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21 protocols using proteoextract albumin igg removal kit

1

Plasma Proteome Profiling of YDLKS and NS Patients

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All the plasma protein detection and analyses were started from 2016. 40 of 120 samples from PCC patients with typical YDLKS (10), PLC patients with typical YDLKS (10), PCC patients with NS (10) and PLC patients with NS (10) were chosen for characteristic proteins detection using iTRAQ combined with LC-MS/MS technology. Plasma samples were thawed on ice. Equal amounts of plasma from individuals in each group were pooled to yield 2 distinct pools of 500 ml each. To deplete the high-abundance proteins of each plasma pool, a ProteoExtract™ Albumin/IgG Removal Kit (Merck, Germany, Cat 122642) was used according to the manufacture’s instruction. Briefly, plasma was loaded onto the column and proteins bound with high specificity to a bead-based library of diverse peptide ligands. High-abundance proteins which saturated their corresponding ligands were washed out of the column. The remaining low- and mid-abundance proteins in the column were then eluted and collected. After elution, protein was precipitated with acetone overnight at 20°C and dissolved with iTRAQ dissolution buffer. The total protein content of each group was quantified with a Bradford protein assay kit. 10 μg purified samples was taken for SDS-PAGE electrophoresis.
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2

Albumin and IgG Removal for Proteomic Analysis

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Following the collection, all samples were placed at room temperature for 2 h and the supernatants were then centrifuged at 15,000 × g and at 4°C to remove lipids. Albumin and IgG were removed using the Proteo Extract Albumin/IgG Removal kit (Merck & Co., Inc.) according to the manufacturer’s instructions. Subsequently, the samples were resuspended in lysis buffer (30 mM Tris-HCl, 7 M urea, 2 M thiourea, 4% CHAPS, at pH 8.5), and incubated on ice for 30 min. The suspended samples were then centrifuged at 15,000 × g and at 4°C for 30 min. Protein concentrations were determined using the 2D Quant kit (GE Healthcare BioSciences) according to the manufacturer’s protocol. Finally, the proteins were freeze-dried. All the other reagents were supplied by Sigma-Aldrich; Merck KGaA unless otherwise indicated.
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3

Cell Lysis and Protein Extraction Protocol

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To prepare the cell lysates, cells were extracted in RIPA buffer (PH 8) followed by sonication to disrupt the cellular membranes and centrifugation (10,000× g, 7 min at 4 °C) to remove the cellular debris. A total amount of protein of 2 µg was used to perform the analysis.
Cellular supernatants (1 mL) were centrifuged (1200× g, 10 min at 4 °C) to remove the remaining cells, concentrated an average of 4–5 fold times in Amicon Ultra-4 kgl filter units (Merck Milipore, Burlington, MA, USA) and depleted for albumin/IgGs with the ProteoExtract Albumin/IgG removal kit (Merck Millipore, Burlington, MA, USA).
Sample extracts from the cellular/supernatant fraction were resolved by SDS-PAGE and electro-transferred to nitrocellulose membranes. Detection of the protein of interest was performed with antibodies against total IL-1β (monoclonal anti-IL-1β, Cell Signaling, 1:1000) and cleaved IL-1β (monoclonal anti-IL-1β, Cell Signaling, 1:1000) and normalized with β-actin (monoclonal anti-β-actin, Abcam, dilution:1/5000) or total protein (ponceau). Western blot bands were detected by chemiluminescence using a peroxidase enzymatic reaction (Supersignal, Pierce) and quantified with a ChemiDocTM XRS system using the Quantity-One 1-D analysis software (Bio-Rad).
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4

Depletion of Albumin and IgG from Serum Samples

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The removal of albumin and IgG from sera was performed using a ProteoExtract Albumin/IgG Removal kit (Merck, Darmstadt, Germany) according to the manufacturer’s instructions. In brief, 60 µL of each serum was diluted with 540 µL of binding buffer and allowed to pass through the column by gravity flow. The flow-through fraction was collected in a collection tube. To wash the column, binding buffer was allowed to pass through the column by gravity flow. The flow-through fraction was collected in the same collection tube. Desalting and concentration were performed by ultrafiltration. The albumin- and IgG-depleted samples were buffer-exchanged and centrifuged using 10-kDa molecular-weight cut-off ultra-filtration VIVASPIN 2 (Sartorius, Gottingen, Germany). The samples were centrifuged at 6,000×g at 4°C until less than 100 µL, and then the buffer was exchanged for PBS (–) with centrifugation at 6,000×g at 4°C until concentrated to less than 50 µL. The concentrated samples were adjusted to a final volume of 60 µL with PBS (–)
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5

Plasma Proteomics Workflow

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The plasma of 20 patients derived from experimental group and control group were mixed and prepared for protein extraction, respectively. After protein extraction, highly abundant plasma proteins were removed by using the Proteo Extract Albumin/IgG Removal Kit (Merck, Germany). The total plasma protein concentration was measured using a Bradford protein assay kit (TIANGEN, Beijing, China) according to the manufacturer’s protocol.
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6

Serum Protein Fractionation Protocol

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Equal amounts of serum from the 5 individuals in each group were combined. A ProteoExtract™ Albumin/IgG Removal Kit (Merck, Germany) was used to remove the high-abundance proteins in serum sample according to the manufacturer’s instructions, and serum pools were then desalted with an ultrafiltration filter (Sartorius, Germany). Finally, the total protein samples were quantified with BCA (bicinchoninic acid) assay.
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7

Serum Proteome Profiling of Tuberculosis

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The serum samples were firstly processed with ProteoExtract Albumin/IgG Removal Kit (Merck, Germany) to remove high abundant albumin and immunolgobulin G as the manufacturer’s instructions. Then the serum pools were ultrafiltered through Millipore 10 KD filters (Merck Millipore, Germany). The peptides were reduced using 5 mM dithiothreitol at 37°C for 45 min and alkylated using 10 mM iodoacetamide at room temperature keep away from light for 30 min. All the peptide mixtures were concentrated using a Speed-vac centrifuge (Eppendorf, Germany), dissolved in 0.1% formic acid, and analyzed in an ultra-performance liquid chromatograph (UPLC) system (Waters, Milford, MA) coupled with an LTQ Orbitrap Velos mass spectrometer (ThermoFisher Scientific, Waltham, MA) as previously reported.26 (link),27 (link) Proteome Discoverer software (version 2.4.0.305, Thermo Fisher Scientific, Waltham, MA) were used to process the raw data with search algorithms SEQUEST (version 1.3, Thermo Fisher Scientific, Waltham, MA) against Mycobacterium tuberculosis (strain ATCC 25618/H37Rv) database from Swiss-Prot database (release 2021_04). All the serum samples from the same condition were pooled and the LC-MS/MS analysis was performed in three technical replicates.
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8

MALDI-TOF/TOF Mass Spectrometry Proteomics

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The major instruments used in this experimental study include UltrafleXtreme MALDI-TOF/TOF mass spectrometer from Bruker Daltonics (USA). The Ettan IPGphor 3 Integrated Isoelectric Focusing Unit Electrophoresis System and Ettan DALT six Electrophoresis Unit from GE Healthcare (USA), and Beckman Coulter AU5800 automatic biochemical analyzer from Beckman Coulter (USA). The 2-D Quant Kit and the CyDye DIGE Fluor Labeling Kit were purchased from GE Healthcare (USA). The ProteoExtract Albumin/IgG removal kit was purchased from Merck KGaA (Germany). Research-grade acetonitrile (ACN), trifluoroacetic acid (TFA), Dimethyl formamide, ammonium bicarbonate, and DL-Dithiothreitol were purchased from Sigma-Aldrich (USA)
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9

Serum Protein Fractionation for 2-D Gel

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For 2-D gel electrophoresis, the serum samples were processed by using the ProteoExtract Albumin/IgG removal kit (Merck, Germany) and following the standard protocol provided by the manufacturer. Briefly, 60 μL of each serum was diluted 10-fold with binding buffer, and then the diluted serum sample was added to the resin column and allowed to pass by gravity-flow. The resin column was washed twice with 600 μL of binding buffer. The flow-through fraction was concentrated using a 3kDa cut off centrifugal filter device (Millipore, USA). The final serum protein concentration was determined with the 2-D Quant kit (GE Healthcare, USA) according to the manufacturer's instructions.
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10

IgG Purification from SLE or HC

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SLE or HC IgG was purified using the ProteoExtract Albumin/IgG Removal Kit (122643, Merck) or Protein A/G (BE6868, Easybio) according to the manufacturer’s protocols. For kit-isolated IgG, 0.75M NaHCO3 was used to neutralize the pH of the eluent. IgG was enriched by centrifugal filters (UFC905096, Merck) and resuspended in PBS.
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