Shotgun Ion-Mobility Mass Spectrometry Sequencing (SIMMS2) for glycosaminoglycan oligosaccharides

Responsible:

Rebecca Miller . University Of Copenhagen . rmiller@sund.ku.dk

Sample preparation

---

1.Sample Origin

General information:
Chemical or Chemoenzymatic synthesised GAG structures

Growth/harvest conditions for recombinantly produced material:
N/A

Treatments and/or storage conditions:
-80oC freezer

For commercial material, vendor and applicable item information:
N/A

Generation of chemically derived material:
Protocol for chemical and chemoenzymatic synthesis of GAG oligosaccharides. 1. Arungundram, S., Al-Mafraji, K., Asong, J., Leach, F. E., Amster, I. J., Venot, A., Turnbull, J. E., and Boons, G.-J. (2009) Modular Synthesis of Heparan Sulfate Oligosaccharides for Structure−Activity Relationship Studies, J. Am. Chem. Soc. 131, 17394-17405. 2. Arungundram, S., Al-Mafraji, K., Asong, J., Leach, F. E., Amster, I. J., Venot, A., Turnbull, J. E., and Boons, G.-J. (2009) Modular Synthesis of Heparan Sulfate Oligosaccharides for Structure−Activity Relationship Studies, J. Am. Chem. Soc. 131, 17394-17405. 3. Zhang, X. et al. Chemoenzymatic synthesis of heparan sulfate and heparin oligosaccharides and NMR analysis: paving the way to a diverse library for glycobiologists. Chemical Science 8, 7932-7940 (2017). 4. Kuberan, B., Beeler, D.L., Lech, M., Wu, Z.L. & Rosenberg, R.D. Chemoenzymatic synthesis of classical and non-classical anticoagulant heparan sulfate polysaccharides. J Biol Chem 278, 52613-52621 (2003).

2. Sample Processing

Purification steps:
Size exclusion chromatography

2. Defined Sample

Sample name:
Glycosaminoglycans

HPLC

---

1. General settings

Instrument: NA

Manufacturer url: NA

Injector: NA

Injector settings: NA

2. Column

Manufacturer: NA

Model: NA

Type of Chromatography: NA

Type of Material: NA

Column diameter: NA

Column length: NA

Particle size: NA

Manufacturer url: NA

3. Method run

Temperature: NA

Solvent a: water

Solvent b: water

Other solvent: NA

Flow rate: 0.1 ml/min

Flow gradient: NA

Run time: NA

Phase: none

MS

---

1. General features

Date stamp: Tue Feb 18 UTC 2020

Instrument: Waters Synapt G2-S HDMS

Customizations from the manufacturer's specification:
DTIMS (Triwave removed)

ion_mode: -

2. Ion sources

(a) Electrospray ionisation - ESI

Sprayer type : static

Interface name: NA

Other data for the Interface: NA

Sprayer name: NanoLock Spray Ionisation Source

Other data for the sprayer: Pd/Pt-coated borosilicate nanoelectrospray ionization (nESI) capillaries

Relevant voltages: Capillary Voltage: 0.65kV, Cone Voltage 2, Source Temp 100oC,

Degree of prompt fragmentation evaluated: Not applicable

In-source dissociation performed: No

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: Argon

CID. Gas pressure: NA

CID. Collision energy: For MS/MS experiments the trap collision energy was increased to 3V–18 V.

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 : Helium

Ion mobility. Pressure: NA

Ion mobility. Instrument parameters: Trap gas flow, 2 ml/min; helium cell gas flow, 180 ml/min; ion mobility gas flow, 20 ml/min; trap bias, 2V; ion mobility wave velocity, 300 m/s; ion mobility wave height, 0 V.

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