Recombinant:Article Title: Protocol for simultaneous profiling of N- and O-glycans on glycoproteins using a one-pot format.
Article Snippet: .. Chemicals, peptides, and recombinant proteins Fetuin A from fetal bovine seruma New England Biolabs P6042S Glycerol-Free PNGase Fa New England Biolabs P0705L Proteinase Ka New England Biolabs P8107S Iodomethanea Millipore Sigma 289566 LCMS-Grade Watera Fisher Scientific W64 LCMS-Grade Methanol (MeOH)a Fisher Scientific A456-1 LCMS-Grade Acetonitrile (ACN)a Fisher Scientific A955-1 LCMS-Grade Trifluoroacetic Acid (TFA)a Fisher Scientific A116-10xAMP LCMS-Grade Acetic Acida Fisher Scientific A11350 1,4-Dithiothreitol (DTT)a Millipore Sigma D0632 Iodoacetamide (IAA)a Abcam ab274286 Ureaa Abcam ab274287 100 mM Tris(hydroxymethyl)aminomethane (Tris-HCl)a Abcam ab274285 Ammonium Bicarbonate (ABC)a Abcam ab274284 Ammonia Boranea Sigma-Aldrich 682098-1G Sodium Hydroxide Beadsa Millipore Sigma 367176-500G Dimethylsulfoxide (DMSO)a Sigma-Aldrich D8418-100ML Sodium Chloride (NaCl)a Research Products International S23020–1000.0 2,5-Dihydroxybenzoic acid (DHB)a Sigma Aldrich 85707-250MG Deposited data MALDI-TOF/MS Mass Spectra of Glycoproteins and STDs Ortega-Rodriguez et al.1 Software and algorithms Glycoworkbenchb Ceroni et al.14 https://code.google.com/archive/p/glycoworkbench/ FlexControl 4.2b Bruker Daltonics N/A FlexAnalysis 4.2b Bruker Daltonics N/A AssignMALDIb Parsons et al.15 https://github.com/FDA/AssignMALDI Other Hypersep NH2 SPE cartridges a Thermo Scientific 60108–424 Hypersep C18 SPE cartridges a Thermo Scientific 60108–390 Mortara Thermo Fisher Scientific FB961A Pestlea Thermo Fisher Scientific FB961K Thermomixera Eppendorf ThermoMixer C Centrifuge tubes (2mL)a Eppendorf 22363352 Centrifuge tubes (1.5mL)a Eppendorf 22363204 Pipette (100 - 1000 μL)a Rainin Pipet-Lite-XLS Pipette (50 - 200 μL)a Rainin Pipet-Lite-XLS (Continued on next page) STAR Protocols 7, 104336, March 20, 2026 3 MATERIALS AND EQUIPMENT .. Pipette (2 - 20 μL)a Rainin Pipet-Lite-XLS Pipette (0.5–2 μL)a Rainin Pipet-Lite-XLS Vortexa Daigger 22220A Benchtop Centrifugea Eppendorf 5425 Micro Centrifugea Daigger SD 110VAC Analytical Scalea OHAUS PR223/E Weighing boatsa Fisher Scientific 01-549-752 Spatulasa Fisher Scientific 18-001-017 Parafilm M Laboratory Filma Amcor PM999 30kDa MWCO Filtersa,c Abcam ab274288 FASP Centrifuge Tubesa Abcam ab280352 Speed Vaca Thermo Scientific SPD111V Abcam Protein Digestion Kita Abcam ab270519 Disposable Borosilicate Glass Pasteur Pipettesa Fisher Scientific 13-678-20C Nitrile Glovesa Fisher Scientific 19-167-54 Ansell MICROFLEXTM 93-260 Polychloroprene Chemical Resistant Glovesa Fisher Scientific 93–260 Eye Protectiona Protective Industrial Products 250-37-0900 Test Tubesa Fisher Scientific 14-961-27 PCR Tubesa Crystalgen L-2082 MALDI-TOF Mass Spectrometera Bruker Daltonics UltrafleXtreme Micro SpinColumns, Empty, 20 μm frita Harvard Apparatus 77–4400 MALDI Target Frameb Bruker Daltonics 8074115 MTP Targets, MALDI Target Plate, Ground Steelb Bruker Daltonics 8280784 aReagent or resource can commonly be bought from other manufacturers (Thermo Fisher, Sigma-Aldrich, VWR, Abcam, etc.). bThe reagent or resource needs to be acquired from the specific manufacturer. cIf the molecular weight of the glycoprotein is below 30kDa, the MWCO filter needs to be changed to a 10kDa or 5kDa MWCO filter.
Article Title: Functional divergence of MdpS and MdpS2 reveals mucin-targeting strategies in Streptococcus oralis
Article Snippet: .. Humanised IgG1 trastuzumab (Roche, Switzerland), human IgG2 panitumumab (Amgen, United States), human plasma IgG3 myeloma (Merck, Germany), human IgG4 nivolumab (Bristol-Myers Squibb, United States), human IgE myeloma (Merck), human serum IgM (Merck), recombinant human PSGL−1/CD162 Fc chimera protein (Bio-Techne, Ireland), foetal calf serum fetuin (NEB, United States), were used. ..
Liquid Chromatography with Mass Spectroscopy:Article Title: Protocol for simultaneous profiling of N- and O-glycans on glycoproteins using a one-pot format.
Article Snippet: .. Chemicals, peptides, and recombinant proteins Fetuin A from fetal bovine seruma New England Biolabs P6042S Glycerol-Free PNGase Fa New England Biolabs P0705L Proteinase Ka New England Biolabs P8107S Iodomethanea Millipore Sigma 289566 LCMS-Grade Watera Fisher Scientific W64 LCMS-Grade Methanol (MeOH)a Fisher Scientific A456-1 LCMS-Grade Acetonitrile (ACN)a Fisher Scientific A955-1 LCMS-Grade Trifluoroacetic Acid (TFA)a Fisher Scientific A116-10xAMP LCMS-Grade Acetic Acida Fisher Scientific A11350 1,4-Dithiothreitol (DTT)a Millipore Sigma D0632 Iodoacetamide (IAA)a Abcam ab274286 Ureaa Abcam ab274287 100 mM Tris(hydroxymethyl)aminomethane (Tris-HCl)a Abcam ab274285 Ammonium Bicarbonate (ABC)a Abcam ab274284 Ammonia Boranea Sigma-Aldrich 682098-1G Sodium Hydroxide Beadsa Millipore Sigma 367176-500G Dimethylsulfoxide (DMSO)a Sigma-Aldrich D8418-100ML Sodium Chloride (NaCl)a Research Products International S23020–1000.0 2,5-Dihydroxybenzoic acid (DHB)a Sigma Aldrich 85707-250MG Deposited data MALDI-TOF/MS Mass Spectra of Glycoproteins and STDs Ortega-Rodriguez et al.1 Software and algorithms Glycoworkbenchb Ceroni et al.14 https://code.google.com/archive/p/glycoworkbench/ FlexControl 4.2b Bruker Daltonics N/A FlexAnalysis 4.2b Bruker Daltonics N/A AssignMALDIb Parsons et al.15 https://github.com/FDA/AssignMALDI Other Hypersep NH2 SPE cartridges a Thermo Scientific 60108–424 Hypersep C18 SPE cartridges a Thermo Scientific 60108–390 Mortara Thermo Fisher Scientific FB961A Pestlea Thermo Fisher Scientific FB961K Thermomixera Eppendorf ThermoMixer C Centrifuge tubes (2mL)a Eppendorf 22363352 Centrifuge tubes (1.5mL)a Eppendorf 22363204 Pipette (100 - 1000 μL)a Rainin Pipet-Lite-XLS Pipette (50 - 200 μL)a Rainin Pipet-Lite-XLS (Continued on next page) STAR Protocols 7, 104336, March 20, 2026 3 MATERIALS AND EQUIPMENT .. Pipette (2 - 20 μL)a Rainin Pipet-Lite-XLS Pipette (0.5–2 μL)a Rainin Pipet-Lite-XLS Vortexa Daigger 22220A Benchtop Centrifugea Eppendorf 5425 Micro Centrifugea Daigger SD 110VAC Analytical Scalea OHAUS PR223/E Weighing boatsa Fisher Scientific 01-549-752 Spatulasa Fisher Scientific 18-001-017 Parafilm M Laboratory Filma Amcor PM999 30kDa MWCO Filtersa,c Abcam ab274288 FASP Centrifuge Tubesa Abcam ab280352 Speed Vaca Thermo Scientific SPD111V Abcam Protein Digestion Kita Abcam ab270519 Disposable Borosilicate Glass Pasteur Pipettesa Fisher Scientific 13-678-20C Nitrile Glovesa Fisher Scientific 19-167-54 Ansell MICROFLEXTM 93-260 Polychloroprene Chemical Resistant Glovesa Fisher Scientific 93–260 Eye Protectiona Protective Industrial Products 250-37-0900 Test Tubesa Fisher Scientific 14-961-27 PCR Tubesa Crystalgen L-2082 MALDI-TOF Mass Spectrometera Bruker Daltonics UltrafleXtreme Micro SpinColumns, Empty, 20 μm frita Harvard Apparatus 77–4400 MALDI Target Frameb Bruker Daltonics 8074115 MTP Targets, MALDI Target Plate, Ground Steelb Bruker Daltonics 8280784 aReagent or resource can commonly be bought from other manufacturers (Thermo Fisher, Sigma-Aldrich, VWR, Abcam, etc.). bThe reagent or resource needs to be acquired from the specific manufacturer. cIf the molecular weight of the glycoprotein is below 30kDa, the MWCO filter needs to be changed to a 10kDa or 5kDa MWCO filter.
Software:Article Title: Protocol for simultaneous profiling of N- and O-glycans on glycoproteins using a one-pot format.
Article Snippet: .. Chemicals, peptides, and recombinant proteins Fetuin A from fetal bovine seruma New England Biolabs P6042S Glycerol-Free PNGase Fa New England Biolabs P0705L Proteinase Ka New England Biolabs P8107S Iodomethanea Millipore Sigma 289566 LCMS-Grade Watera Fisher Scientific W64 LCMS-Grade Methanol (MeOH)a Fisher Scientific A456-1 LCMS-Grade Acetonitrile (ACN)a Fisher Scientific A955-1 LCMS-Grade Trifluoroacetic Acid (TFA)a Fisher Scientific A116-10xAMP LCMS-Grade Acetic Acida Fisher Scientific A11350 1,4-Dithiothreitol (DTT)a Millipore Sigma D0632 Iodoacetamide (IAA)a Abcam ab274286 Ureaa Abcam ab274287 100 mM Tris(hydroxymethyl)aminomethane (Tris-HCl)a Abcam ab274285 Ammonium Bicarbonate (ABC)a Abcam ab274284 Ammonia Boranea Sigma-Aldrich 682098-1G Sodium Hydroxide Beadsa Millipore Sigma 367176-500G Dimethylsulfoxide (DMSO)a Sigma-Aldrich D8418-100ML Sodium Chloride (NaCl)a Research Products International S23020–1000.0 2,5-Dihydroxybenzoic acid (DHB)a Sigma Aldrich 85707-250MG Deposited data MALDI-TOF/MS Mass Spectra of Glycoproteins and STDs Ortega-Rodriguez et al.1 Software and algorithms Glycoworkbenchb Ceroni et al.14 https://code.google.com/archive/p/glycoworkbench/ FlexControl 4.2b Bruker Daltonics N/A FlexAnalysis 4.2b Bruker Daltonics N/A AssignMALDIb Parsons et al.15 https://github.com/FDA/AssignMALDI Other Hypersep NH2 SPE cartridges a Thermo Scientific 60108–424 Hypersep C18 SPE cartridges a Thermo Scientific 60108–390 Mortara Thermo Fisher Scientific FB961A Pestlea Thermo Fisher Scientific FB961K Thermomixera Eppendorf ThermoMixer C Centrifuge tubes (2mL)a Eppendorf 22363352 Centrifuge tubes (1.5mL)a Eppendorf 22363204 Pipette (100 - 1000 μL)a Rainin Pipet-Lite-XLS Pipette (50 - 200 μL)a Rainin Pipet-Lite-XLS (Continued on next page) STAR Protocols 7, 104336, March 20, 2026 3 MATERIALS AND EQUIPMENT .. Pipette (2 - 20 μL)a Rainin Pipet-Lite-XLS Pipette (0.5–2 μL)a Rainin Pipet-Lite-XLS Vortexa Daigger 22220A Benchtop Centrifugea Eppendorf 5425 Micro Centrifugea Daigger SD 110VAC Analytical Scalea OHAUS PR223/E Weighing boatsa Fisher Scientific 01-549-752 Spatulasa Fisher Scientific 18-001-017 Parafilm M Laboratory Filma Amcor PM999 30kDa MWCO Filtersa,c Abcam ab274288 FASP Centrifuge Tubesa Abcam ab280352 Speed Vaca Thermo Scientific SPD111V Abcam Protein Digestion Kita Abcam ab270519 Disposable Borosilicate Glass Pasteur Pipettesa Fisher Scientific 13-678-20C Nitrile Glovesa Fisher Scientific 19-167-54 Ansell MICROFLEXTM 93-260 Polychloroprene Chemical Resistant Glovesa Fisher Scientific 93–260 Eye Protectiona Protective Industrial Products 250-37-0900 Test Tubesa Fisher Scientific 14-961-27 PCR Tubesa Crystalgen L-2082 MALDI-TOF Mass Spectrometera Bruker Daltonics UltrafleXtreme Micro SpinColumns, Empty, 20 μm frita Harvard Apparatus 77–4400 MALDI Target Frameb Bruker Daltonics 8074115 MTP Targets, MALDI Target Plate, Ground Steelb Bruker Daltonics 8280784 aReagent or resource can commonly be bought from other manufacturers (Thermo Fisher, Sigma-Aldrich, VWR, Abcam, etc.). bThe reagent or resource needs to be acquired from the specific manufacturer. cIf the molecular weight of the glycoprotein is below 30kDa, the MWCO filter needs to be changed to a 10kDa or 5kDa MWCO filter.
Transferring:Article Title: Protocol for simultaneous profiling of N- and O-glycans on glycoproteins using a one-pot format.
Article Snippet: .. Chemicals, peptides, and recombinant proteins Fetuin A from fetal bovine seruma New England Biolabs P6042S Glycerol-Free PNGase Fa New England Biolabs P0705L Proteinase Ka New England Biolabs P8107S Iodomethanea Millipore Sigma 289566 LCMS-Grade Watera Fisher Scientific W64 LCMS-Grade Methanol (MeOH)a Fisher Scientific A456-1 LCMS-Grade Acetonitrile (ACN)a Fisher Scientific A955-1 LCMS-Grade Trifluoroacetic Acid (TFA)a Fisher Scientific A116-10xAMP LCMS-Grade Acetic Acida Fisher Scientific A11350 1,4-Dithiothreitol (DTT)a Millipore Sigma D0632 Iodoacetamide (IAA)a Abcam ab274286 Ureaa Abcam ab274287 100 mM Tris(hydroxymethyl)aminomethane (Tris-HCl)a Abcam ab274285 Ammonium Bicarbonate (ABC)a Abcam ab274284 Ammonia Boranea Sigma-Aldrich 682098-1G Sodium Hydroxide Beadsa Millipore Sigma 367176-500G Dimethylsulfoxide (DMSO)a Sigma-Aldrich D8418-100ML Sodium Chloride (NaCl)a Research Products International S23020–1000.0 2,5-Dihydroxybenzoic acid (DHB)a Sigma Aldrich 85707-250MG Deposited data MALDI-TOF/MS Mass Spectra of Glycoproteins and STDs Ortega-Rodriguez et al.1 Software and algorithms Glycoworkbenchb Ceroni et al.14 https://code.google.com/archive/p/glycoworkbench/ FlexControl 4.2b Bruker Daltonics N/A FlexAnalysis 4.2b Bruker Daltonics N/A AssignMALDIb Parsons et al.15 https://github.com/FDA/AssignMALDI Other Hypersep NH2 SPE cartridges a Thermo Scientific 60108–424 Hypersep C18 SPE cartridges a Thermo Scientific 60108–390 Mortara Thermo Fisher Scientific FB961A Pestlea Thermo Fisher Scientific FB961K Thermomixera Eppendorf ThermoMixer C Centrifuge tubes (2mL)a Eppendorf 22363352 Centrifuge tubes (1.5mL)a Eppendorf 22363204 Pipette (100 - 1000 μL)a Rainin Pipet-Lite-XLS Pipette (50 - 200 μL)a Rainin Pipet-Lite-XLS (Continued on next page) STAR Protocols 7, 104336, March 20, 2026 3 MATERIALS AND EQUIPMENT .. Pipette (2 - 20 μL)a Rainin Pipet-Lite-XLS Pipette (0.5–2 μL)a Rainin Pipet-Lite-XLS Vortexa Daigger 22220A Benchtop Centrifugea Eppendorf 5425 Micro Centrifugea Daigger SD 110VAC Analytical Scalea OHAUS PR223/E Weighing boatsa Fisher Scientific 01-549-752 Spatulasa Fisher Scientific 18-001-017 Parafilm M Laboratory Filma Amcor PM999 30kDa MWCO Filtersa,c Abcam ab274288 FASP Centrifuge Tubesa Abcam ab280352 Speed Vaca Thermo Scientific SPD111V Abcam Protein Digestion Kita Abcam ab270519 Disposable Borosilicate Glass Pasteur Pipettesa Fisher Scientific 13-678-20C Nitrile Glovesa Fisher Scientific 19-167-54 Ansell MICROFLEXTM 93-260 Polychloroprene Chemical Resistant Glovesa Fisher Scientific 93–260 Eye Protectiona Protective Industrial Products 250-37-0900 Test Tubesa Fisher Scientific 14-961-27 PCR Tubesa Crystalgen L-2082 MALDI-TOF Mass Spectrometera Bruker Daltonics UltrafleXtreme Micro SpinColumns, Empty, 20 μm frita Harvard Apparatus 77–4400 MALDI Target Frameb Bruker Daltonics 8074115 MTP Targets, MALDI Target Plate, Ground Steelb Bruker Daltonics 8280784 aReagent or resource can commonly be bought from other manufacturers (Thermo Fisher, Sigma-Aldrich, VWR, Abcam, etc.). bThe reagent or resource needs to be acquired from the specific manufacturer. cIf the molecular weight of the glycoprotein is below 30kDa, the MWCO filter needs to be changed to a 10kDa or 5kDa MWCO filter.
Activity Assay:Article Title: Enzymes for glycan analysis
Article Snippet: Enzymes (0.05 μg) were mixed with a substrate (25 μM) in 20 mM Tris-HCl pH 6.8, and incubated for 30 minutes at 37° C., after which free sialic acids in the mixture were quantified, according to manufacturer's instructions (Sialic Acid Quantification Kit, Abcam). .. Activity Assessment Using Protein Substrate TNFαR, EPO, Enbrel and fetuin (0.5 μg) were mixed together with varying concentrations of tested sialidases (1:40) or commercial sialidase (from NEB, according to manufacturer) and incubated for 30 minutes, after which the proteins were separated on 4-20% Novex gradient SDS-PAGE, and/or analyzed with SNA lectin blots. .. Lectin Blots Separated proteins were transferred to PVDF membranes using the Trans-Blot Turbo Transfer System (BioRad).
Incubation:Article Title: Enzymes for glycan analysis
Article Snippet: Enzymes (0.05 μg) were mixed with a substrate (25 μM) in 20 mM Tris-HCl pH 6.8, and incubated for 30 minutes at 37° C., after which free sialic acids in the mixture were quantified, according to manufacturer's instructions (Sialic Acid Quantification Kit, Abcam). .. Activity Assessment Using Protein Substrate TNFαR, EPO, Enbrel and fetuin (0.5 μg) were mixed together with varying concentrations of tested sialidases (1:40) or commercial sialidase (from NEB, according to manufacturer) and incubated for 30 minutes, after which the proteins were separated on 4-20% Novex gradient SDS-PAGE, and/or analyzed with SNA lectin blots. .. Lectin Blots Separated proteins were transferred to PVDF membranes using the Trans-Blot Turbo Transfer System (BioRad).
Clinical Proteomics:Article Title: Functional divergence of MdpS and MdpS2 reveals mucin-targeting strategies in Streptococcus oralis
Article Snippet: .. Humanised IgG1 trastuzumab (Roche, Switzerland), human IgG2 panitumumab (Amgen, United States), human plasma IgG3 myeloma (Merck, Germany), human IgG4 nivolumab (Bristol-Myers Squibb, United States), human IgE myeloma (Merck), human serum IgM (Merck), recombinant human PSGL−1/CD162 Fc chimera protein (Bio-Techne, Ireland), foetal calf serum fetuin (NEB, United States), were used. ..
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