Azoxymethane (Sigma, United States), dextran sulfate sodium (36–50 kDa, MP Biomedicals, United States), phosphate-buffered saline (Hyclone, United States), PageRuler Plus Prestained Protein Ladder (ThermoFisher, United States), TMT® Mass Tagging Kits and Reagents (ThermoFisher, United States), dithiothreitol (Sigma, United States), iodoacetamide (Sigma, United States), sodium dodecyl sulfate (Sigma, United States), urea (Sigma, United States), pancreatin (Promega, China), ammonium bicarbonate (Sigma, United States), UltraPure water (ThermoFisher, United States), triethylammonium bicarbonate buffer (Sigma, United States), acetonitrile (ThermoFisher, United States), formic acid (ThermoFisher, United States), acetone (ThermoFisher, United States), ProteoMiner Low-Abundance Protein Enrichment Kit (Bio-Rad, United States), and trifluoroacetate (Sigma, United States) were used in this study.
Triethylammonium bicarbonate buffer
Manufactured by Merck Group
Sourced in United States, Germany
Triethylammonium bicarbonate buffer is a laboratory reagent used to maintain a specific pH range in various chemical and biological applications. It is a salt of triethylamine and carbonic acid, providing a buffering system that helps stabilize the pH of solutions. The core function of this buffer is to control and regulate the acidity or basicity of the reaction environment, enabling optimal conditions for various experiments and analyses.
Automatically generated - may contain errors
Lab products found in correlation
Formic acid, by Thermo Fisher Scientific (9 mentions)
Iodoacetamide, by Merck Group (6 mentions)
Trypsin, by Promega (6 mentions)
Acetonitrile, by Thermo Fisher Scientific (6 mentions)
Pierce bca protein assay kit, by Thermo Fisher Scientific (4 mentions)
Sodium dodecyl sulfate (sds), by Merck Group (3 mentions)
Dithiothreitol (dtt), by Merck Group (3 mentions)
Rapigest, by Waters Corporation (3 mentions)
Formic acid, by Merck Group (3 mentions)
Sucrose, by Merck Group (3 mentions)
Acetone, by Thermo Fisher Scientific (2 mentions)
Urea, by Merck Group (2 mentions)
γ globin, by Bio-Rad (2 mentions)
D biotin, by Thermo Fisher Scientific (2 mentions)
Ha agarose beads, by Merck Group (2 mentions)
Sodium dodecyl sulfate (sds), by Serva Electrophoresis (2 mentions)
Ethylenediaminetetraacetic acid, by Merck Group (2 mentions)
Methanol, by Thermo Fisher Scientific (2 mentions)
Trifluoroacetic acid, by Merck Group (2 mentions)
Pngase f, by Promega (2 mentions)
23 protocols using triethylammonium bicarbonate buffer
1
Proteomic Analysis of Colorectal Cancer
2
Tandem Affinity Purification of Protein Complexes
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Tandem affinity purifications were performed as previously described (15 (link), 61 (link)). Affinity purifications were performed as biological replicates and cell lines expressing SH-tagged GFP were used as negative controls. In brief, cell lines were incubated with 1–2 μg/ml doxycycline for 7–24 h to induce expression of SH-tagged bait proteins. Whole cell extracts were prepared in 50 mm HEPES (pH 8.0), 150 mm NaCl, 5 mm EDTA, 0.5% Nonidet P-40, 50 mm NaF, 1 mm Na3VO4, 1 mm PMSF, and protease inhibitor mixture. Cell lysates were cleared by centrifugation (13000 rpm, 20 min, 4 °C). Proteins were quantitated by Bradford assay using γ-globin as standard (Bio-Rad). 50 mg total lysate were incubated with StrepTactin Sepharose beads (IBA, Göttingen, Germany). Tagged proteins were eluted with d -biotin (Alfa-Aesar, Ward Hill, MA) followed by a second purification step using HA-agarose beads (Sigma-Aldrich). Protein complexes were eluted with 100 mm formic acid and immediately neutralized with triethylammonium bicarbonate buffer (Sigma-Aldrich). Samples were digested with trypsin (Promega, Fitchburg, WI), and the resultant peptides desalted and concentrated with customized reversed-phase tips (62 (link)). The volume of the eluted samples was reduced to ∼2 μl in a vacuum centrifuge and reconstituted with 5% formic acid.
3
Tandem Affinity Purification of Protein Complexes
4
LC/MS Sample Preparation Protocols
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
For LC/MS sample preparation, LC/MS-grade water and acetonitrile (ACN) were used, if not otherwise stated, and were purchased together with acetone from Merck, Darmstadt, Germany. Triethylammonium bicarbonate buffer (TEAB), formic acid (FA), EDTA tris(2 carboxyethyl)phosphine (TCEP) and iodoacetamide (IAA) and trifluoroethanol (TFE) were purchased from Sigma-Aldrich, Taufkirchen, Germany. SDS was purchased from Serva Electrophoresis GmbH, Heidelberg, Germany. TFA was obtained from Roth, Karlsruhe, Germany. Rapigest was obtained from Waters, Milford, United States. 15N-labeled αSyn was purchased from rPeptide, Watkinsville, United States. MS-grade trypsin and LysN were obtained from Promega, Madison, United States. TMT10plex and TMT11-131C were purchased from Thermo Fisher Scientific, Bleiswijk, Netherlands.
5
Quantitative Analysis of Bispecific Protein
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The proprietary TFP, consisting of human immunoglobulin G4 (human IgG4) targeting the cell surface CD38 fused to a modified form of human interferon alpha, was prepared in-house. Anti-CD38 and human interferon alpha part were cloned into the pTT5 mammalian expressing vector [26 (link)]. Anti-human IgG (Fc specific) highly cross-adsorbed biotinylated antibody, DL-dithiothreitol (DTT), formic acid, iodoacetamide, and triethylammonium bicarbonate buffer were purchased from Sigma Aldrich (St. Louis, MO, USA). Sequencing grade modified trypsin was from Promega (Fitchburg, WI, USA). The signature peptides for human IgG4 (SLSLSLGK and SLSLSLG[K]) and interferon alpha (EDSILAVR and EDSILAV[R]), where [R] and [K] indicate 13C615N4-R and 13C615N2-K, respectively), Thermo KingFisher™ magnetic beads processor, T-PER tissue protein extraction reagent, and Halt protease inhibitor cocktail were from Thermo Fisher Scientific (Waltham, MA, USA). Dynabeads™ M-280 Streptavidin was from Invitrogen (Carlsbad, CA, USA). AffiniPure goat anti-human IgG (H+L) antibody is from Jackson ImmunoResearch (West Grove, PA, USA). MSD GOLD SULFO-TAG NHS-Ester is from Meso Scale Discovery (Rockville, MD, USA). Mouse anti-interferon alpha 2b antibody is from Abcam (Cambridge, MA, USA). FastPrep-24 is from MP Biomedicals (Santa Ana, CA, USA).
6
Kiwifruit Protein Identification Protocol
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Dithiothreitol (DTT), iodoacetamide (IAA), ethanol, ammonia, formic acid, formaldehyde (37% solution in H2O), formaldehyde-D2 (20% solution in H2O), phenol, sodium deoxycholate (SDC), trichloroacetic acid (TCA), ethylenediaminetetraacetic acid (EDTA), β-mercaptoethanol, and triethylammonium bicarbonate buffer (TEAB) were purchased from Sigma-Aldrich (St. Louis, MO, USA). Acrylamide, ammonium persulfate, sodium dodecyl sulfate (SDS), N,N′-methylene-bis-Acrylamide, glycine, and N,N,N′,N′-tetraethylmethylenediamine were obtained from Bio-Rad (Hercules, CA, USA). MS grade trypsin was provided by Fisher Scientific (Houston, TX, USA). Acetonitrile (MS grade), acetone, Coomassie brilliant blue, methanol, Tris-Base, and ammonium acetate were from J.T.Baker (Phillipsburg, NJ, USA). Sodium cyanoborohydride was purchased from Alfa Aesar (purity 95%, Haverhill, MA, USA). Urea was from VWR International (Radnor, PA, USA). Ammonium sulfate was obtained from Taiwan Fertilizer Co. (Hsinchu, Taiwan). The peptide standards, IVALSTGWYNGGSR (SPA1), NNIVDGSNAVWSALGLDK (SPA5), and GEHNSVTWTFHYEK (SPA11) were synthesized at the National Institute of Infectious Diseases and Vaccinology (Taipei, Taiwan). Kiwifruits were purchased from a local market in Taipei city.
7
Protein Extraction and Quantification
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The procedure was performed as described previously [4 ]. Briefly, protein extraction was performed on ice with pre‐chilled lysis buffer (12 mm sodium deoxycholate; SDC; FUJIFILM Wako Pure Chemical Corporation), 12 mm sodium N‐dodecanoylsarcosinate (FUJIFILM Wako Pure Chemical Corporation), protease inhibitor (Complete, EDTA‐free; Roche Life Science), phosphatase inhibitor (PhosSTOP Phosphatase inhibitor cocktail; Roche Life Science) in 100 mm triethylammonium bicarbonate buffer (pH 8.5; Sigma‐Aldrich). Five hundred specimens in a 1.5‐mL tube were carefully ground using a plastic grinder (Biomasher II; Nippi Inc., Tokyo, Japan) with 200 μL of lysis buffer. Homogenates were sonicated at 4 °C for 20 min using a Bioruptor II (BM Equipment Co., Ltd). The protein concentration was measured using a PIERCE BCA protein assay kit (Thermo Fisher Scientific) and absorbance at 534 nm was measured using a TECAN plate reader (Tecan).
8
Proteomic Quantification in Diabetic Mice
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Triethylammonium
bicarbonate buffer (1 M,
pH 8.5) and aniline were obtained from Sigma-Aldrich (St. Louis, MO).
DiART 6-plex reagents and CILAT 2-plex reagents were synthesized in-house.15 ,19 (link) HPLC-grade solvents were purchased from Honeywell Burdick &
Jackson (Muskegon, MI). 4-[3-(Perfluorooctyl)-propyl-1-oxy]benzaldehyde
was obtained from Fluorous Technologies Inc. (Ambridge, PA). Strepavidin
Sepharose high-performance beads were purchased from GE Healthcare
Life Sciences (Pittsburgh, PA). Diabetic (BKS.Cg-m+/+Leprdb/J, BKS-db/db) and control (BKS-db/+) mice were purchased from Jackson Laboratories (Bar
Harbor, ME). Mice were housed in a pathogen-free environment, with
continuous access to food (Purina 5053 chow) and water on a 12 h light–12
h dark schedule, and cared for following the University of Michigan
Committee on the Care and Use of Animals guidelines (approval no.
07675).20 (link)
bicarbonate buffer (1 M,
pH 8.5) and aniline were obtained from Sigma-Aldrich (St. Louis, MO).
DiART 6-plex reagents and CILAT 2-plex reagents were synthesized in-house.15 ,19 (link) HPLC-grade solvents were purchased from Honeywell Burdick &
Jackson (Muskegon, MI). 4-[3-(Perfluorooctyl)-propyl-1-oxy]benzaldehyde
was obtained from Fluorous Technologies Inc. (Ambridge, PA). Strepavidin
Sepharose high-performance beads were purchased from GE Healthcare
Life Sciences (Pittsburgh, PA). Diabetic (BKS.Cg-m+/+Leprdb/J, BKS-db/db) and control (BKS-db/+) mice were purchased from Jackson Laboratories (Bar
Harbor, ME). Mice were housed in a pathogen-free environment, with
continuous access to food (Purina 5053 chow) and water on a 12 h light–12
h dark schedule, and cared for following the University of Michigan
Committee on the Care and Use of Animals guidelines (approval no.
07675).20 (link)
9
Quantitative Phosphoproteomics Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
All the chemicals including triethylammonium bicarbonate buffer, 2-chloroacetamide, ammonium acetate, Radioimmunoprecipitation assay (RIPA) buffer, and protease inhibitors were purchased from Sigma-Aldrich (St. Louis, MO, USA). HPLC-grade water, acetonitrile, methanol, and formic acid were acquired from Fisher Scientific (Waltham, MA, USA). Trypsin was purchased from Promega (Madison, WI, USA). bicinchoninic acid (BCA) protein assay, High select TiO2 Phosphopeptide Enrichment Kit (Lot number: SF243171), and TMTsixplex™ Isobaric Label Reagent kits (Lot number: SH254566) were purchased from Thermo Fisher (Waltham, MA, USA).
10
Proteomics Sample Preparation Protocol
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
All solutions were prepared with ultrapure water produced in-house with a MilliQ® Integral 3 instrument (Millipore, Billerica, MA, USA). Methanol (MeOH, ≥99.9%) and acetonitrile (ACN, ≥99.9%) were acquired from VWR International (Vienna, Austria). Triethylammonium bicarbonate buffer (TEAB, pH 8.5 ± 0.1, 1 mol/L), sodium dodecyl sulfate (SDS, ≥99.5%), tris(2-carboxyethyl)phosphin-hydrochlorid (TCEP, ≥98.0%), iodoacetamide (IAA, ≥99.0%), formic acid–(FA, 98–100%) and trifluoroacetic acid (TFA ≥ 99.0%) were purchased from Sigma-Aldrich (Vienna, Austria). Ortho-phosphoric acid (85%) was obtained from Merck (Darmstadt, Germany). Trypsin (sequencing grade modified, porcine) was purchased from Promega (Madison, WI, USA).
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!