The Glycomic MS Database and Repository

Responsible:

Vignesh Venkatakrishnan . Sahlgrenska Academy, University of Gothenburg . vignesh.venkatakrishnan@gu.se

Sample preparation


1.Sample Origin

General information:
O-glycans released from soluble and insoluble pig mucins isolateed from healthy and Brachyspira hyodysenteriae infected colon tissues

Growth/harvest conditions for recombinantly produced material:

Treatments and/or storage conditions:
Soluble and insoluble mucins were purified from pig colon tissues using isopycnic gradient centrifugation. O-glycans were released chemically using reductive beta-elimination

For commercial material, vendor and applicable item information:

Generation of chemically derived material:


2. Sample Processing

Purification steps:
Released O-glycans were desalted using strong cation exchange Dowex resin packed as a microcolumn in top of hydrphobic C18 material


2. Defined Sample

Sample name:
O-linked oligosaccharides



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HPLC


1. General settings

Instrument: Thermo Fisher 1100 Series

Manufacturer url: NA

Injector: NA

Injector settings: NA


2. Column

Manufacturer: In-house

Model: Custom made Hypercarb

Type of Chromatography: Liquid chromatography

Type of Material: Porous graphitized carbon

Column diameter: 0.25

Column length: 100

Particle size: 5

Manufacturer url: NA


3. Method run

Temperature:

Solvent a: 10mM ammonium bicarbonate

Solvent b: 10mM ammonium bicarbonate in 80% Acetonitrile

Other solvent:

Flow rate: 250 nL/min

Flow gradient:

Run time: 78 minutes

Phase: Normal

}

MS



1. General features

Date stamp: Tue Aug 04 00:00:00 CEST 2015

Instrument: Thermo Fisher LTQ Linear Ion Trap ESI

Customizations from the manufacturer's specification:

ion_mode: -


2. Ion sources

(a) Electrospray ionisation - ESI

Sprayer type : Liquid chromatography

Interface name:

Other data for the Interface:

Sprayer name: need to check

Other data for the sprayer:

Relevant voltages:

Degree of prompt fragmentation evaluated: No

In-source dissociation performed: No

Other parameters if discriminant for the experiment:


(b) MALDI

Plate composition (or type): NA

Matrix composition: NA

Deposition technique: NA

Relevant voltages: NA

Degree of prompt fragmentation evaluated: NA

PSD (or LID/ISD) summary: NA

Operation with or without delayed extraction: NA

Laser type: NA

Other laser related parameters: NA

url: NA


3. Ion transfer optics

Hardware options:


3. Post-source componentry

Collision-Induced Dissociation - CID

CID. Gas composition: NA

CID. Gas pressure: NA

CID. Collision energy: NA

Electron Transfer Dissociation - ETD

ETD. Reagent gas: NA

ETD. Pressure: NA

ETD. Reaction time: NA

ETD. Reagent atoms: NA

Electron Capture Dissociation - ECD

ECD. Emitter type: NA

ECD. Voltage: NA

ECD. Current: NA

TOF drift tube

TOF. Reflectron status: NA

Ion Trap

Ion trap. Final MS stage achieved: NA

Ion mobility

Ion mobility. Gas type : NA

Ion mobility. Pressure: NA

Ion mobility. Instrument parameters: NA

FT-ICR

Peak selection: NA

FT-ICR. Pulse: NA

FT-ICR. Width: NA

FT-ICR. IR: Decay time: NA

FT-ICR. IR: NA

FT-ICR. Other parameters: NA

Detectors

Detector type: NA