The root node of the unimod modifications ontology.
Cyanogen bromide (CNBr) cleavage converts the C-term Met to either homoserine or homoserine lactone, depending on pH.
Azidohomoalanine (AHA) bound to propargylglycine-NH2 (alkyne).
Methionine (C5H11NO2S) is substituted in culture with azidohomoalanine (AHA - C4H8N4O2). The azide group reacts with the alkyne group propargylglycine-NH2. As a result the side chain of methionine (C3H7S) is substituted by C7H12N5O.
Azidohomoalanine (AHA) bound to DDDDK-propargylglycine-NH2 (alkyne).
Methionine (C5H11NO2S) is substituted in culture with azidohomoalanine (AHA - C4H8N4O2). The azide group reacts with the alkyne group DDDDK-propargylglycine-NH2. As a result the side chain of methionine (C3H7S) is substituted by C29H44N11O14.
2H(3) 13C(1) monomethylated Arg13C(6) 15N(4).
Carboxyamidomethylation of selenocysteine
C-terminal homoserine lactone and two aminohexanoic acids.
Water-quenched monolink of DSS/BS3 crosslinker.
Water quenched monolink of EGS cross-linker.
Ethylene glycolbis(succinimidylsuccinate)
Water quenched monolink of DST crosslinker.
Water quenched monolink of DSP/DTSSP crosslinker.
Water quenched monolink of DMP crosslinker.
Dimethyl pimelimidate dead-end crosslink
Cleavage product of EGS protein crosslinks by hydroylamine treatment.
desthiobiotin-GTP desthiobiotin-ADP desthiobiotin-ATP
Tyrosine caged with 2-nitrobenzyl (ONB).
Dethiobiotin-FP was designed to label the active site serine of serine hydrolases (e.g. esterases, peptidases, lipases).
TAMRA fluorophosphonate modification of serine.
ActivX TAMRA-FP Serine Hydrolase Probe TAMRA-alkyl-FP
TAMRA-FP was designed to label the active site serine of serine hydrolases (e.g. esterases, peptidases, lipases).
Deoxyhypusine synthase catalyzes the formation of a deoxyhypusine by transferring an aminobutyl moiety from spermidine onto a conserved lysine residue within the eIF5A.
Regulation of eIF5A by deoxyhypusine acetylation/deacetylation.
Regulation of eIF5A by hypusine acetylation/deacetylation.
Misacylation of the tRNA or editing of the charged tRNA
Applied Biosystems cleavable ICAT(TM) light.
Applied Biosystems cleavable ICAT(TM) heavy.
only with Listeria monocytogenes (gram-positive bacteria)
Oxidized lysine biotinylated with biotin-LC-hydrazide, reduced.
Oxidized lysine biotinylated with biotin-LC-hydrazide.
Oxidized proline biotinylated with biotin-LC-hydrazide, reduced.
Oxidized Proline biotinylated with biotin-LC-hydrazide.
Oxidized arginine biotinylated with biotin-LC-hydrazide.
Oxidized arginine biotinylated with biotin-LC-hydrazide, reduced.
Applied Biosystems original ICAT(TM) d8.
SUMOylation leaving GG tag glycineglycine
The two glycine residues left on ubiquitinylated lysine after tryptic digestion.
Can occur under CNBr cleavage conditions (70% HCOOH)
A protein in which either the N-terminal N-formylmethionine has not been processed by the methionyl-tRNA formyltransferase or which is posttranslationally modified by the attachment of at least one formyl group.
N-iodoacetyl, p-chlorobenzyl-12C6-glucamine.
N-iodoacetyl, p-chlorobenzyl-13C6-glucamine.
Azidohomoalanine coupled to reductively cleaved tag.
Carbamidomethylated form of reductively cleaved tag coupled to azidohomoalanine.
Sulfo-SBED Label Photoreactive Biotin Crosslinker.
Sulfo-SBED Label Transfer ReagentrnReaction path that does not remove one Hidrogen atom from the target peptide
Sulfo-SBED Label Photoreactive Biotin Crosslinker minus Hydrogen.
Sulfo-SBED Label Transfer Reagent. Reaction path that removes one Hydrogen atom from the target peptide
Believed to be created in a secondary reaction after initial formation of an adduct between the organophosphate 2-(o-cresyl)-4H-1,3,2-benzodioxaphosphorane-2-one and Tyr or Ser in proteins.
Created by hydrolysis of the product of the reaction of 2-(o-cresyl)-4H-1,3,2-benzodioxaphosphorane-2-one with amino acids residues in proteins.
Created by reaction of 2-(o-cresyl)-4H-1,3,2-benzodioxaphosphorane-2-one with amino acid residues in proteins.
Active site DUB cystine modification with Br Ub probe Trypsin Digestion reminant of Ub Br probe
Active site DUB cystine modification with VME Ub probe Trypsin Digestion reminant of Ub VMEr probe
Cleaved and reduced DSP/DTSSP crosslinker.
Can also be the product of reaction with EZ-Link Sulfo-NHS-SS-Biotin (Sulfosuccinimidyl 2-(biotinamido)-ethyl-1, 3-dithiopropionate) followed by reduction with DTT.
Active site DUB cystine modification with Fluorescein Ub probe Trypsin Digestion reminant of Ub Fluorescein probe
Unpublished chemically synthesized protein modification tool.
Occasionally used as chemical tag. In most cases, +57 is actually over-alkylation with iodoacetamide.
N-Homocysteine thiolactone is an acylating agent and can react with the E amino group of lysine residues
Homocysteine can take part in disulfide exchange reactions with S-S bonds in proteins, thus forming S-homocysteinylated proteins
Side product of the three component Ugi-Joullie reaction. Pirrolidine is reacted with a isocianide modificated peptide (CNGGHHHHHH) to get a Pro-Gly-GGHHHHHH. The main product is the C-terminal modified protein. Unlikely Asp and Glu can react.
Cysteine residue reacts with a chlorinated dipyridyl ligand to get a monoalkylated Cys-L1. The only product is this single cys mutant modified on that position.
Chemical modification of the iodinated sites of thyroglobulin by Suzuki reaction.
Chemical modification of the diiodinated sites of thyroglobulin by Suzuki reaction.
5-Iodoacetamidofluorescein (Molecular Probe, Eugene, OR).
(4-hydroxy-1-methyl-4-phenylpiperidin-3-yl)(phenyl)methanone 3-benzoyl-1-methyl-4-phenyl-4-piperidinol
Side reaction of PG with Side chain of aspartic or glutamic acid.
Side product of the three component Ugi-Joullie reaction. Pirrolidine is reacted with a isocianide modificated glycine to get Protein-Pro-Gly. The main product is the C-terminal modified protein. Unlikely Asp and Glu can react.
Side reaction of PGPG with Side chain of aspartic or glutamic acid.
Side product of the three component Ugi-Joullie reaction. Pirrolidine is reacted with a isocianide modificated glycine to get Protein-Pro-Gly-Pro-Gly. The main product is the C-terminal modified protein. Unlikely Asp and Glu can react.
Glycosylation with IME linked Hex(2) NeuAc.
(2-Imino-2-methoxyethyl 1-thioglycoside)
Modification by Hex(2) NeuAc using IME coupling to get glycosylated proteins.
Loss of arginine due to transpeptidation.
Addition of arginine due to transpeptidation.
This peptide is generated from a trypsin/chymotrypsin dual digest.
Applied Biosystems original ICAT(TM) d0.
Addition of lysine due to transpeptidation.
Biotin hydrazide labeled acrolein addition +298.
3-benzoyl-1-methyl-4-phenyl-4-piperidinol demethyl damino
Accurate mass for DiLeu 115 isobaric tag.
Different channels have the same nominal mass but slightly different exact masses.
Accurate mass for DiLeu 116 isobaric tag.
Representative, nominal mass for all four tags
Accurate mass for DiLeu 117 isobaric tag.
Accurate mass for DiLeu 118 isobaric tag.
Chemical reaction with 2,4-dinitro-1-chloro benzene (DNCB).
Chemical reaction with 2,4-dinitro-1-chloro benzene (DNCB) by nucleophilic attack on electrophilic amino acid side chains.
myristoyl with one double bond C14:1 acylation
Found on vision signal transduction proteins.
iodoTMTzero iodoTMT0 Tandem Mass Tag® and TMT® are registered Trademarks of Proteome Sciences plc.
This modification describes the native iodoTMT Reagent without isotopic label. Upon CID, this reagent releases a reporter ion of 126.127725(monoisotopic mass).
iodoTMTsixplex iodoTMT6 Tandem Mass Tag® and TMT® are registered Trademarks of Proteome Sciences plc.
This modification describes the native iodoTMT Reagent without isotopic label. Upon CID, this reagent releases a reporter ions of 126.127725, 127.124760, 128.134433, 129.131468, 130.141141, and 131.138176 (monoisotopic mass).
Cy3 mono-functional maleimides are used for the selective labeling of molecules containing free sulfhydryl groups, such as cysteine residues in proteins and peptides and oligonucleotides.
Modification of the lysine side chain from NH2 to guanidine with a H removed in favor of a benzyl group.
(cis,cis-delta 5, delta 8)-tetradecadienoyl.
myristoyl with 2 double bonds C14:2 fatty acylation
A fixed +1 charge tag attached to the N-terminus of peptides.
Added mass is reduced by 1 H to reflect that first charge state requires no proton addition Replaces one of the N-terminal H atoms with C9H12N2O
Formation of five membered aromatic heterocycle.
Lab based observation that D5 NEM hydrolyses in an analogous way to NEM.
Labeling reagent light form (N-term & K).
Adduct formed upon reaction of the organophosphate tabun with the active site serine of serine esterases/proteases such as butyrylcholinestease.
This adduct is a consequence of hydrolysis of the initial adduct formed by tabun (aging) on the active site serine of serine esterases/proteases such as butyrylcholinesterase.
3-fold methylated lysine labelled with Acetyl_heavy.
Core structure of high-mannose N-linked oligosaccharides.
3-fold methylation with deuterated methyl groups.
protein alkylation by Michael acceptor methyl vinyl sulfone
protein alkylation by Michael acceptor ethyl vinyl sulfone
protein alkylation by Michael acceptor phenyl vinyl sulfone
PLP bound to lysine reduced by sodium borohydride (NaBH4) to create amine linkage.
This is a chemical derivatization of the PLP imine with sodium borohydride to reduce imine bound through lysine epsilon amine group to chemical stable amine linkage
Methionine oxidation to homocysteic acid.
ADP-ribosylation followed by conversion to hydroxamic acid via hydroxylamine.
Conversion of carboxylic acid to hydroxamic acid
From exposure to hydroxylamine (used with TMT)
Modification by hydroxylated mechloroethamine (HN-2).
Modification by hydroxylated tris-(2-chloroethyl)amine (HN-3).
N-ethylmaleimide on cysteine sulfenic acid.
Representative mass and accurate mass for 114.
Isobaric labeling reagent from Omic Biosystems, Inc. AKA DiART6plex114
Different tags have the same nominal mass but slightly different exact masses. Use this modification for all tags for quantitation purposes. Monoisotopic masses of the fragment ions to be quantified are 114.12827, 115.12531, 116.14082, 117.13786, 118.14752, 119.14456.
Isobaric labeling reagent from Omic Biosystems, Inc.
Different tags have the same nominal mass but slightly different exact masses.
Accurate mass for DiART6plex 116 and 119.
13C labelled iodoacetanilide derivative.
Addition of gram negative peptidoglycan amino acid (DAP) plus monolinked DSP.
Decarboxylation of C-terminus as reaction inside the mass spectrometer
MS/MS experiments of mass spectrometric a-ions (MS^3) can be used for protein identification by library searching. T3-sequencing is such a technique (see reference). Search engines must recognize this 'virtual modification' for this purpose.
Virtual Modification for MS/MS of a-type ions corrected by subtraction of a further -O at 8.6.2010
Gram negative peptidoglycan saccharide amide bonded to Alanine.
Sumoylation by SUMO-1 after Cyanogen bromide (CNBr) cleavage.
Sumoylation by SUMO-2/3 after Cyanogen bromide (CNBr) cleavage.
The cleavage products of SUMO-2 and SUMO-3 are indistinguishable
Amidination of lysines or N-terminal amines with methyl acetimidate.
3-fold methylation with fully labelled methyl groups.
pyruvic acid from N-term ser oxobutanoic acid from N term Thr
Pyro-carbamidomethyl as a delta from Carbamidomethyl-Cys
Hex(2) HexNAc(2) NeuAc ---OR--- dHex Hex HexNAc(2) NeuGc.
Hex(4) HexNAc(2) NeuAc ---OR--- Hex(3) HexNAc(2) dHex NeuGc.
Hex(3) HexNAc(4) NeuAc ---OR--- Hex(2) HexNAc(4) dHex NeuGc.
DHex Hex(3) HexNAc(3) Pent(3) ---OR--- Hex(4) HexNAc(2) dHex(2) NeuAc.
DHex Hex(4) HexNAc(3) NeuAc ---OR--- dHex(2) Hex(3) HexNAc(3) NeuGc.
DHex Hex(4) HexNAc(3) NeuGc ---OR--- Hex(5) HexNAc(3) NeuAc.
DHex Hex(5) HexNAc(3) NeuGc ---OR--- Hex(6) HexNAc(3) NeuAc.
HexNAc Kdn(2) ---OR--- Hex(2) HexNAc HexA.
DHex Hex HexNAc Kdn ---OR--- Hex(2) dHex NeuAc.
DHex Hex HexNAc NeuGc ---OR--- Hex(2) HexNAc NeuAc.
Hex HexNAc NeuAc(2) ---OR--- Hex HexNAc(3) HexA.
DHex Hex HexNAc(2) Kdn ---OR--- Hex(2) HexNAc dHex NeuAc.
Selenocysteine conventionally represented by 1 letter code U
DHex(2) Hex HexNAc(2) Kdn ---OR--- Hex(2) HexNAc dHex(2) NeuAc.
DHex(2) Hex HexNAc(2) NeuGc ---OR--- Hex(2) HexNAc(2) dHex NeuAc ---OR--- Hex HexNAc(3) dHex Kdn.
DHex Hex(2) HexNAc(2) NeuGc ---OR--- Hex(3) HexNAc(2) NeuAc.
DHex Hex HexNAc(3) NeuGc ---OR--- Hex(2) HexNAc(3) NeuAc.
DHex(2) Hex(2) HexNAc(2) NeuAc ---OR--- Hex HexNAc(3) dHex(2) Kdn.
DHex(2) Hex(2) HexNAc(2) NeuGc ---OR--- Hex(3) HexNAc(2) dHex NeuAc ---OR--- Hex(2) HexNAc(3) dHex Kdn.
Hex(3) HexNAc(3) NeuAc ---OR--- Hex(2) HexNAc(3) dHex NeuGc ---OR--- Hex(2) HexNAc(4) Kdn.
Conversion of glycosylated asparagine residues upon deglycosylation with PGNase F in 18O labelled water.
DHex(2) Hex(3) HexNAc(2) NeuGc ---OR--- Hex(4) HexNAc(2) dHex NeuAc.
DHex(2) Hex(2) HexNAc(3) NeuGc ---OR--- Hex(3) HexNAc(3) dHex NeuAc ---OR--- Hex(2) HexNAc(4) dHex Kdn.
DHex(3) Hex(2) HexNAc(3) Kdn ---OR--- Hex(3) HexNAc(2) dHex(3) NeuAc.
DHex(2) Hex(3) HexNAc(3) NeuAc ---OR--- Hex(2) HexNAc(4) dHex(2) Kdn.
Michael addition of BHT quinone methide to Cysteine and Lysine.
BHT metabolism has been studied in rats and mice in relation to tumor promotion.
Secondary adduct - much less common as C
Hex(4) HexNAc(3) NeuAc ---OR--- Hex(3) HexNAc(4) Kdn.
DHex(2) Hex(4) HexNAc(4) ---OR--- Hex(4) HexNAc(4) dHex Pent Me.
DAET = 2-(dimethylamino)ethanethiol; The phosphorylation to amine is the beta elimination of phosphate and Michael addition of 2-(dimethylamino)ethanethiol to the site.
DHex Hex(4) HexNAc(4) NeuAc ---OR--- Hex(3) HexNAc(5) dHex Kdn.
Ammonium-quenched monolink of DSS/BS3 crosslinker.
Fluorescein-tyramine adduct by peroxidase activity.
Transamidation of glycine ethyl ester to glutamine.
GEE (glycine ethyl ester) is a substrate for the enzyme Factor XIII for cross-linking to fibrinogen
LRGG ubiquitin remnant with methylated Arg
LRGG remnant of ubiquitin remaining attached to lysine with missed cleavage due to methylation of arginine.
LRGG ubiquitin remnant with dimethylated Arg
LRGG remnant of ubiquitin remaining attached to lysine with missed cleavage due to dimethylation of arginine.
Only observed on a small fraction of residues (~2%). See doi: 10.1038/nmeth.4465
Tris adduct causes 104 Da addition at asparagine-succinimide intermediate.
tris adduct at asparagine tris adduct at IgG causes 104 Da addition
NG sequence specifically after deamidation - Deamidated Asparagine with adjacent glycine are prone for this modification.
Iodoacetamide derivative of stilbene (reaction product with thiol).
4-acetamido-4'-((iodoacetyl)amino)stilbene-2,2'-disulfonic acid
Covalently bound structure in Manglik et al., Fig. 1b-Fig1c. Chemical formula % Sigma catalog entry.
Cys alkylation by dimethylaminoethyl halide.
OH-PGO and PGO react with arginine at a stoichiometry of 2:1.
Tris-quenched monolink of DSS/BS3 crosslinker.
Water-quenched monolink of DSSO crosslinker.
Ammonia-quenched monolink of DSSO crosslinker.
Tris-quenched monolink of DSSO crosslinker.
Sulfenic acid fragment of DSSO crosslinker.
Ammonia quenched monolink of BuUrBu crosslinker.
Water quenched monolink of BuUrBu crosslinker.
Tris quenched monolink of BuUrBu crosslinker.
Ammonium-quenched monolink of BS2-G crosslinker.
Water-quenched monolink of BS2-G crosslinker.
Tris-quenched monolink of BS2-G crosslinker.
Ammonia quenched monolink of DMP crosslinker.
Methionine oxidation to aspartic semialdehyde.
Adduction of aflatoxin B1 Dialdehyde to lysine.
Proline oxidation to 5-hydroxy-2-aminovaleric acid.
Tryptophan oxidation to beta-unsaturated-2,4-bis-tryptophandione.
Tryptophan oxidation to hydroxy-bis-tryptophandione.
Tryptophan oxidation to dihydroxy-N-formaylkynurenine.
Methylglyoxal-derived carboxyethyllysine.
Note that Table 3 in the reference has the delta as H(3) C(3) O(2) = 71 Da
Crotonaldehyde-derived dimethyl-FDP-lysine.
Methylglyoxal-derived tetrahydropyrimidine.
6-aminoquinolyl-N-hydroxysuccinimidyl carbamate.
Unidentified modification of 162.1258 found in open search.
The elemental composition should be assumed incorrect Although it happens to be that of Diethylene glycol butyl ether, a common solvent.
Unidentified modification of 176.7462 found in open search.
The elemental composition should be assumed incorrect
Unidentified modification of 210.1616 found in open search.
Unidentified modification of 216.1002 found in open search.
Unidentified modification of 234.0742 found in open search.
Unidentified modification of 248.1986 found in open search.
Unidentified modification of 249.981 found in open search.
Unidentified modification of 301.9864 found in open search.
Unidentified modification of 306.0952 found in open search.
Unidentified modification of 420.0506 found in open search.
Probable non-covalent adduct of CAM-DTT-DTT-CAM
Created by auto-catalytic dealkylation of the O-dimethylphosphothione adduct.
Ubiquitin D (FAT10) leaving after chymotrypsin digestion Cys-Ile-Gly-Gly.
Ubiquitin D (FAT10) leaving after trypsin digestion Gly-Asn-Leu-Leu-Phe-Leu-Ala-Cys-Tyr-Cys-Ile-Gly-Gly.
Heavy tris(2,4,6-trimethoxyphenyl)phosphonium acetic acid N-hydroxysuccinimide ester derivative.
The formula is reduced from H(34) to H(33) so as to give correct observed m/z values. The charge on the TMPP means that ions have one less proton than would be expected.
possible side chain reaction when labeling N-term
DST crosslinker cleaved by sodium periodate.
MS/MS experiments of mass spectrometric c-ions (MS^3) can be used for protein identification by library searching. T3-sequencing is such a technique (see reference). Search engines must recognize this as a virtual modification.
Glutamine-donor substrate for transglutaminase.
Loss of O2; nitro photochemical decomposition.
Tandem Mass Tag and TMT are registered Trademarks of Proteome Sciences plc. Super Heavy TMT
This modification describes the Super Heavy TMT Reagent. Upon HCD, this reagent releases a reporter ion of 132.14153 (monoisotopic mass).
Tandem Mass Tag and TMT are registered Trademarks of Proteome Sciences plc. Also applies to TMTpro 18plex mass tags
Tandem Mass Tag and TMT are registered Trademarks of Proteome Sciences plc.
This modification describes the native TMTpro Reagent without isotopic label with reporter mass m/z 126.127726.
Glycosylation of Serine/Threonine residues with KDO.
3-deoxy-D-manno-oct-2-ulosonic acid 2-Keto-3-Deoxy-D-Mannooctanoic Acid
Oxidative cross-link of free methionine to histidine residue in protein.
Loss of MBS, peptide from KLH after trypsin digestion
RNA-protein UVC-crosslinked, hydrofluoride-digested uridine adduct.
Crosslink to all 20 amino acids. Not C-term (Missed cleavage). Partial in-source fragmentation to Uracil (loss of ribose): H(4) C(4) N(2) O(2)
Tandem Mass Tag and TMT are registered Trademarks of Proteome Sciences plc. TMTpro-SH 13C15 H25 15N3 O3
This modification describes the Super Heavy TMTpro Reagent. Upon HCD, this reagent releases a reporter ion of 135.151600 (monoisotopic mass).
Methionine is substituted in culture with azidohomoalanine. The azide group reacts with the alkyne group of DADPS Biotin Alkyne.
Methionine is substituted in culture with azidohomoalanine. The azide group reacts with the alkyne group of PC Biotin Alkyne.
RNA-protein UVA-crosslinked, hydrofluoride-digested 4-thiouridine adduct.
Crosslink to all 20 amino acids. Not C-term (Missed cleavage). Partial in-source fragmentation & near-complete HCD-mediated fragmentation to 4-thiouracil form: H(2) C(4) N(2) O(1)
RNA-protein UVA-crosslinked, hydrofluoride-digested 6-thioguanosine adduct.
Crosslink to all 20 amino acids. Not C-term (Missed cleavage). Partial in-source fragmentation & near-complete HCD-mediated fragmentation to 6-thioguanine form: H(3) C(5) N(5)
Iodoacetamido-LC-Phosphonic Acid derivative.
PhoX, tBu-PhoX (acid deprotected) A52286, A52287
Water-quenched monolink of DSPP/TBDSPP crosslinker.
A52286, A52287 PhoX, tBu-PhoX (acid deprotected) water quench
Tris-quenched monolink of DSPP/TBDSPP crosslinker.
C12 H14 N O8 P PhoX, tBu-PhoX (acid deprotected) Tris quench A52286, A52287
Ammonia-quenched monolink of DSPP/TBDSPP crosslinker.
PhoX, tBu-PhoX (acid deprotected) ammonia quench A52286, A52287
Desthiobiotinylation of cysteine with DBIA probe.
Monomodification of Nγ-propargyl-L-Gln probe with clicked desthiobiotin-azide.
Enrichment of modified peptides using desthiobiotin-tag on streptavidin beads
- desthiobiotin-azide to enrich L-Gln-propargyl modified peptides.
Dimodification of L-Glu and Nγ-propargyl-L-Gln probe with clicked desthiobiotin-azide.
Dimodification of L-Gln and Nγ-propargyl-L-Gln probe with clicked desthiobiotin-azide.
Plain N6-Propargyl-AMP modified proteins without any clicked enrichment tag.
DABCYL-C2-maleimide Thiol-reactive dye for fluorescence labelling of proteins.
4-Chloro-7-nitrobenzofurazan NBD Chloride
Use for enrichment of cysteine oxidation Cleaved Cysteine Sulfenic Acid Probe (DCP-Bio1)
SUMOylation by Endogenous SUMO2/3 following Lys C and Asp-N serial digestion.
Neutral loss of phosphate is typically observed from Y/H/D/E/K/C, rather than the preferential loss of phosphoric acid from S/T.
Representative mass and accurate mass for 116 & 117.
AKA iTRAQ4plex116/7 Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry
Different channels have the same nominal mass but slightly different exact masses. Use this value for all channels for quantitation purposes. mTRAQ heavy is identical to iTRAQ4plex 117.
didehydroalanine C-terminal imide Prompt loss of phosphate from phosphorylated residue D-Succinimide
Pyro-carboxymethyl as a delta from Carboxymethyl-Cys
Lys modification is formation of Schiff base.
Reduction of Schiff base formed between K amino group and acetaldehyde.
S-carbamoylmethylcysteine cyclization (N-terminus).
Carboxymethyl-Cys cyclization (N-terminus) Carbamidomethyl-Cys cyclization (N-terminus)
Cyclisation of N-term Carbamidomethyl-Cys or Carboxymethyl-Cys. The delta is relative to Cys. For a delta relative to alkylated Cys, see Ammonia-loss and Dehydrated.
PET = 2-[4-pyridyl]ethanethiol. This modification is a chemical derivative, based on a alkaline catalysed beta-elimination of phosphoserines and phosphothreonines and subsequent 1,4-addition of 2-[4-pyridine]ethanethiol. These modified serines and threonines produce in MS/MS a characteristic fragment which can be used for precursor-ion-scan experiments.
Result of conversion of 13C6, 15N4 arginine to 13C5, 15N1 proline
Cytopiloyne is a polyacetylenic glucoside isolated form Bidens pilosa which can modulate T helper cell differentiation. Biotinylated cytopiloyne might be use to identify its receptor in T cell.
Nucleophilic addition to cytopiloyne+H2O.
Cytopiloyne is a polyacetylenic glucoside isolated form Bidens pilosa which can modulated T helper cell differentiation. Biotinylated cytopiloyne might be use to identify its receptor in T cell.
N-terminal sulfonation of diglycine to detect ubiquitination sites.
Potential protein modification when using AEBSF (Pefabloc) as a serine protease inhibitor.
from reaction of SH group with iodoethanol
C-Terminal/Glutamate/Aspartate sulfonation
The cleavage of a peptide bond between Try-Xxx with oxidation of tryptophan to the oxolactone occurs in the presence of BNPS-skatole. This is a useful method for the chemical cleavage of proteins specifically at tryptophan residues.
EDC crosslinker is used to couple biotin PEO-amine to carboxyl groups or 5' phosphate groups.
EDC-coupled modification of D, E and C-terminus
UV induced linkage of Iodo-U-amp with WFY
One note about this chemistry is that for W you have to take care of O2 big time (and extract the I-uracil monophosphate with organics to get rid of residual iodide).
Used in base/residue interactions (in principle?)
Used in base/residue interactions (observed)
3-thiopropanoyl moiety from reduced DSP crosslinker or NHS-SS-biotin, modified with Iodoacetamide
esterification of carboxylic acids using D3-Methanolic HCl
SILAC labelling with L-Methionine-(methyl-d3)
dHex Hex(4) HexNAc(4) ---OR--- Hex(4) HexNAc(4) Pent Me
Usually major adduct formed from malondialdehyde (MDA) with the amino group of lysine residues.
5-hydro-5-methylimidazol-4-one, Methylglyoxal adduct
O-ethyl-N-(biotinamidopentyl)decanamido phosphonate
FP-biotin was designed to label the active site serine of serine esterases/proteases.
Phosphoserine to S-ethylcystine via Beta elimination/Michael addition of ethylthiol.
6-N-biotinylaminohexyl isopropyl phosphate.
O-isopropyl-N-biotinylaminohexyl phosphonate
Commercially available from Toronto Research Chemicals Inc, as of 2005. Designed to label the active site serine of serine esterases/proteases.
Michael addition adduct of 4-hydroxynonenal with histidine, cystein and lysine residues stabilized by reduction with NaBH4.
Oxidized Arginine biotinylated with biotin hydrazide.
Arginine oxidation to glutamic semialdehyde.
Arginine oxidation to gamma-glutamyl semialdehyde
Could also be classed as chemical derivative
Hydroxyglycine derivative in amidation pathway
Tryptophan oxidation to hydroxykynurenin.
Lysine oxidation to aminoadipic semialdehyde.
Oxidized Lysine biotinylated with biotin hydrazide.
Oxidized proline biotinylated with biotin hydrazide.
Oxidized Threonine biotinylated with biotin hydrazide.
A selective label for the active site serine of the serine esterase/protease family. It has also been shown to label tyrosine in serum albumin.
Created by auto-catalytic dealkylation of the O-Diisopropylphosphate adduct.
Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, heavy form.
Attention: As the digest is typically applied AFTER ICPL_light/heavy labeling, only ProteinN-term labeling and Lys-specific labeling is applied.
Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, light form.
Michael addition of hydroxymethylvinyl ketone to cysteine.
Labeling with diethylpyrocarbonate (DEPC)
oxobutanoic acid from N term Thr pyruvic acid from N-term ser
Phycocyanobilin and phycobiliviolin have different structures but the same empirical formula.
Because the modification is quantitatively lost on CID, site assigment is not possible when there is a choice of sites
Lactone formation from C-terminal hydroxylysine
L-selenocysteinyl molybdenum bis(molybdopterin guanine dinucleotide).
This group is normally a substituent on N6 of a lysine residue of an enzyme or other protein.
Addition of a single sulfur atom by Pi3-Tryptophan reagent to create thiol
Molybdenum bis(molybdopterin guanine dinucleotide).
phenylalanine oxidation to dihydroxyphenylalanine
The amine derivative of a hexose formed by replacing a hydroxyl group with an amino group.(+acetyl group).
Cis-14-hydroxy-10,13-dioxo-7-heptadecenoic ester.
Copper sulfido molybdopterin cytosine dinuncleotide.
Serine to Alanine Threonine to a-aminobutyrate
Beta elimination of O-glycosylation under alkaline conditions followed by reduction
Microcin E492 siderophore ester from serine.
The co-enzyme derivative of vitamin B6. Forms Schiff's bases of substrate amino acids during catalysis of transamination, decarboxylation and racemisation reactions.
4-sulfophenyl isothiocyanate (Heavy C13).
Palmitoylation is a post-translational modification that consists in the addition of a 16 carbons fatty acid, palmitate, to a cysteine residue through the creation of a thioester link.
Modification procedure used for phosphopeptide mapping.
Dehydropyrrolizidine alkaloid (dehydroretronecine) on cysteines.
Protein which contains at least one phosphopantetheine as the prosthetic group. In acyl carrier proteins (ACP) for example, it serves as a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups.
Bisphenol A diglycidyl ether derivative.
Michael addition of t-butyl hydroxylated BHT (BHTOH) to C, H or K.
BHTOH is formed upon metabolism of BHT with P450 enzymes. The BHTOH is further metabolized to its quinone methide (electrophile) which reacts with -SH and -NH2 groups.
Carbamylation is an irreversible process of non-enzymatic modification of proteins by the breakdown products of urea isocyanic acid reacts with the N-term of a proteine or side chains of lysine and arginine residues.
Levuglandinyl - lysine hydroxylactam adduct.
Levuglandinyl - arginine hydroxylactam adduct.
Lactosylation of bovine Beta-Lactoglobulin.
In a recent publication (see reference), we have shown that family 84 glycoside hydrolases contain a deep pocket beneath the 2-acetamido group of its substrate (N-acetyl-glucosamine). With this strucual feature in mind, we have designed a specific inhibitor that contains a chloride group appended to the end of the propyl chain on a known inhibitor termed propyl-NAG-thiazoline. We have shown kinetically that this molecule is a potent suicide inhibitor of this enzyme famiy and now wish to know the precise residue which is acting as the nucleophile to dispace the choride atom. We have included all residues that are in the vacinity of the chloride atom that could potentially act in a nucleophilic manner.
Diethylation, analogous to Dimethylation.
4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid.
Specific for sidechain of lysine. Does not modify the N-termini except for glycine at a slower rate than the side chain of lysine.
CLIP-TRAQ-2 H(17) C(10) C13 N(3) O(4) is an in-house made compound that reacts with primary amines through a N-hydroxysuccinimide group leading to a 141.0983 Da mass shift (monoisotopic) in MS mode. The reporter ion in MS/MS mode can either be 113 or 114 m/z depending on the position of isotopic C13 in the molecule. (Fahlman, R. and Overall, C.M. ; in preparation).
Prompt loss of side chain from oxidised Met.
A lipid-type modification. HNE forms a Michael addition product on Cysteine, Histidine and Lysines. Unusually, it doesn't replace a hydrogen on the amino acid side chain.
Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry
CLIP_TRAQ_3 (H(20) C(11) C13 N(3) O(4) is an in-house made compound that reacts with primary amines through a N-hydroxysuccinimide group leading to a 155.1 Da mass shift (monoisotopic) in MS mode. The reporter ion in MS/MS mode can either be 127 or 128 m/z depending on the position of isotopic C13 in the molecule. (Fahlman, R. and Overall, C.M. ; in preparation).
CLIP_TRAQ_4 is an in-house made compound that reacts with primary amines through a N-hydroxysuccinimide group leading to a 128.1 Da mass shift (monoisotopic) in MS mode. The reporter ion in MS/MS mode can either be 100 or 101 m/z depending on the position of isotopic C13 in the molecule. (Fahlman, R. and Overall, C.M. ; in preparation).
15-deoxy-delta 12,14-Prostaglandin J2-biotinimide
The addition of a sugar unit to a protein amino acid, e.g. the addition of glycan chains to proteins. Addition of glucuronic acid. Observed for N-term G.
Acetate labeling reagent (N-term & K) (heavy form, +3amu).
Propionate labeling reagent light form (N-term & K).
Propionate labeling reagent heavy form (+3amu), N-term & K.
Quaternary amine labeling reagent light form (N-term & K).
Quaternary amine labeling reagent heavy (+3amu) form, N-term & K.
Quaternary amine labeling reagent heavy form (+6amu), N-term & K.
Quaternary amine labeling reagent heavy form (+9amu), N-term & K.
Succinic anhydride labeling reagent light form (N-term & K).
Succinic anhydride labeling reagent, heavy form (+4amu, 4H2), N-term & K.
Succinic anhydride labeling reagent, heavy form (+4amu, 4C13), N-term & K.
Michael addition of nitro-linoleic acid to Cys and His
Reversible post-translational modification of proteins by nitrated fatty acids.
Michael addition of nitro-oleic acid to Cys and His
Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, medium form.
phenyllactyl from N-term Phe Citrullination
Convertion of glycosylated asparagine residues upon deglycosylation with PNGase F in H2O
Protein which is post-translationally modified by the de-imination of one or more arginine residues; Peptidylarginine deiminase (PAD) converts protein bound to citrulline
Mass Spectroscopic Characterization of Protein Modification by 4-Hydroxy-2-(E)-nonenal and 4-Oxo-2-(E)-nonenal.
Covalent adduction of nucleophilic amino acids by 4-hydroxynonenal and 4-oxononenal.
Created by auto-catalytic dealkylation of the O-Dimethylphosphate adduct.
Created by auto-catalytic dealkylation of the O-Diethylphosphate adduct.
Created by auto-catalytic dealkylation of either the O-pinacolylmethylphosphonate adduct, or the O-isopropylmethylphosphonate adduct.
Representative mass and accurate mass for 113, 114, 116 & 117.
Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry AKA iTRAQ8plex:13C(7)15N(1)
Other 4 channels have the same nominal mass but slightly different exact mass. For quantitation purposes, use this entry for all channels.
Other 4 channels have the same nominal mass but slightly different exact mass. For quantitation purposes, use iTRAQ8plex for all channels.
Carboxyl modification with ethanolamine.
Carbodiimide mediated blocking of free carboxylic acids (Asp/Glu sidechains and C-termini) with ethanolamine; reaction yields an amide-bond between the carboxylic acid of the peptide/protein and the primary amine of ethanolamine; reaction irreversibly modifies carboxylic acids. Shown above is the composition of the mass adduct, after substraction of water.
Beta elimination of modified S or T followed by Michael addition of DTT.
threo-1,4-dimercaptobutane-2,3-diol Was DTT_ST
Beta-elimination and Michael addition of dithiothreitol (DTT) to serine and threonine adds a weight of approximately 136.2.
The addition of DTT adds 136.2 not 154.2 to Serine due to loss of water in reaction
The addition of DTT adds 136.2 not 154.2 to Threonine due to loss of water in reaction
Beta elimination of alkylated Cys followed by Michael addition of DTT.
When the beta-elimination and Michael addition of dithiothreitol (DTT) (BEMAD) reaction is used with alkylated cysteine a sulfur group is lost leaving the addition of approximately 120.2 in the chemical reaction.
Tandem Mass Tag® and TMT® are registered Trademarks of Proteome Sciences plc. Also applies to TMT10plex Tandem Mass Tag sixplex labelling kit Proteome Sciences This is a nominal. representative mass
Tandem Mass Tag® and TMT® are registered Trademarks of Proteome Sciences plc. Tandem Mass Tag Duplex labelling kit Proteome Sciences
Duplex-TMT® reagents 2TMT-126, 2TMT-127. m/z values of the TMT® fragment ions to be quantified: 126.12773 127.13108.
Tandem Mass Tag® and TMT® are registered Trademarks of Proteome Sciences plc.
This modification describes the "native" TMT Reagent without isotopic label.
ExacTag Thiol label mass for 2-4-7-10 plex.
ExacTag Amine label mass for 2-4-7-10 plex.
Accurate mass for Exactag Amine labels. Includes the mass of the conjugation reagent.
Mass Spectorscopic Characterization of Protein Modification by 4-hydroxy-2-(E)-nonenal and 4-oxo-2-(E)-nonenal.
Nitroso Sulfamethoxazole Sulphenamide thiol adduct.
Synthesis and Reactions of Nitroso Sulphamethoxazole with Biological Nucleophiles: Implications for Immune Mediated Toxicity.
Nitroso Sulfamethoxazole Sulfinamide thiol adduct.
Derivatization by N-term modification using 3-Sulfobenzoic succinimidyl ester.
Trifluoroleucine replacement of leucine.
Modified peptides identified by isotope pattern. Restriction to cysteine-containing peptides combined with high mass accuracy allows peptide identification.
Beta elimination of modified S or T followed by Michael addition of labelled DTT.
Can be used for quantitative analysis of O-linked post-translational modifications. Same reaction can be used for quantitative analysis of cysteine-containing peptides, but then the modification is 16 Da less in mass; i.e. isotopically labeled reagent adds 126 Da in mass.
Beta elimination of alkylated Cys followed by Michael addition of labelled DTT.
Was DTT_C:2H(6) Isotopically labeled Dithiothreitol (DTT) modification of cysteines
Can be used for quantitative analysis of cysteine-containing peptides. Same reaction can be used for quantitative analysis of O-linked post-translational modifications to serines and threonines, but then the modification is 16 Da more in mass; i.e. isotopically labeled reagent adds 142 Da in mass.
Removal of initiator methionine from protein N-terminus.
N-terminal initiator methionine is removed by a methionine aminopeptidase from proteins where the residue following the methionine is Ala, Cys, Gly, Pro, Ser, Thr or Val. This is generally the final N-terminal state for proteins where the following residue was a Cys, Pro or Val.
Removal of initiator methionine from protein N-terminus, then acetylation of the new N-terminus.
The N-terminal initiator methionine is removed by a methionine aminopeptidase from proteins whose residue following the methionine is Ala, Cys, Gly, Pro, Ser, Thr or Val. Proteins whose following residue was Ala, Gly, Ser or Thr are then acetylated by an N(alpha)-acetyltransferase on the new N-terminus.
Mono-methylated lysine labelled with Acetyl_heavy.
Lapachenole photochemically added to cysteine.
Simple cyclic compound C16H16O2 adds to cysteine forming fluorescent derivative.
Result of Arg to Pro conversion of 13C(6) labelled Arg
Alkylation by biotinylated form of phenacyl bromide.
Phenacyl bromide conjugated with a linker and biotin tag, details not published yet.
Iodoacetic acid derivative w/ 13C label.
Deuterium cysteamine modification to S or T.
The two glycine residues left on SILAC labeled ubiquitinylated lysine after tryptic digestion.
Used for labeling glutamine-donor substrate of transglutaminase
Labeling transglutaminase substrate on glutamine side chain.
Pierce EZ link biotin hydrazide prod no. 21360
hydrazide reacts at any activated carboxyl group
Cy3b meleimide reacted with Cysteine Formula requires confirmation
Enzymatic glycine removal leaving an amidated C-terminus.
Amidation requires presence of glycine at peptide terminus
Tris(2,4,6-trimethoxyphenyl)phosphonium acetic acid N-hydroxysuccinimide ester derivative.
The formula has been reduced from H(34) to H(33) on 13 May 2009 so as to give correct observed m/z values. The charge on the TMPP means that ions have one less proton than would be expected.
Both isotopiclabel and post translational mod
Arginine replacement by Nitropyrimidyl ornithine.
Sumo mutant Smt3-WT tail following trypsin digestion.
The reaction product of Arg with phenylglyoxal has been shown to be a 2:1 adduct
Protein which is posttranslationally modified by the attachment of cGMP on the sulfur atom of Cys or hydroxyl group of Ser residues.
Protein which is posttranslationally modified by the attachment of cGMP that has lost ribose 3',5'-cyclic monophosphate moiety on the sulfur atom of Cys or hydroxyl group of Ser.
NHS ester linked Green Fluorescent Bodipy Dye.
Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, +10 Da form.
Attention: As the digest is typically applied AFTER ICPL labeling, only ProteinN-term labeling and Lys-specific labeling is applied.
Oxidised methionine 13C(1)2H(3) SILAC label.
2-ammonio-6-[4-(hydroxymethyl)-3-oxidopyridinium-1-yl]- hexanoate.
Covalent linkage of maleimidyl coumarin probe (Molecular Probes D-10253).
CAS 156571-46-9 7-diethylamino-3-((((2-maleimidyl)ethyl)amino)carbonyl)coumarin
MDCC is used extensively as a fluorescent probe to report changes in protein conformation.
Due to the mechanism of maleimidyl modification of Cys, the molecular weight of MDCC equals the mass shift created upon crossllinking (no chemical leaving group). During MS/MS, MDCC can reasonably be predicted to fragment readily and at various positions.
mTRAQ medium is identical to iTRAQ4plex 117 Applied Biosystems mTRAQ(TM) reagent
Thiol-reactive dye for fluorescence labelling of proteins.
Carbamidomethylated DTT modification of cysteine.
Carboxymethylated DTT modification of cysteine.
Methionine (C5H11NO2S) is substituted in cell culture by Azidohomoalanine (C4H8N4O2). The azido group reacts with an alkyne group attached to a linker (PEO) with a biotin group at the end (C27H45N5O7S). As a result the side chain of Met (C3H7S) is substitued by C29H49N8O7S.
Methionine replacement by azido homoalanine.
Metabolic labeling with ammonium sulfate (15N)
Methionine replacement by homopropargylglycine.
2,3,4,6-tetra-O-Acetyl-1-allyl-alpha-D-galactopyranoside modification of cysteine.
Reaction with dimethylarsinous (AsIII) acid.
Protein from animals exposed to organoarsenicals.
Lys->Cys substitution and carbamidomethylation.
Phe->Cys substitution and carbamidomethylation.
Leu->Met substitution and sulfoxidation.
Lys->Met substitution and sulfoxidation.
Monolink of SMCC terminated with 3-(dimethylamino)-1-propylamine.
Asn-linked glycan from Gram-negative Bacterium DATDH
Cys modification by (1-oxyl-2,2,5,5-tetramethyl-3-pyrroline-3-methyl)methanesulfonate (MTSL).
4-hydroxy-2-nonenal and biotinamidohexanoic acid hydrazide, reduced.
Product of beta elimination of phospho- or glycosylated-Ser with addition of ethylamine.
Product of beta elimination of phospho- or glycosylated-Ser with addition of beta Mercapto Ethanol.
Deamidation followed by esterification with ethanol.
SUMOylation by SUMO-2/3 (formic acid cleavage).
This peptide is generated from a formic acid digest
SUMOylation by SUMO-1 (formic acid cleavage).
Photocleavable Biotin + GalNAz on O-GlcNAc.
High molecular absorption maleimide label for proteins.
The electrophilic moiety of the chemical forms a direct bond with the thiol bond of the cysteine. As a result, there are no losses of elements and the final adduct has the monoisotopic mass of the chemical at 820.3360 added to a cysteine at SH side chain.
Carbamidomethylated Cys that undergoes beta-elimination and Michael addition of methylamine.
2-methoxy-4,5-dihydro-1H-imidazole derivative Lys imidazole
Carbamidomethylated Cys that undergoes beta-elimination and Michael addition of ethylamine.
Trp modification with 2,4-Dinitrobenzenesulfenyl
Fontana A. Biochemistry. vol 7. 980-986 (1968)
derivatization of Trp residues using the 2,4-dinitrophenyl-sulfenyl chloride (DNPS-Cl) reagent, that leads to a Trp derivative with the DNPS label attached at 2-position of the indole nucleus.
High molecular absorption label for proteins.
Levuglandinyl-lysine anhydrolactam adduct.
15-deoxy-PGJ2 (15d-PGJ2) influences multiple signaling pathways by covalently binding with key signaling molecules
Levuglandinyl-lysine anhyropyrrole adduct.
Condensation product of 3-deoxyglucosone.
2-methoxy-4,5-dihydro-1H-imidazole derivative
SUMOylation by SUMO-1 after tryptic cleavage.
SUMOylation by SUMO-2/3 after tryptic cleavage.
Created for Michael (Brad) Strader 2/12/10.
2,3-dihydro-2,2-dimethyl-7-benzofuranol N-methyl carbamate.
Native cysteine-reactive Tandem Mass Tag®.
This modification describes the native cysteine-reactive cysTMT Reagent without isotopic label. Upon CID, this reagent releases a reporter ion of 126.127725 (monoisotopic mass).
Cysteine-reactive Sixplex Tandem Mass Tag®.
This modification describes the isobaric sixplex cysteine-reactive cysTMT6 Reagents with isotopic labels. Upon CID, these reagents release reporter ions of 126.127725, 127.131079, 128.134433, 129.137787, 130.141141, and 131.138176 (monoisotopic mass).
Replacement of proton with ammonium ion.
Sometimes observed after elution of phosphopeptides from TiO2 with ammonium hydroxide.
this is a virtual modification, as it only accounts for the structure of the MS/MS fragment as it occurs in Top-Down MS/MS analyses. This must be accounted for in MS³-analysis of z+2 ions