I would like to suggest the following additions and minor changes to CHMO to facilitate annotation of glycomics methods and reflect recent technical development in the field of mass spectrometry. In addition to common sample treatments, I also suggest including the action noun "orbitrap mass spectrometry", and categorizing both orbitrap and Fourier transform ion cyclotron resonance mass spectrometry as "ion trap mass spectrometry" and/or "Fourier transform mass spectrometry". Both are correct, and consistent with the current definition of "ion trap mass spectrometry" in the ontology. "Fourier transform mass spectrometry" is a subclass of "ion trap mass spectrometry". The term "Fourier transform mass spectrometer" could also be added, but I left it out as the Fourier transform typically happens in the computer that is arguably separate from the instrument.
The suggestions:
[Term]
id: CHMO:XXXXXXX
name: Smith degradation
def: "A selective degradation of polysaccharides by periodate oxidation."
is_a: OBI:0000094 ! material processing
[Term]
id: CHMO:XXXXXXX
name: beta elimination
def: "A chemical reaction in which atoms or groups are removed from adjacent atoms."
synonym: "β-elimination" EXACT []
is_a: OBI:0000094 ! material processing
[Term]
id: CHMO:XXXXXXX
name: hydrazine treatment
def: "Treatment of a sample with hydrazine."
synonym: "hydrazinolysis" EXACT []
is_a: OBI:0000094 ! material processing
[Term]
id: CHMO:XXXXXXX
name: PNGase A digestion
def: "An enzymatic removal of N-linked glycans from a peptide or protein using the enzyme PNGase A (N-Glycosidase A), including those with core α1-3 fucosylation."
synonym: "PNGase A treatment" EXACT []
synonym: "PNGase A glycan release" EXACT []
synonym: "PNGase A glycan cleavage" EXACT []
is_a: CHMO:0001494 ! enzyme digestion
[Term]
id: CHMO:XXXXXXX
name: PNGase F digestion
def: "An enzymatic removal of N-linked glycans from a peptide or protein using the enzyme PNGase F (N-Glycosidase F)."
synonym: "PNGase F treatment" EXACT []
synonym: "PNGase F glycan release" EXACT []
synonym: "PNGase F glycan cleavage" EXACT []
is_a: CHMO:0001494 ! enzyme digestion
[Term]
id: CHMO:XXXXXXX
name: high-performance anion-exchange chromatography
def: "A high-performance liquid chromatography method where the components are distributed between two phases, one of which is stationary and retains anions by positively charged functional groups."
synonym: "HPAEC" EXACT []
synonym: "high-performance AEC" EXACT []
is_a: CHMO:0001009 ! high-performance liquid chromatography
is_a: CHMO:0001209 ! anion-exchange chromatography
[Term]
id: CHMO:XXXXXXX
name: graphitized carbon liquid chromatography
def: "A separation method where the components are distributed between two phases, one of which is stationary and made from graphitized carbon and the other moves in a definite direction."
synonym: "porous graphitic carbon chromatography" EXACT []
synonym: "PGC chromatography" EXACT []
synonym: "graphitized carbon HPLC" EXACT []
is_a: CHMO:0001000 ! chromatography
[Term]
id: CHMO:XXXXXXX
name: Orbitrap mass spectrometry
def: "Mass spectrometry where the mass-to-charge ratio of the sample ions is measured by their oscillations along the centre electrode in an Orbitrap mass analyzer."
synonym: "Orbitrap-mass spectroscopy" EXACT []
synonym: "Orbitrap-MS" EXACT []
is_a: CHMO:0000500 ! ion trap mass spectrometry
is_a: CHMO:XXXXXXX ! Fourier transform mass spectrometry
[Term]
id: CHMO:XXXXXXX
name: Fourier transform mass spectrometry
def: "Mass spectrometry where the mass-to-charge ratio of the sample ions is determined by Fourier transform of a recorded time-domain transient."
synonym: "FTMS" EXACT []
synonym: "FT-MS" EXACT []
is_a: CHMO:0000500 ! ion trap mass spectrometry
Suggested changes (to reflect that both Orbitraps and FTICRs are (Kingdon and Penning) ion traps used to perform Fourier transform mass spectrometry, which is a subclass of ion trap mass spectrometry):
id: CHMO:0000968
name: orbitrap
def: "A mass-to-charge analyser that consists of two coaxial axially symmetric electrodes, the outer one in the shape of a barrel, the inner one in the shape of a spindle, that traps ions in oscillating trajectories along the z-axis according to their mass-to-charge ratio." [ISBN:9780470516348]
is_a: CHMO:0002657 ! ion trap mass spectrometer
[Term]
id: CHMO:0000965
name: Fourier transform ion cyclotron resonance mass spectrometer
def: "A mass spectrometer that uses an ion cyclotron resonance cell (a piece of apparatus that measures the frequency at which ions precesses in a fixed magnetic field and subjects the frequency output to a Fourier transform) as a mass-to-charge analyser and detector." [ISBN:9780470516348]
synonym: "FT-ICR MS" RELATED []
synonym: "FTICR MS" RELATED []
synonym: "FTICR spectrometer" EXACT []
is_a: CHMO:0002657 ! ion trap mass spectrometer
intersection_of: CHMO:0000982 ! mass spectrometer
intersection_of: BFO:0000174 CHMO:0000964 ! has proper continuant part at some time ion cyclotron resonance cell
relationship: BFO:0000174 CHMO:0000964 ! has proper continuant part at some time ion cyclotron resonance cell
[Term]
id: CHMO:0000502
name: Fourier transform ion cyclotron resonance mass spectrometry
def: "Mass spectrometry where the mass-to-charge ratio of the sample ions is determined by measuring their cyclotron frequency (the frequency at which they precesses in a fixed magnetic field) and subjecting it to a Fourier transform." [https://doi.org/10.1351/goldbook.F02492, FIX:0000083]
synonym: "Fourier transform ion cyclotron resonance mass spectroscopy" EXACT []
synonym: "Fourier transform mass spectrometry" EXACT []
synonym: "Fourier transform mass spectroscopy" EXACT []
synonym: "FT ICR MS" EXACT []
synonym: "FT-ICR mass spectrometry" EXACT []
synonym: "FT-ICR mass spectroscopy" EXACT []
synonym: "FT-ICR MS" EXACT []
synonym: "FT-ICR-MS" EXACT []
synonym: "FT-ICRMS" EXACT []
synonym: "FT/ICR mass spectrometry" EXACT []
synonym: "FT/ICR mass spectroscopy" EXACT []
synonym: "FTICRMS" EXACT []
synonym: "ICR-FT-MS" EXACT []
synonym: "in-beam Fourier-transform ion cyclotron resonance" EXACT []
synonym: "ion cyclotron resonance Fourier transform mass spectrometry" EXACT []
is_a: CHMO:0000501 ! ion cyclotron resonance mass spectrometry
is_a: CHMO:XXXXXXX ! Fourier transform mass spectrometry
I would like to suggest the following additions and minor changes to CHMO to facilitate annotation of glycomics methods and reflect recent technical development in the field of mass spectrometry. In addition to common sample treatments, I also suggest including the action noun "orbitrap mass spectrometry", and categorizing both orbitrap and Fourier transform ion cyclotron resonance mass spectrometry as "ion trap mass spectrometry" and/or "Fourier transform mass spectrometry". Both are correct, and consistent with the current definition of "ion trap mass spectrometry" in the ontology. "Fourier transform mass spectrometry" is a subclass of "ion trap mass spectrometry". The term "Fourier transform mass spectrometer" could also be added, but I left it out as the Fourier transform typically happens in the computer that is arguably separate from the instrument.
The suggestions:
[Term] id: CHMO:XXXXXXX name: Smith degradation def: "A selective degradation of polysaccharides by periodate oxidation." is_a: OBI:0000094 ! material processing
[Term] id: CHMO:XXXXXXX name: reductive beta elimination def: "A beta elimination under reducing conditions." synonym: "reductive β-elimination" EXACT [] is_a: CHMO:XXXXXXX ! beta elimination
[Term] id: CHMO:XXXXXXX name: non-reductive beta elimination def: "A beta elimination under non-reducing conditions." synonym: "non-reductive β-elimination" EXACT [] is_a: CHMO:XXXXXXX ! beta elimination
[Term] id: CHMO:XXXXXXX name: beta elimination def: "A chemical reaction in which atoms or groups are removed from adjacent atoms." synonym: "β-elimination" EXACT [] is_a: OBI:0000094 ! material processing
[Term] id: CHMO:XXXXXXX name: hydrazine treatment def: "Treatment of a sample with hydrazine." synonym: "hydrazinolysis" EXACT [] is_a: OBI:0000094 ! material processing
[Term] id: CHMO:XXXXXXX name: PNGase A digestion def: "An enzymatic removal of N-linked glycans from a peptide or protein using the enzyme PNGase A (N-Glycosidase A), including those with core α1-3 fucosylation." synonym: "PNGase A treatment" EXACT [] synonym: "PNGase A glycan release" EXACT [] synonym: "PNGase A glycan cleavage" EXACT [] is_a: CHMO:0001494 ! enzyme digestion
[Term] id: CHMO:XXXXXXX name: PNGase F digestion def: "An enzymatic removal of N-linked glycans from a peptide or protein using the enzyme PNGase F (N-Glycosidase F)." synonym: "PNGase F treatment" EXACT [] synonym: "PNGase F glycan release" EXACT [] synonym: "PNGase F glycan cleavage" EXACT [] is_a: CHMO:0001494 ! enzyme digestion
[Term] id: CHMO:XXXXXXX name: high-performance anion-exchange chromatography def: "A high-performance liquid chromatography method where the components are distributed between two phases, one of which is stationary and retains anions by positively charged functional groups." synonym: "HPAEC" EXACT [] synonym: "high-performance AEC" EXACT [] is_a: CHMO:0001009 ! high-performance liquid chromatography is_a: CHMO:0001209 ! anion-exchange chromatography
[Term] id: CHMO:XXXXXXX name: graphitized carbon liquid chromatography def: "A separation method where the components are distributed between two phases, one of which is stationary and made from graphitized carbon and the other moves in a definite direction." synonym: "porous graphitic carbon chromatography" EXACT [] synonym: "PGC chromatography" EXACT [] synonym: "graphitized carbon HPLC" EXACT [] is_a: CHMO:0001000 ! chromatography
[Term] id: CHMO:XXXXXXX name: Orbitrap mass spectrometry def: "Mass spectrometry where the mass-to-charge ratio of the sample ions is measured by their oscillations along the centre electrode in an Orbitrap mass analyzer." synonym: "Orbitrap-mass spectroscopy" EXACT [] synonym: "Orbitrap-MS" EXACT [] is_a: CHMO:0000500 ! ion trap mass spectrometry is_a: CHMO:XXXXXXX ! Fourier transform mass spectrometry
[Term] id: CHMO:XXXXXXX name: Fourier transform mass spectrometry def: "Mass spectrometry where the mass-to-charge ratio of the sample ions is determined by Fourier transform of a recorded time-domain transient." synonym: "FTMS" EXACT [] synonym: "FT-MS" EXACT [] is_a: CHMO:0000500 ! ion trap mass spectrometry
Suggested changes (to reflect that both Orbitraps and FTICRs are (Kingdon and Penning) ion traps used to perform Fourier transform mass spectrometry, which is a subclass of ion trap mass spectrometry):
id: CHMO:0000968 name: orbitrap def: "A mass-to-charge analyser that consists of two coaxial axially symmetric electrodes, the outer one in the shape of a barrel, the inner one in the shape of a spindle, that traps ions in oscillating trajectories along the z-axis according to their mass-to-charge ratio." [ISBN:9780470516348] is_a: CHMO:0002657 ! ion trap mass spectrometer
[Term] id: CHMO:0000965 name: Fourier transform ion cyclotron resonance mass spectrometer def: "A mass spectrometer that uses an ion cyclotron resonance cell (a piece of apparatus that measures the frequency at which ions precesses in a fixed magnetic field and subjects the frequency output to a Fourier transform) as a mass-to-charge analyser and detector." [ISBN:9780470516348] synonym: "FT-ICR MS" RELATED [] synonym: "FTICR MS" RELATED [] synonym: "FTICR spectrometer" EXACT [] is_a: CHMO:0002657 ! ion trap mass spectrometer intersection_of: CHMO:0000982 ! mass spectrometer intersection_of: BFO:0000174 CHMO:0000964 ! has proper continuant part at some time ion cyclotron resonance cell relationship: BFO:0000174 CHMO:0000964 ! has proper continuant part at some time ion cyclotron resonance cell
[Term] id: CHMO:0000502 name: Fourier transform ion cyclotron resonance mass spectrometry def: "Mass spectrometry where the mass-to-charge ratio of the sample ions is determined by measuring their cyclotron frequency (the frequency at which they precesses in a fixed magnetic field) and subjecting it to a Fourier transform." [https://doi.org/10.1351/goldbook.F02492, FIX:0000083] synonym: "Fourier transform ion cyclotron resonance mass spectroscopy" EXACT [] synonym: "Fourier transform mass spectrometry" EXACT [] synonym: "Fourier transform mass spectroscopy" EXACT [] synonym: "FT ICR MS" EXACT [] synonym: "FT-ICR mass spectrometry" EXACT [] synonym: "FT-ICR mass spectroscopy" EXACT [] synonym: "FT-ICR MS" EXACT [] synonym: "FT-ICR-MS" EXACT [] synonym: "FT-ICRMS" EXACT [] synonym: "FT/ICR mass spectrometry" EXACT [] synonym: "FT/ICR mass spectroscopy" EXACT [] synonym: "FTICRMS" EXACT [] synonym: "ICR-FT-MS" EXACT [] synonym: "in-beam Fourier-transform ion cyclotron resonance" EXACT [] synonym: "ion cyclotron resonance Fourier transform mass spectrometry" EXACT [] is_a: CHMO:0000501 ! ion cyclotron resonance mass spectrometry is_a: CHMO:XXXXXXX ! Fourier transform mass spectrometry