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XLMOD.obo
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format-version: 1.2
data-version: release/2019-10-28
ontology: xlmod
date: 05:02:2022 20:08
saved-by: Joshua Klein
auto-generated-by: OBO-Edit 2.3.1
default-namespace: XLMOD
remark: version: 1.1.12
remark: coverage: cross-linking reagents, cross-linker related post-translational modifications, and derivatization reagents for GC-MS and LC-MS
remark: creator: Lutz Fischer <lfischer <-at-> staffmail.ed.ac.uk>
remark: creator: Alexander Leitner <leitner <-at-> imsb.biol.ethz.ch>
remark: creator: Nils Hoffmann <nils.hoffmann <-at-> isas.de>
remark: creator: Gerhard Mayer <mayerg97 <-at-> rub.de>
remark: This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.
remark: To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.
[Typedef]
id: part_of
name: part_of
is_transitive: true
def: "The basic part of relationship indicating a top-level branch of this ontology." [OBO:defs]
[Typedef]
id: is_activatable
name: is_activatable
def: "Indicates how the cross-linking reagent can be activated." [OBO:defs]
[Typedef]
id: is_analog_of
name: is_analog_of
def: "Indicates biochemical analogues of nucleobases, nucleosides or amino acids." [OBO:defs]
[Typedef]
id: is_cleavable
name: is_cleavable
def: "Indicates that the cross-linking reagent is cleavable." [OBO:defs]
[Typedef]
id: is_labelled
name: is_labelled
def: "Indicates that the cross-linking or derivatization reagent has an isotopic label." [OBO:defs]
[Typedef]
id: is_partially_reacted
name: is_partially_reacted
def: "Specifies the type of the cross-linker related chemical modification." [OBO:defs]
[Typedef]
id: is_reactive_with
name: is_reactive_with
def: "Indicates the chemical group that can react with the cross-linking or derivatization reagent." [OBO:defs]
[Typedef]
id: is_side_product_of
name: is_side_product_of
def: "Indicates the cross-linking reagent from which the chemical modification is derived." [OBO:defs]
[Typedef]
id: has_handle
name: has_handle
def: "Indicates that the cross-linking reagent has a handle that can be used for detection/identification, enrichment or purification." [OBO:defs]
[Typedef]
id: has_click_enabled_linker
name: has_click_enabled_linker
def: "Indicates that the cross-linking reagent has a linker that can be enabled by click chemistry." [OBO:defs]
[Typedef]
id: has_neutral_loss_reporter
name: has_neutral_loss_reporter
def: "Indicates that the cross-linking reagent has a neutral loss reporter." [OBO:defs]
[Typedef]
id: has_property
name: has_property
def: "Indicates a property of a cross-linking or derivatization reagent." [OBO:defs]
[Typedef]
id: has_chromophore
name: has_chromophore
def: "Indicates that the derivatization reagent can be detected by the specified chromophore." [OBO:defs]
[Typedef]
id: has_electrophore
name: has_electrophore
def: "Indicates that the derivatization reagent can be detected by the specified electrophore." [OBO:defs]
[Typedef]
id: has_fluorophore
name: has_fluorophore
def: "Indicates that the derivatization reagent can be detected by the specified fluorophore." [OBO:defs]
[Typedef]
id: has_reactive_group
name: has_reactive_group
def: "Indicates that the cross-linking or derivatization reagent has the specified reactive group." [OBO:defs]
[Term]
id: XLMOD:00000
name: Proteomics Standards Initiative cross-linking and derivatization controlled vocabulary
def: "Proteomics Standards Initiative cross-linking and derivatization controlled vocabulary." [PSI:XL]
[Term]
id: XLMOD:00001
name: cross-linking entity
def: "Entity relevant to the domain of cross-linking in proteomics." [PSI:XL]
relationship: part_of XLMOD:00000 ! Proteomics Standards Initiative cross-linking and derivatization controlled vocabulary
[Term]
id: XLMOD:00002
name: cross-linker related chemical modification
def: "Dead-end modification resulting from a cross-linker reagent reacting only with one peptide." [PSI:XL]
relationship: part_of XLMOD:00000 ! Proteomics Standards Initiative cross-linking and derivatization controlled vocabulary
[Term]
id: XLMOD:00003
name: label transfer reagent
def: "A cross-linker acting as label transfer reagent." [PSI:XL]
relationship: part_of XLMOD:00000 ! Proteomics Standards Initiative cross-linking and derivatization controlled vocabulary
[Term]
id: XLMOD:00004
name: cross-linker
def: "Compound that can link two or more polymer chains." [PSI:XL]
is_a: XLMOD:00001 ! cross-linking entity
[Term]
id: XLMOD:00005
name: homofunctional cross-linker
def: "A cross-linking reagent with identical reactive groups at each end of the spacer arm." [PSI:XL]
is_a: XLMOD:00004 ! cross-linker
[Term]
id: XLMOD:00006
name: heterofunctional cross-linker
def: "A cross-linking reagent with at least two different reactive groups." [PSI:XL]
is_a: XLMOD:00004 ! cross-linker
[Term]
id: XLMOD:00007
name: photoreactive cross-linker
def: "OBSOLETE A cross-linking reagent that becomes reactive when exposed to ultraviolet or visible light." [PSI:XL]
comment: This term was made obsolete because photo-reactivity is now encoded for the reactive groups of the cross-linkers, see (XLMOD:00108).
is_obsolete: true
[Term]
id: XLMOD:00008
name: zero-length cross-linker
def: "A cross-linking reagent causing direct conjugation without becoming part of the final cross-link between the target molecules." [PSI:XL]
is_a: XLMOD:00004 ! cross-linker
[Term]
id: XLMOD:00009
name: cross-linking attribute
def: "An attribute describing a cross-linker." [PSI:XL]
is_a: XLMOD:00001 ! cross-linking entity
[Term]
id: XLMOD:00010
name: deuterium labelled
def: "Indicates that a cross-linker is deuterium labelled." [PSI:XL]
is_a: XLMOD:00009 ! cross-linking attribute
[Term]
id: XLMOD:00011
name: hydrolyzed
def: "Indicates that a cross-linker is hydrolyzed, for example for NHS-type reagents -C(=O)-NHS was converted to -C(=O)-OH." [PSI:XL]
is_a: XLMOD:00009 ! cross-linking attribute
[Term]
id: XLMOD:00012
name: amidated
def: "Indicates that a cross-linker is amidated." [PSI:XL]
is_a: XLMOD:00009 ! cross-linking attribute
[Term]
id: XLMOD:00013
name: membrane permeable
def: "Indicates that a cross-linker is membrane permeable." [PSI:XL]
is_a: XLMOD:00009 ! cross-linking attribute
[Term]
id: XLMOD:00014
name: hydrophilic
def: "Indicates that a cross-linker is hydrophilic." [PSI:XL]
is_a: XLMOD:00009 ! cross-linking attribute
[Term]
id: XLMOD:00015
name: fluorescent
def: "Indicates that a cross-linker is fluorescent." [PSI:XL]
is_a: XLMOD:00009 ! cross-linking attribute
[Term]
id: XLMOD:00016
name: cleavable
def: "Indicates that a cross-linker is cleavable." [PSI:XL]
is_a: XLMOD:00009 ! cross-linking attribute
[Term]
id: XLMOD:00017
name: chemically cleavable
def: "Indicates that a cross-linker is chemically cleavable." [PSI:XL]
is_a: XLMOD:00016 ! cleavable
[Term]
id: XLMOD:00018
name: cleavable by MS2 labile bond
def: "Indicates that a cross-linker is mass-spectrometrically cleavable, i.e. contains a MS2 labile bond leading to fragments detected in MS3." [PSI:XL]
is_a: XLMOD:00016 ! cleavable
[Term]
id: XLMOD:00019
name: enrichable
def: "Indicates that a cross-linker facilitates enrichment." [PSI:XL]
is_a: XLMOD:00009 ! cross-linking attribute
[Term]
id: XLMOD:00020
name: iodinatable
def: "Indicates that a cross-linker is iodinatable, e.g. for autoradiographic detection by radio-labelling with J-131." [PSI:XL]
is_a: XLMOD:00009 ! cross-linking attribute
[Term]
id: XLMOD:00021
name: ammonium amidated
def: "Indicates a dead-end modification that was amidated by an ammonium salt, like e.g. bicarbonate, phosphate, chloride, for example for NHS-type reagents -C(=O)-NHS was converted to -C(=O)-NH2." [PSI:XL]
is_a: XLMOD:00012 ! amidated
[Term]
id: XLMOD:00022
name: Tris amidated
def: "Indicates a dead-end modification that was amidated by Tris(hydroxymethyl)-aminomethane, for example for NHS-type reagents -C(=O)-NHS was converted to -C(=O)-NHC(CH2OH)3." [PSI:XL]
is_a: XLMOD:00012 ! amidated
[Term]
id: XLMOD:00023
name: cleavable S-S bond
def: "Indicates that a cross-linker contains a cleavable S-S bond, which is chemically cleavable by reducing agents like e.g. thiols, beta-mercaptoethanol, dithiothreitol (DTT), mercaptomethylamine or Tris(2-carboxyethyl)phosphin (TCEP)." [PSI:XL]
is_a: XLMOD:00017 ! chemically cleavable
relationship: is_cleavable XLMOD:00041 ! thiol cleavable
relationship: is_cleavable XLMOD:00038 ! DTT cleavable
relationship: is_cleavable XLMOD:00042 ! TCEP cleavable
relationship: is_cleavable XLMOD:00043 ! mercaptoethanol cleavable
[Term]
id: XLMOD:00024
name: periodate cleavable
def: "Indicates that a cross-linker is chemically cleavable by the oxidizing agent periodate." [PSI:XL]
is_a: XLMOD:00017 ! chemically cleavable
[Term]
id: XLMOD:00025
name: hydroxylamine cleavable
def: "Indicates that a cross-linker is chemically cleavable by hydroxylamine." [PSI:XL]
is_a: XLMOD:00017 ! chemically cleavable
[Term]
id: XLMOD:00026
name: reactive group attribute
def: "An attribute describing a reactive group." [PSI:XL]
relationship: part_of XLMOD:00001 ! cross-linking entity
[Term]
id: XLMOD:00027
name: chemically reactive
def: "Indicates that a reactive group reacts with specific functional groups." [PSI:XL]
is_a: XLMOD:00026 ! reactive group attribute
[Term]
id: XLMOD:00028
name: primary amine reactive
def: "Indicates that a reactive group is reactive with primary amino (-NH2) groups." [PSI:XL]
is_a: XLMOD:00027 ! chemically reactive
[Term]
id: XLMOD:00029
name: sulfhydryl reactive
def: "Indicates that a reactive group is reactive with sulfhydryl (-SH) groups." [PSI:XL]
is_a: XLMOD:00027 ! chemically reactive
[Term]
id: XLMOD:00030
name: carboxyl reactive
def: "Indicates that a reactive group is reactive with carboxyl (-COOH) groups." [PSI:XL]
is_a: XLMOD:00027 ! chemically reactive
[Term]
id: XLMOD:00031
name: aldehyde reactive
def: "Indicates that a reactive group is reactive with aldehyde (-CHO) or carbonyl (-CO) groups." [PSI:XL]
is_a: XLMOD:00027 ! chemically reactive
[Term]
id: XLMOD:00032
name: hydroxyl reactive
def: "Indicates that a reactive group is reactive with hydroxyl (-OH) groups." [PSI:XL]
is_a: XLMOD:00027 ! chemically reactive
[Term]
id: XLMOD:00033
name: azide reactive
def: "Indicates that a reactive group is reactive with azide (-N3) groups." [PSI:XL]
is_a: XLMOD:00027 ! chemically reactive
[Term]
id: XLMOD:00034
name: photo cleavable
def: "Indicates that a cross-linker is cleavable by light." [PSI:XL]
is_a: XLMOD:00016 ! cleavable
[Term]
id: XLMOD:00035
name: CID cleavable
def: "Indicates that a cross-linker is mass-spectrometrically cleavable by collission induced dissociation." [PSI:XL]
is_a: XLMOD:00016 ! cleavable
[Term]
id: XLMOD:00036
name: 13C labelled
def: "Indicates that a cross-linker is labelled with carbon-13." [PSI:XL]
is_a: XLMOD:00009 ! cross-linking attribute
[Term]
id: XLMOD:00037
name: non-selective
def: "Indicates that a cross-linker is non-selective (i.e. can react with different amino acids, but also with DNA/RNA and carbohydrates (aldehyde reactive))." [PSI:XL]
is_a: XLMOD:00026 ! reactive group attribute
[Term]
id: XLMOD:00038
name: DTT cleavable
def: "Indicates that a cross-linker is chemically cleavable by the reducing agent DTT (dithiothreitol)." [PSI:XL]
is_a: XLMOD:00017 ! chemically cleavable
[Term]
id: XLMOD:00039
name: ammonium cleavable
def: "Indicates that a cross-linker is chemically cleavable by ammonium hydroxide." [PSI:XL]
is_a: XLMOD:00017 ! chemically cleavable
[Term]
id: XLMOD:00040
name: ISD cleavable
def: "Indicates that a cross-linker is mass-spectrometrically cleavable by in-source decay." [PSI:XL]
is_a: XLMOD:00016 ! cleavable
[Term]
id: XLMOD:00041
name: thiol cleavable
def: "Indicates that a cross-linker is mass-spectrometrically cleavable (reducible) by thiols." [PSI:XL]
synonym: "DTT cleavable" RELATED []
synonym: "TCEP cleavable" RELATED []
synonym: "mercaptoethanol cleavable" RELATED []
is_a: XLMOD:00016 ! cleavable
[Term]
id: XLMOD:00042
name: TCEP cleavable
def: "Indicates that a cross-linker is chemically cleavable by the reducing agent TCEP (Tris(2-carboxyethyl)phosphin)." [PSI:XL]
is_a: XLMOD:00017 ! chemically cleavable
[Term]
id: XLMOD:00043
name: mercaptoethanol cleavable
def: "Indicates that a cross-linker is chemically cleavable by the reducing agent mercaptoethanol." [PSI:XL]
is_a: XLMOD:00017 ! chemically cleavable
[Term]
id: XLMOD:00044
name: mass defect labelled
def: "Indicates that a cross-linker is mass defect labelled." [PSI:XL]
is_a: XLMOD:00009 ! cross-linking attribute
[Term]
id: XLMOD:00045
name: thioether reactive
def: "Indicates that a reactive group is reactive with thioether (R1-S-R2) groups." [PSI:XL]
is_a: XLMOD:00027 ! chemically reactive
[Term]
id: XLMOD:00046
name: imidazole reactive
def: "Indicates that a reactive group is reactive with the heterocyclic imidazole groups." [PSI:XL]
is_a: XLMOD:00027 ! chemically reactive
[Term]
id: XLMOD:00047
name: thioesterized
def: "Indicates that a cross-linker is thioesterized." [PSI:XL]
is_a: XLMOD:00009 ! cross-linking attribute
[Term]
id: XLMOD:00048
name: nucleic acid reactive
def: "Indicates that a reactive group is reactive with RNA or DNA." [PSI:XL]
is_a: XLMOD:00027 ! chemically reactive
[Term]
id: XLMOD:00049
name: amino acid derivative
def: "An amino acid derivative used in cross-linking experiments." [PSI:XL]
is_a: XLMOD:00001 ! cross-linking entity
[Term]
id: XLMOD:00050
name: handle
def: "A handle attached to a cross-linker used for detection, affinity enrichment or purification." [PSI:XL]
is_a: XLMOD:00001 ! cross-linking entity
relationship: part_of XLMOD:00004 ! cross-linker
[Term]
id: XLMOD:00051
name: biotin
def: "A Biotin affinity handle, enrichable with avidin, streptavidin or neutravidin, attached to a cross-linker." [PSI:XL]
is_a: XLMOD:00050 ! handle
is_a: XLMOD:00019 ! enrichable
[Term]
id: XLMOD:00052
name: NO2 neutral loss reporter
def: "A NO2 detection tag." [PMID:19496583]
is_a: XLMOD:00050 ! handle
[Term]
id: XLMOD:00053
name: alkyne
def: "An alkyne (hadrocarbon with at least one C-C triple bond) tag, e.g. BARAC (biarylazacycloctynone) to enable enrichment of cross-linked peptides by either coupling of an affinity group with alkyne-azido click chemistry or by using immobilized azide linkers." [PMID:19496583]
is_a: XLMOD:00050 ! handle
is_a: XLMOD:00019 ! enrichable
[Term]
id: XLMOD:00054
name: DNB
def: "A dinitrobenzole affinity handle for enrichment with anti-DNB antibodies, attached to a cross-linker." [PSI:XL]
is_a: XLMOD:00050 ! handle
is_a: XLMOD:00019 ! enrichable
[Term]
id: XLMOD:00055
name: azide
def: "A photoreactive azide (-N3) tag to enable enrichment of cross-linked peptides with either immobilized alkyne linkers or by azide-alkyne click chemistry using biotin-alkyne respective biotin-phosphine." [PMID:20472459]
is_a: XLMOD:00050 ! handle
is_a: XLMOD:00019 ! enrichable
is_a: XLMOD:00100 ! reactive group
relationship: is_activatable XLMOD:00149 ! photoactivatable
relationship: is_reactive_with XLMOD:00037 ! non-selective
[Term]
id: XLMOD:00056
name: CHCA
def: "An alpha-cyano-4-hydroxycinnamic acid UV-absorbing label for signal enhancement." [PMID:19902427]
is_a: XLMOD:00050 ! handle
[Term]
id: XLMOD:00057
name: generic neutral loss reporter
def: "A generic neutral loss reporter." [PXI:XL]
is_a: XLMOD:00050 ! handle
[Term]
id: XLMOD:00058
name: amino acid
def: "An amino acid compound." [PSI:XL]
is_a: XLMOD:00001 ! cross-linking entity
[Term]
id: XLMOD:00059
name: L-Leucine
def: "The amino acid L-Leucine." [PXI:XL]
is_a: XLMOD:00058 ! amino acid
[Term]
id: XLMOD:00060
name: L-Methionine
def: "The amino acid L-Methionine." [PXI:XL]
is_a: XLMOD:00058 ! amino acid
[Term]
id: XLMOD:00061
name: base cleavable
def: "Indicates that a cross-linker is chemically cleavable by bases." [PSI:XL]
is_a: XLMOD:00017 ! chemically cleavable
[Term]
id: XLMOD:00062
name: hydrazine reactive
def: "Indicates that a reactive group is reactive with hydrazines (N2H4)." [PSI:XL]
is_a: XLMOD:00027 ! chemically reactive
[Term]
id: XLMOD:00063
name: carbonyl reactive
def: "Indicates that a reactive group is reactive with carbonyl (R1-CO-R2) groups." [PSI:XL]
is_a: XLMOD:00027 ! chemically reactive
[Term]
id: XLMOD:00064
name: oxidized
def: "Indicates that a cross-linker is oxidized, e.g. by oxidizing a carbonyl to a carboxyl functional group." [PSI:XL]
is_a: XLMOD:00009 ! cross-linking attribute
[Term]
id: XLMOD:00065
name: alkenized
def: "Indicates that a cross-linker is modified to it's alkene form (loss of two hydrogen atoms by forming a C=C double bond)." [PSI:XL]
is_a: XLMOD:00009 ! cross-linking attribute
[Term]
id: XLMOD:00066
name: acid cleavable
def: "Indicates that a cross-linker is chemically cleavable by acids." [PSI:XL]
is_a: XLMOD:00017 ! chemically cleavable
[Term]
id: XLMOD:00067
name: CID cleavable C-S bond
def: "Indicates that a cross-linker contains a CID (Collision Induced Dissociation) cleavable C-S bond." [PSI:XL]
is_a: XLMOD:00035 ! CID cleavable
relationship: is_cleavable XLMOD:00018 ! cleavable by MS2 labile bond
[Term]
id: XLMOD:00068
name: L-Isoleucine
def: "The amino acid L-Isoleucine." [PXI:XL]
is_a: XLMOD:00058 ! amino acid
[Term]
id: XLMOD:00069
name: 18O labelled
def: "Indicates that a cross-linker is labelled with oxygen-18." [PSI:XL]
is_a: XLMOD:00009 ! cross-linking attribute
[Term]
id: XLMOD:00070
name: L-Phenylalanine
def: "The amino acid L-Phenylalanine." [PXI:XL]
is_a: XLMOD:00058 ! amino acid
[Term]
id: XLMOD:00071
name: iminobiotintrifluoroacetamide
def: "A Iminobiotin trifluoroacetamide affinity handle, enrichable with avidin, streptavidin or neutravidin, attached to a cross-linker." [PSI:XL]
is_a: XLMOD:00050 ! handle
is_a: XLMOD:00019 ! enrichable
relationship: is_reactive_with XLMOD:00072 ! avidin reactive
[Term]
id: XLMOD:00072
name: avidin reactive
def: "Indicates that a reactive group is reactive with either of the glycoproteins avidin, streptavidin or neutravidin." [PSI:XL]
is_a: XLMOD:00027 ! chemically reactive
[Term]
id: XLMOD:00073
name: nucleobase
def: "A nitrogeneous base occurring in nucleic acids." [PSI:XL]
is_a: XLMOD:00001 ! cross-linking entity
[Term]
id: XLMOD:00074
name: purine base
def: "A purine base occurring in nucleic acids." [PSI:XL]
is_a: XLMOD:00073 ! nucleobase
[Term]
id: XLMOD:00075
name: pyrimidine base
def: "A pyrimidine base occurring in nucleic acids." [PSI:XL]
is_a: XLMOD:00073 ! nucleobase
[Term]
id: XLMOD:00076
name: adenine
def: "The nucleobase adenine." [PXI:XL]
is_a: XLMOD:00074 ! purine base
[Term]
id: XLMOD:00077
name: guanine
def: "The nucleobase guanine." [PXI:XL]
is_a: XLMOD:00074 ! purine base
[Term]
id: XLMOD:00078
name: cytosine
def: "The nucleobase cytosine." [PXI:XL]
is_a: XLMOD:00075 ! pyrimidine base
[Term]
id: XLMOD:00079
name: thymine
def: "The nucleobase thymine." [PXI:XL]
is_a: XLMOD:00075 ! pyrimidine base
[Term]
id: XLMOD:00080
name: uracil
def: "The nucleobase uracil." [PXI:XL]
is_a: XLMOD:00075 ! pyrimidine base
[Term]
id: XLMOD:00081
name: nucleobase derivative
def: "A nucleobase derivative used in cross-linking experiments for protein-oligonucleotide cross-linking." [PSI:XL]
is_a: XLMOD:00001 ! cross-linking entity
relationship: is_analog_of XLMOD:00073 ! nucleobase
[Term]
id: XLMOD:00082
name: nucleoside
def: "A combination of a nucleobase and a sugar (either ribose or deoxyribose)." [PSI:XL]
is_a: XLMOD:00001 ! cross-linking entity
[Term]
id: XLMOD:00083
name: adenosine
def: "The nucleoside adenosine." [PXI:XL]
is_a: XLMOD:00082 ! nucleoside
[Term]
id: XLMOD:00084
name: guanosine
def: "The nucleoside guanosine." [PXI:XL]
is_a: XLMOD:00082 ! nucleoside
[Term]
id: XLMOD:00085
name: cytidine
def: "The nucleoside cytidine." [PXI:XL]
is_a: XLMOD:00082 ! nucleoside
[Term]
id: XLMOD:00086
name: uridine
def: "The nucleoside uridine." [PXI:XL]
is_a: XLMOD:00082 ! nucleoside
[Term]
id: XLMOD:00087
name: 5-methyluridine
def: "The nucleoside 5-methyluridine." [PXI:XL]
is_a: XLMOD:00082 ! nucleoside
[Term]
id: XLMOD:00088
name: nucleoside derivative
def: "A nucleoside derivative used in cross-linking experiments for protein-oligonucleotide cross-linking." [PSI:XL]
is_a: XLMOD:00001 ! cross-linking entity
relationship: is_analog_of XLMOD:00082 ! nucleoside
[Term]
id: XLMOD:00089
name: RNA-SH
def: "Thiol-modified RNA." [PSI:XL]
is_a: XLMOD:00001 ! cross-linking entity
[Term]
id: XLMOD:00090
name: biotin-alkyne
def: "A biotin-alkyne affinity handle, which can be used for enrichment with click-chemistry." [PSI:XL]
is_a: XLMOD:00050 ! handle
is_a: XLMOD:00019 ! enrichable
relationship: is_reactive_with XLMOD:00033 ! azide reactive
[Term]
id: XLMOD:00091
name: tetramethylrhodamine-alkyne
def: "A tetramethylrhodamine-alkyne affinity handle, which can be used for enrichment with click-chemistry." [PSI:XL]
synonym: "TAMRA" EXACT []
is_a: XLMOD:00050 ! handle
is_a: XLMOD:00019 ! enrichable
relationship: is_reactive_with XLMOD:00033 ! azide reactive
[Term]
id: XLMOD:00092
name: lipid analogue
def: "A lipid analogue used in cross-linking experiments for lipid-protein cross-linking." [PSI:XL]
is_a: XLMOD:00001 ! cross-linking entity
[Term]
id: XLMOD:00093
name: sialic acid analogue
def: "A sialic acid analogue used in cross-linking experiments for glycan-protein cross-linking." [PSI:XL]
is_a: XLMOD:00001 ! cross-linking entity
[Term]
id: XLMOD:00094
name: alkenized cross-linker related chemical modification
def: "Alkenization dead-end modification resulting from a cross-linker reagent reacting only with one peptide." [PSI:XL]
is_a: XLMOD:00002 ! cross-linker related chemical modification
[Term]
id: XLMOD:00095
name: ammonium amidation cross-linker related chemical modification
def: "Ammonium amidation dead-end modification resulting from a cross-linker reagent reacting only with one peptide." [PSI:XL]
is_a: XLMOD:00002 ! cross-linker related chemical modification
[Term]
id: XLMOD:00096
name: hydrolization cross-linker related chemical modification
def: "Hydrolization dead-end modification resulting from a cross-linker reagent reacting only with one peptide." [PSI:XL]
is_a: XLMOD:00002 ! cross-linker related chemical modification
[Term]
id: XLMOD:00097
name: oxidation cross-linker related chemical modification
def: "Oxidition dead-end modification resulting from a cross-linker reagent reacting only with one peptide." [PSI:XL]
is_a: XLMOD:00002 ! cross-linker related chemical modification
[Term]
id: XLMOD:00098
name: thioesterization cross-linker related chemical modification
def: "Thio-esterization dead-end modification resulting from a cross-linker reagent reacting only with one peptide." [PSI:XL]
is_a: XLMOD:00002 ! cross-linker related chemical modification
[Term]
id: XLMOD:00099
name: formic acid cleavable
def: "Indicates that a cross-linker is chemically cleavable by formic acid." [PSI:XL]
is_a: XLMOD:00017 ! chemically cleavable
[Term]
id: XLMOD:00100
name: reactive group
def: "Part of a cross-linker that reacts with the amino-acids of the protein." [PSI:XL]
is_a: XLMOD:00009 ! cross-linking attribute
[Term]
id: XLMOD:00101
name: NHS ester
def: "A reactive group (N-hydroxysuccinimide) that reacts with lysines and N-termini but also serines, threonines and tyrosines." [PSI:XL]
synonym: "N-hydroxysuccinimide ester" EXACT []
property_value: specificities: "(K,Protein N-term)" xsd:string
property_value: secondarySpecificities: "(S,T,Y)" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: has_property XLMOD:00013 ! membrane permeable
relationship: is_reactive_with XLMOD:00028 ! primary amine reactive
[Term]
id: XLMOD:00102
name: Sulfo NHS ester
def: "A reactive group (N-hydroxysulfosuccinimide) that reacts with lysines and N-termini but also serines, threonines and tyrosines." [PSI:XL]
synonym: "N-hydroxysulfosuccinimide ester" EXACT []
property_value: specificities: "(K,Protein N-term)" xsd:string
property_value: secondarySpecificities: "(S,T,Y)" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: has_property XLMOD:00014 ! hydrophilic
relationship: is_reactive_with XLMOD:00028 ! primary amine reactive
[Term]
id: XLMOD:00103
name: diazirine
def: "Photoreactive group (R1-CN2-R2) that inserts into any C-H or N-H bond." [PSI:XL]
property_value: waveLengthRange: "330-370 nm" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: is_activatable XLMOD:00149 ! photoactivatable
relationship: is_reactive_with XLMOD:00037 ! non-selective
[Term]
id: XLMOD:00104
name: N-hydroxyphthalimide
def: "A reactive group that reacts with amines." [PMID:19994840]
property_value: specificities: "(K,N,Q,R,Protein N-term)" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: is_reactive_with XLMOD:00028 ! primary amine reactive
[Term]
id: XLMOD:00105
name: carbodiimide
def: "A Carboxyl-to-amine (R1-N=C=N_R2) reactive chemical group." [PSI:XL]
property_value: specificities: "(K,N,Q,R,Protein N-term)&(E,D,Protein C-term)" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: is_reactive_with XLMOD:00028 ! primary amine reactive
relationship: is_reactive_with XLMOD:00030 ! carboxyl reactive
[Term]
id: XLMOD:00106
name: maleimide
def: "A reactive group that reacts with sulfhydryl groups." [PSI:XL]
property_value: specificities: "(C)" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: is_reactive_with XLMOD:00029 ! sulfhydryl reactive
[Term]
id: XLMOD:00107
name: nitrophenyl azide
def: "A nitrophenyl azide photoreactive group." [PSI:XL]
property_value: waveLengthRange: "320-370 nm" xsd:string
is_a: XLMOD:00114 ! aryl azide
relationship: is_activatable XLMOD:00149 ! photoactivatable
relationship: is_reactive_with XLMOD:00037 ! non-selective
relationship: is_reactive_with XLMOD:00089 ! RNA-SH
[Term]
id: XLMOD:00108
name: photoreactive
def: "Indicates that a reactive group is photoreactive." [PSI:XL]
is_a: XLMOD:00026 ! reactive group attribute
[Term]
id: XLMOD:00109
name: pyridinyldisulfide
def: "A pyridinyldisulfide reactive group that reacts with sulfhydryl groups to form disulfide bonds." [PSI:XL]
synonym: "pyridyl disulfide" EXACT []
synonym: "pyridyldithiol" EXACT []
property_value: specificities: "(C)" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: is_cleavable XLMOD:00023 ! cleavable S-S bond
relationship: is_reactive_with XLMOD:00029 ! sulfhydryl reactive
[Term]
id: XLMOD:00110
name: hydrazide
def: "A hydrazide reactive group (-CO-NH-NH2) that reacts with carbonyls to form hydrazone bonds." [PSI:XL]
property_value: specificities: "(D,E,Protein C-term)" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: is_reactive_with XLMOD:00030 ! carboxyl reactive
relationship: is_reactive_with XLMOD:00031 ! aldehyde reactive
relationship: is_reactive_with XLMOD:06510 ! ketone reactive
[Term]
id: XLMOD:00111
name: imidoester
def: "An amine-reactive chemical group (R1-C(=NH)-OR2)." [PSI:XL]
property_value: specificities: "(K,N,Q,R,Protein N-term)" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: is_reactive_with XLMOD:00028 ! primary amine reactive
[Term]
id: XLMOD:00112
name: haloacetyl
def: "A reactive group (alpha-haloacetyl, halo-C2H5), mostly a iodoacetyl, bromoacetyl or chloroacetyl group, that reacts with sulfhydryl groups." [PSI:XL]
property_value: specificities: "(C)" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: is_reactive_with XLMOD:00029 ! sulfhydryl reactive
[Term]
id: XLMOD:00113
name: alkoxyamine
def: "A reactive group (R-O-N-R2) that conjugates to carbonyls." [PSI:XL]
property_value: specificities: "(D,E,Protein C-term)" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: is_reactive_with XLMOD:00031 ! aldehyde reactive
[Term]
id: XLMOD:00114
name: aryl azide
def: "Photoreactive aryl(Ar)-substitited azide (N=N=N) group, that initiates addition reactions with double bonds or insertion into C-H and N-H bonds or reacts with primary amines." [PSI:XL]
property_value: waveLengthRange: "250-350 nm" xsd:string
is_a: XLMOD:00055 ! azide
relationship: is_activatable XLMOD:00149 ! photoactivatable
relationship: is_reactive_with XLMOD:00028 ! primary amine reactive
relationship: is_reactive_with XLMOD:00037 ! non-selective
[Term]
id: XLMOD:00115
name: glyoxal
def: "An arginine-specific reactive group (H-CO-CO-H)." [PSI:XL]
property_value: baseSpecificities: "(Guanine)" xsd:string
property_value: specificities: "(R)" xsd:string
is_a: XLMOD:00100 ! reactive group
[Term]
id: XLMOD:00116
name: aldehyde group
def: "An aldehyde (R-CO-H) reactive group." [PSI:XL]
property_value: specificities: "(K,N,R,Q,Y,Protein N-term)" xsd:string
property_value: secondarySpecificities: "(C,F,H,S,T,W)" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: is_reactive_with XLMOD:00028 ! primary amine reactive
[Term]
id: XLMOD:00117
name: acryl
def: "A reactive group (CH2=CH-CO-R) that reacts with sulfhydryl (-SH) groups." [PMID:22641729]
property_value: specificities: "(C)" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: is_reactive_with XLMOD:00029 ! sulfhydryl reactive
[Term]
id: XLMOD:00118
name: tetrafluorophenyl azide
def: "Tetrafluorophenyl (TFP) azide (N=N=N) photoreactive group." [PMID:22641729]
is_a: XLMOD:00114 ! aryl azide
relationship: is_activatable XLMOD:00149 ! photoactivatable
relationship: is_reactive_with XLMOD:00037 ! non-selective
[Term]
id: XLMOD:00119
name: benzophenone
def: "Benzophenone photoreactive group." [PMID:22641729]
property_value: waveLengthRange: "350-360 nm" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: is_activatable XLMOD:00149 ! photoactivatable
relationship: is_reactive_with XLMOD:00037 ! non-selective
relationship: is_reactive_with XLMOD:00089 ! RNA-SH
[Term]
id: XLMOD:00120
name: pentafluorophenyl
def: "A reactive group (F5-Ph) that reacts with amines." [PMID:22067100]
synonym: "PFP ester" EXACT []
property_value: specificities: "(K,N,Q,R,Protein N-term)" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: is_reactive_with XLMOD:00028 ! primary amine reactive
[Term]
id: XLMOD:00121
name: methanethiosulfonate
def: "A reactive group (Ch3-SO2-S-R) that reacts with sulfhydryl (-SH) groups." [PSI:XL]
synonym: "MTS" EXACT []
property_value: specificities: "(C)" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: is_reactive_with XLMOD:00029 ! sulfhydryl reactive
[Term]
id: XLMOD:00122
name: 4-azido-2,3,5,6-tetrafluorobenzene
def: "Photoreactive group that inserts into any C-H bond." [PSI:XL]
synonym: "ATFB" EXACT []
property_value: waveLengthRange: "UV" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: is_activatable XLMOD:00149 ! photoactivatable
relationship: is_reactive_with XLMOD:00037 ! non-selective
[Term]
id: XLMOD:00123
name: thermoreactive
def: "Indicates that a reactive group is thermoreactive." [PSI:XL]
is_a: XLMOD:00026 ! reactive group attribute
[Term]
id: XLMOD:00124
name: isocyanate
def: "An isocyanate (-N=C=O) that reacts with hydroxyl groups." [PMID:21557289]
property_value: specificities: "(S,T,Y)" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: is_reactive_with XLMOD:00028 ! primary amine reactive
relationship: is_reactive_with XLMOD:00032 ! hydroxyl reactive
relationship: is_reactive_with XLMOD:06500 ! secondary amine reactive
[Term]
id: XLMOD:00125
name: hydroxyphenyl azide
def: "A hydroxyphenyl azid photoreactive group." [PSI:XL]
property_value: waveLengthRange: "320-350 nm" xsd:string
is_a: XLMOD:00114 ! aryl azide
relationship: is_activatable XLMOD:00149 ! photoactivatable
relationship: is_reactive_with XLMOD:00037 ! non-selective
[Term]
id: XLMOD:00126
name: phenyl azide
def: "A phenyl azide photoreactive group." [PSI:XL]
synonym: "aryl nitrene" EXACT []
property_value: waveLengthRange: "320-350 nm" xsd:string
is_a: XLMOD:00114 ! aryl azide
relationship: is_activatable XLMOD:00149 ! photoactivatable
relationship: is_reactive_with XLMOD:00037 ! non-selective
[Term]
id: XLMOD:00127
name: iodoacetyl
def: "A iodoacetyl reactive group, that reacts with sulfhydryl groups." [PSI:XL]
property_value: specificities: "(C,H)" xsd:string
is_a: XLMOD:00112 ! haloacetyl
relationship: is_reactive_with XLMOD:00029 ! sulfhydryl reactive
[Term]
id: XLMOD:00128
name: bromoacetyl
def: "A bromoacetyl reactive group, that reacts with sulfhydryl groups." [PSI:XL]
property_value: specificities: "(C,H)" xsd:string
is_a: XLMOD:00112 ! haloacetyl
relationship: is_reactive_with XLMOD:00029 ! sulfhydryl reactive
[Term]
id: XLMOD:00129
name: hydroxybenzotriazole
def: "A reactive group that reacts with amines." [PMID:19994840]
property_value: specificities: "(K,N,Q,R,Protein N-term)" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: is_reactive_with XLMOD:00028 ! primary amine reactive
[Term]
id: XLMOD:00130
name: 1-hydroxy-7-azabenzotriazole
def: "A reactive group that reacts with amines." [PMID:19994840]
property_value: specificities: "(K,N,Q,R,Protein N-term)" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: is_reactive_with XLMOD:00028 ! primary amine reactive
[Term]
id: XLMOD:00131
name: thioimidate
def: "A reactive group that reacts with amines." [PMID:20795639]
property_value: specificities: "(K,N,Q,R,Protein N-term)" xsd:string
is_a: XLMOD:00100 ! reactive group
relationship: is_reactive_with XLMOD:00028 ! primary amine reactive