Glycoprotein Enrichment and Characterization

Sodium deoxycholate (SDC), Tris(2-carboxyethyl)phosphine (TCEP), Tris(hydroxymethyl)aminomethane, chloroacetamide (CAA), sodium hydroxide, and TFA were purchased from Sigma–Aldrich. Formic acid (FA) was purchased from Merck. Acetonitrile (ACN) was purchased from Biosolve. Oasis μElution HLB and PRiME HLB plates were purchased from Waters. Milli-Q was produced by an in-house system (Millipore). Both phosphoSTOP and cOmplete Mini EDTA-free were purchased from Roche. GluC was obtained from Roche. Recombinant tissue nonspecific alkaline phosphatase (TNAP) was a gift from Copenhagen Centre of Glycomics. Histidine-rich glycoprotein (HRG) was purified from human plasma with a cobalt-loaded resin (Thermo Scientific) using immobilized metal affinity chromatography–based enrichment (34 (link)). Commercial sialylglycopeptide (α2,6-SGP) and asialo-SGP were purchased from Fushimi Pharmaceutical Co, Ltd. Commercial pooled human plasma was purchased from Affinity Biologicals. Purified human neutrophils, prepared as described previously (35 (link)), were a kind gift from the Department of Molecular and Cellular Homeostasis, Sanquin Research.

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Mukherjee S., Jankevics A., Busch F., Lubeck M., Zou Y., Kruppa G., Heck A.J., Scheltema R.A, & Reiding K.R. (2022). Oxonium Ion–Guided Optimization of Ion Mobility–Assisted Glycoproteomics on the timsTOF Pro. Molecular & Cellular Proteomics : MCP, 22(2), 100486.

Publication 2022

Sodium deoxycholate chloroacetamide sodium hydroxide Formic acid Acetonitrile Milli-Q phosphoSTOP cOmplete Mini EDTA-free GluC cobalt-loaded resin

Acetonitrile Affinity chromatography Aminomethane Biologicals Cellular Chloroacetamide Cobalt Edta Formic acid Histidine rich glycoprotein Homeostasis Human Metal Neutrophils Oasis Pharmaceutical Phosphine Plasma Resin Sodium deoxycholate Sodium hydroxide Tcep Tissue nonspecific alkaline phosphatase Tris

Corresponding Organization : Netherlands Metabolomics Centre

Other organizations : Bruker (Germany), Knorr-Bremse (Germany)

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Variable analysis

independent variables

Sodium deoxycholate (SDC)
Tris(2-carboxyethyl)phosphine (TCEP)
Tris(hydroxymethyl)aminomethane
Chloroacetamide (CAA)
Sodium hydroxide
Formic acid (FA)
Acetonitrile (ACN)
Oasis μElution HLB and PRiME HLB plates
Recombinant tissue nonspecific alkaline phosphatase (TNAP)
Histidine-rich glycoprotein (HRG)
Commercial sialylglycopeptide (α2,6-SGP) and asialo-SGP
Commercial pooled human plasma
Purified human neutrophils

dependent variables

Measured outcomes

control variables

Milli-Q water produced by an in-house system (Millipore)
PhosphoSTOP and cOmplete Mini EDTA-free from Roche

positive controls

Recombinant tissue nonspecific alkaline phosphatase (TNAP)
Commercial sialylglycopeptide (α2,6-SGP) and asialo-SGP

negative controls

None specified

Annotations

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