Cardicola forsteri glycome

Announcement date

2022/03/22

Responsible:

Paul Ramsland . RMIT University

Description

The glycome of Cardicola forsteri (a parasitic blood fluke of bluefin tuna) was profiled with PGC-LC-ESI-MS/MS.

Sample preparation

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1. Sample Origin

General information:
Reduced N-glycans carrying released from a lysate of Cardicola forsteri.

1.1 Biologically derived material

Biologically derived material - Recombinantly produced material

Cell type:
N/A

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

Biologically derived material - Biological origin of Material

Origin (biological fluid, tissue, etc):
tissue

Species:
Caenorhabditis elegans

Treatments and/or storage conditions:
Lysate from multiple specimens, stored in RNA preservation medium.

Glycoprotein:
N/A

Biologically derived material - Purchased from commercial manufacturer

Vendor and applicable item information:
N/A

1.2 Chemically derived material

Synthesis steps or specify where the equivalent reaction protocol is available:
N/A

Description of starting material:
N/A

2. Sample Processing

2.1 Sample Processing - Isolation

Enzymatic treatments

Enzymes used for oligosaccharide removal or modification of starting material:
Release method-PNGaseF TREATMENT

Describe vendor or expression and purification procedure:
New England BioLabs

Sample material treated in-solution or immobilized? State also temperature, duration, volume, enzyme concentration:
500 U, overnight at 37 °C.

Chemical treatments

Define the technique for oligosaccharide release or other chemical modifications:
N/A

Reaction conditions (temperature, duration, volume and chemical concentrations):
N/A

2.2 Sample Processing - Modification

Enzymatic modifications

Describe any treatments made to the isolated material:
N/A

Enzyme concentration, supplier, biological source, incubation time and temperature:
N/A

If novel glycosidase was used, provide information indicating the origin (i.e. species) of the enzyme:
N/A

Chemical modifications

Describe any treatments made to the isolated material:
N/A

Explain the type of modification employed:
N/A

Source of materials, description of kits used, reaction conditions and detailed workflow:
N/A

2.3 Sample Processing - Purification

Purification steps:
1. Acidified with acetic acid. 2. Desalted with cation exchange resin. 3. Purified with PGC-packed C18 column.

3. Defined Sample

Sample name:
N-linked oligosaccharides

Liquid chromatography

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N/A

MS

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1. General features

(a) Global descriptors

Instrument manufacturer:
Bruker Daltonics

Instrument model:
Other

Customizations:
N/A

Ion mode:
Negative

(b) Control and analysis software

Software name:
DataAnalysis

Version:
4.4

Upgrades not reflected in version number:
N/A

Switching criteria (tandem only):
N/A

Isolation width (global, or by MS level):
N/A

Location of ‘parameters’ file:
N/A

2. Ion sources

(a) Electrospray Ionisation (ESI)

Supply type (static, or fed):
Q-TOF ESI

Interface name:
N/A

Catalog number, vendor, and any modifications made to the standard specification:
N/A

Sprayer name:
nano ESI - CaptiveSpray

Sprayer type, coating, manufacturer, model and catalog number (where available):
N/A

Relevant voltages where appropriate (tip, cone, acceleration):
N/A

Degree of prompt fragmentation evaluated:
N/A

Whether in-source dissociation performed:
N/A

Other parameters if discriminant for the experiment (such as nebulizing gas and pressure):
N/A

(b) MALDI

Plate composition (or type):
N/A

Matrix composition (if applicable):
N/A

Deposition technique:
N/A

Relevant voltages where appropriate:
N/A

Degree of prompt fragmentation evaluated:
N/A

PSD (or LID/ISD) summary, if performed:
N/A

Operation with or without delayed extraction:
N/A

Laser type (e.g., nitrogen) and wavelength (nm):
N/A

Other laser related parameters, if discriminating for the experiment:
N/A

3. Ion transfer optics

Hardware options:
N/A

(a) Post-source componentry - Collision cell

Collision-Induced Dissociation (CID)

Gas composition:
Helium

Gas pressure:
N/A

Collision energy CID/function:
Basic stepping mode was applied for the MS/MS collision energy (80 and 140%) each for 50% of the time. Collision energies were set as follows: For singly charged precursors 45 eV at m/z 500, 60 eV at m/z 800, 80 eV at m/z 1300; for doubly charged precursors 25 eV at m/z 500, 47 eV at m/z 800, 60 eV at m/z 1300, for precursors with three and more charges 20 eV at m/z 500, 45 eV at m/z 800, 65 eV at m/z 1300. MS/MS was performed on the 3 most abundant precursor ions above an m/z value of 550.

Electron Transfer Dissociation (ETD)

Reagent gas:
N/A

Pressure:
N/A

Reaction time:
N/A

Number of reagent atoms:
N/A

Electron Capture Dissociation (ECD)

Emitter type:
N/A

Voltage:
N/A

Current:
N/A

(b) Post-source componentry - TOF drift tube

Reflectron status (on, off, none):
on

(c) Post-source componentry - Ion trap

Final MS stage achieved:
N/A

(d) Post-source componentry - Ion mobility

Gas:
N/A

Pressure:
N/A

Instrument-specific parameters:
N/A

(e) Post-source componentry - FT-ICR

Peak selection:
N/A

Pulse:
N/A

Width:
N/A

Voltage:
N/A

Decay time:
N/A

IR:
N/A

Other parameters:
N/A

(f) Post-source componentry - Detectors

Detector type:
N/A