Occurrence of a D-arabinose-containing complex-type free-N-glycan in the urine of cancer patients

Responsible:

Yasuhide Miyamoto . Department of Molecular Biology, Osaka International Cancer Institute . miyamoto-ya@mc.pref.osaka.jp

Sample preparation

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1.Sample Origin

General information:
Urine from cancer patients

Growth/harvest conditions for recombinantly produced material:
NA

Treatments and/or storage conditions:
store in -80°C

For commercial material, vendor and applicable item information:
NA

Generation of chemically derived material:
NA

2. Sample Processing

Purification steps:
NA

2. Defined Sample

Sample name:
Oligosaccharides

HPLC

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1. General settings

Instrument: Shimadzu 1100 Series

Manufacturer url: NA

Injector: NA

Injector settings: NA

2. Column

Manufacturer: NA

Model: NA

Type of Chromatography: LC

Type of Material: C18

Column diameter: 1

Column length: 50

Particle size: 3

Manufacturer url: NA

3. Method run

Temperature: RT

Solvent a: 5mM Acetic acid/Triethylamine (pH6.0)

Solvent b: 50% acetonitrile

Other solvent: NA

Flow rate: 0.05ml/min

Flow gradient: NA

Run time: 14min

Phase: reversed

MS

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1. General features

Date stamp: Fri Feb 25 UTC 2022

Instrument: Thermo Fisher LTQ Linear Ion Trap ESI

Customizations from the manufacturer's specification:
NA

ion_mode: +

2. Ion sources

(a) Electrospray ionisation - ESI

Sprayer type : HPLC

Interface name: syringe pump

Other data for the Interface: NA

Sprayer name: ESI

Other data for the sprayer: HESI-II

Relevant voltages: NA

Degree of prompt fragmentation evaluated: Yes

In-source dissociation performed: Yes

Other parameters if discriminant for the experiment: NA

(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: NA

3. Post-source componentry

Collision-Induced Dissociation - CID

CID. Gas composition: He

CID. Gas pressure: NA

CID. Collision energy: 0.35

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