade ACN, Optima LC-MS grade water and ammonium bicarbonate were purchased from Fisher Scientific (Pittsburgh, PA, USA). Deionized water (18.2 MΩ cm) was prepared with a Milli-Q Millipore system. Formic acid (≥98%) was obtained from Fluka (Buchs, Switzerland). DL-Dithiothreitol (DTT), Protease-Max surfactant and sequencing-grade modified trypsin were purchased from Promega (Madison, WI, USA). Recombinant lactadherin protein was purchased from R&D Systems (Minneapolis, MN, USA; product 2805-MF/CF).
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3

Protein Digestion Protocol for LC-MS/MS

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According to the quantitative results of the electrophoretic diagram, 200 μL of protein lysate was taken from each sample and placed in a centrifugal tube for an enzyme digestion. We added 2 μL of 1 M DTT (DL-Dithiothreitol, Promega, Beijing, China) to each tube, mixed it, heated it at 56 °C for 15 min, and the briefly spun it by centrifuging, after which it was cooled to room temperature. Each sample was divided into four tubes: 50 μL per tube, to which 150 μL of 50 mM ABC (Vectastain ABC Kit, Jinpan, Shanghai, China) was added to attain a 2 M-urea concentration. Next, we added 1.5 μg trypsin (Putai, Hangzhou, China) to each tube, mixed it with a pipette gun, cut by enzymatic at 37 °C for 4 h, then added 1.5 μg trypsin, cut by enzymatic at 37 °C overnight. After this enzyme digestion process, 20 μL 10% FA (Fisher Scientific, A117-50, Fisher, America) was added and centrifuged at 14 000 × g, from which supernatant was removed for desalting. Finally, one sample was taken from each group, and each analyzed by liquid chromatography-tandem mass spectrometry for 1 h.
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4

Quantitative Protein Profiling via LC-MS/MS

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According to the quantitative results of the electrophoretic diagram, 200 µL of protein lysate was taken from each sample and placed in a centrifugal tube for an enzyme digestion. We added 2 µL of 1M DTT (DL-Dithiothreitol, Promega, Beijing, China) to each tube, mixed it, heated it at 56°C for 15 min, and the brie y spun it by centrifuging, after which it was cooled to room temperature. Each sample was divided into four tubes: 50 µL per tube, to which 150 µL of 50 mM ABC (Vectastain ABC Kit, Jinpan, Shanghai, China) was added to attain a 2M-urea concentration. Next, we added 1.5 µg trypsin (Putai, Hangzhou, China) to each tube, mixed it with a pipette gun, cut by enzymatic at 37°C for 4 h, then added 1.5 µg trypsin, cut by enzymatic at 37°C overnight. After this enzyme digestion process, 20 µL 10% FA (Fisher Scienti c, A117-50, Fisher, America) was added and centrifuged at 14 000 × g, from which supernatant was removed for desalting. Finally, one sample was taken from each group, and each analyzed by liquid chromatography-tandem mass spectrometry for 1 h.
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