SDRF-Proteomics

gc-ms-metabolomics

v1.0.0-dev experiment

SDRF template for GC-MS-based metabolomics experiments. Extends ms-metabolomics with derivatization and GC-specific columns.

Key Guidance

The gc-ms-metabolomics template constrains technology type to GC-MS-based metabolomics and

adds derivatization and GC-specific columns (derivatization, GC column, carrier gas, oven

program). It also tightens comment[ion source] to GC-typical sources (EI, CI).

Polar metabolite analyses on GC-MS routinely require derivatization (e.g. methoximation

followed by silylation with MSTFA), so comment[derivatization] is required. Use none to

explicitly indicate that no derivatization was performed (rare for polar metabolites,

acceptable for volatiles).

Combine with an organism template (human, vertebrates, invertebrates, plants) and optionally

with clinical-metadata or oncology-metadata for clinical studies.

Inheritance

base → sample-metadata → ms-metabolomics → gc-ms-metabolomics

Columns

7 own + 48 inherited = 55 total · click a row for details
Column Requirement Source Description
▶ technology type required gc-ms-metabolomics Type of technology used
Type of technology used
PRIDE:0000663
single_cardinality_validator
values — values: GC-MS-based metabolomics
For gc-ms-metabolomics the technology type must be 'GC-MS-based metabolomics'
▶ comment[ion source] required gc-ms-metabolomics Ion source used for ionization (e.g. ESI, APCI, EI, MALDI). Should be a child of MS:1000008.
Ion source used for ionization (e.g. ESI, APCI, EI, MALDI). Should be a child of MS:1000008.
MS:1000008
values — values: electron ionization, chemical ionization, electron impact ionization
GC-MS typically uses electron ionization (EI) or chemical ionization (CI)
▶ comment[derivatization] required gc-ms-metabolomics Derivatization protocol applied to the sample prior to GC injection. Use `none` if no derivatizat...
Derivatization protocol applied to the sample prior to GC injection. Use `none` if no derivatization was performed (e.g. volatiles analysis).
pattern — pattern: ^.+$
Free-text derivatization protocol
MSTFA, MOX + MSTFA, BSTFA, methoximation followed by trimethylsilylation, none
▶ comment[derivatization agent] recommended gc-ms-metabolomics Chemical reagent(s) used for derivatization
Chemical reagent(s) used for derivatization
allows N/A allows not available multiple cardinality
ontology — ontologies: chebi
Derivatization agent should be a valid ChEBI term when possible
N-methyl-N-(trimethylsilyl)trifluoroacetamide, N,O-bis(trimethylsilyl)trifluoroacetamide, methoxyamine hydrochloride
▶ comment[gc column] recommended gc-ms-metabolomics GC column used for separation, including stationary phase and dimensions
GC column used for separation, including stationary phase and dimensions
allows N/A allows not available
pattern — pattern: ^.+$
Free-text GC column description
DB-5MS 30 m x 0.25 mm x 0.25 um, HP-5MS 30 m x 0.25 mm x 0.25 um, Rxi-5Sil MS 30 m x 0.25 mm x 0.25 um
▶ comment[carrier gas] optional gc-ms-metabolomics Carrier gas used in the GC system
Carrier gas used in the GC system
allows N/A allows not available
values — values: helium, hydrogen, nitrogen
Carrier gas should be helium, hydrogen, or nitrogen
▶ comment[oven program] optional gc-ms-metabolomics Free-text description of the GC oven temperature program
Free-text description of the GC oven temperature program
allows N/A allows not available
pattern — pattern: ^.+$
Free-text oven program description
60C 1 min, ramp 10C/min to 300C, hold 5 min, 70C 2 min, ramp 5C/min to 320C, hold 10 min

Contributors