The Glycomic MS Database and Repository

Responsible:

John Benktander . Gothenburg University . Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9A, 405 30 Gothenburg

Sample preparation


1.Sample Origin

General information:
Atlantic Salmon mucus from skin, pyloric caeca and distal intestine.

Growth/harvest conditions for recombinantly produced material:

Treatments and/or storage conditions:
Stored in -80 C

For commercial material, vendor and applicable item information:

Generation of chemically derived material:


2. Sample Processing

Purification steps:
Crude mucin fraction obtained after dissolved in GuHCl extraction buffer and centrifugation to remove insoluble material.


2. Defined Sample

Sample name:
O-linked oligosaccharides



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HPLC


1. General settings

Instrument: Agilent 1100 Series

Manufacturer url: https://www.agilent.com/home

Injector: HTC PAL

Injector settings: 3 ul


2. Column

Manufacturer: In-house

Model:

Type of Chromatography:

Type of Material: Porous graphitized carbon

Column diameter: 250 um

Column length: 10 cm

Particle size: 5 um

Manufacturer url: NA


3. Method run

Temperature: RT

Solvent a: 10 mM (NH4)HCO3 in water

Solvent b: 10 mM (NH4)HCO3 in 80% acetontirile

Other solvent:

Flow rate: 10 ul/min

Flow gradient: 0-40%

Run time: 40 min

Phase: reverse phase

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MS



1. General features

Date stamp: Fri Nov 23 00:00:00 CET 2018

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 : Fed

Interface name:

Other data for the Interface:

Sprayer name: IonMax standard ESI source

Other data for the sprayer: Equipped with a stainless steel needle

Relevant voltages: Electrospray voltage of 3.5 kV and capillary voltage of −33.0 V..

Degree of prompt fragmentation evaluated: Yes

In-source dissociation performed: Yes

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: He

CID. Gas pressure:

CID. Collision energy: Collision energy 35%

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