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 Cyanogen bromide (CNBr) cleavage converts the C-term Met to either homoserine or homoserine lactone, depending on pH. Cyanogen bromide (CNBr) cleavage converts the C-term Met to either homoserine or homoserine lactone, depending on pH. Protein which is posttranslationally modified by the attachment of at least one phosphate group usually on serine, threonine or tyrosine residues, but also on aspartic acid or histidine residues. 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. Proton replaced by sodium cation This group is normally a substituent on N6 of a lysine residue of an enzyme or other protein The amine derivative of a hexose formed by replacing a hydroxyl group with an amino group.(+acetyl group) The co-enzyme derivative of vitamin B6. Forms Schiff\'s bases of substrate amino acids during catalysis of transamination, decarboxylation and racemisation reactions. 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. 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. Specific for sidechain of lysine. Does not modify the N-termini except for glycine at a slower rate than the side chain of lysine. 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. 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 Reduction of Schiff base formed between K amino group and acetaldehyde Lys modification is formation of Schiff base. The two glycine residues left on ubiquitinylated lysine after tryptic digestion Reduced product of reaction with 3,3-Dithio-bis-(sulfosuccinimidyl)propionate. Note that name thioacyl is misleading and subject to change in a future revision. 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 Found on vision signal transduction proteins Found on vision signal transduction proteins Core structure of high-mannose N-linked oligosaccharides 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. Conversion of glycosylated asparagine residues upon deglycosylation with PGNase F in 18O labelled water. BHT metabolism has been studied in rats and mice in relation to tumor promotion. Phosphoserine to S-ethylcystine\r\nvia Beta elimination/Michael addition of ethylthiol DAET = 2-(dimethylamino)ethanethiol; The phosphorylation to amine is the beta elimination of phosphate and Michael addition of 2-(dimethylamino)ethanethiol to the site. OH-PGO and PGO react with arginine at a stoichiometry of 2:1 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 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. 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. 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. N-terminal sulfonation of diglycine to detect ubiquitination sites Protein which is posttranslationally modified by the attachment of a nitric oxide group on the sulfur atom of one or more cysteine residues. Potential protein modification when using AEBSF (Pefabloc) as a serine protease inhibitor. EDC crosslinker is used to couple biotin PEO-amine to carboxyl groups or 5\' phosphate groups 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. 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). usually major adduct formed from malondialdehyde (MDA) with the amino group of lysine residues Invitrogen X-link reagent imidoester cross-linker FP-biotin was designed to label the active site serine of serine esterases/proteases. 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 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. Attention: As the digest is typically applied AFTER ICPL_light/heavy labeling, only ProteinN-term labeling and Lys-specific labeling is applied. Attention: As the digest is typically applied AFTER ICPL_light/heavy labeling, only ProteinN-term labeling and Lys-specific labeling is applied. Observed phycocyanobilin and phycobiliviolin have different structures but the same empirical formula fluorescent derivative Modification procedure used for phosphopeptide mapping Found in canned food products For SILAC experiments 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 Lactosylation of bovine Beta-Lactoglobulin Dethiobiotin-FP was designed to label the active site serine of serine hydrolases (e.g. esterases, peptidases, lipases) 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). 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. More commonly seen as a neutral loss Different channels have the same nominal mass but slightly different exact masses. Different channels have the same nominal mass but slightly different exact masses. 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). Reversible post-translational modification of proteins by nitrated fatty acids Reversible post-translational modification of proteins by nitrated fatty acids Attention: As the digest is typically applied AFTER ICPL_light/heavy labeling, only ProteinN-term labeling and Lys-specific labeling is applied. Other 4 channels have the same nominal mass but slightly different exact mass. For quantitation purposes, use this entry for all channels 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. Other 4 channels have the same nominal mass but slightly different exact mass. For quantitation purposes, use iTRAQ8plex for all channels Beta-elimination and Michael addition of dithiothreitol (DTT) to serine and threonine adds a weight of approximately 136.2. 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. Sixplex-TMT® reagents 6TMT-126, 6TMT-127, 6TMT-128, 6TMT-129, 6TMT-130, 6TMT-131 Masses of the TMT® fragment ions to be quantified:126.1283 127.1316 128.1350 129.1383 130.1417 131.1387 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. Duplex-TMT® reagents 2TMT-126, 2TMT-127 Masses of the TMT® fragment ions to be quantified: 126.1283 127.1316 This modification describes the \"native\" TMT Reagent without isotopic label. Accurate mass for Exactag Thiol labels Accurate mass for Exactag Amine labels. Includes the mass of the conjugation reagent Synthesis and Reactions of Nitroso Sulphamethoxazole with Biological Nucleophiles: Implications for Immune Mediated Toxicity. Mass Spectorscopic Characterization of Protein Modification by 4-hydroxy-2-(E)-nonenal and 4-oxo-2-(E)-nonenal Synthesis and Reactions of Nitroso Sulphamethoxazole with Biological Nucleophiles: Implications for Immune Mediated Toxicity. Synthesis and Reactions of Nitroso Sulphamethoxazole with Biological Nucleophiles: Implications for Immune Mediated Toxicity. phenacyl bromide conjugated with a linker and biotin tag, details not published yet 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. Modified peptides identified by isotope pattern. Restriction to cysteine-containing peptides combined with high mass accuracy allows peptide identification. 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. 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. 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. 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 The two glycine residues left on SILAC labeled ubiquitinylated lysine after tryptic digestion For SILAC experiments, + PTM 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. Attention: As the digest is typically applied AFTER ICPL labeling, only ProteinN-term labeling and Lys-specific labeling is applied. MDCC is used extensively as a fluorescent probe to report changes in protein conformation. 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. Protein from animals exposed to organoarsenicals for Brad Strader for Brad Strader for Brad Strader for Brad Strader for Bindu Abraham structural isomer to succinyl 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. 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 Created for Bindu Abraham 12/22/09 Created for Bindu Abraham 12/22/09 Created for Michael (Brad) Strader 2/12/10 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). 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). sometimes observed after elution of phosphopeptides from TiO2 with ammonium hydroxide 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. 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. Created for Bindu Abraham 2010-10-05 Created for Bindu Abraham 2010-10-05 formaldeyde induced formation of thioproline Created for Bindu Abraham 2011-01-25 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 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. Unpublished chemically synthesized protein modification tool. Unpublished chemically synthesized protein modification tool. 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. 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. 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. 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. Modification by Hex(2) NeuAc using IME coupling to get glycosylated proteins Mentioned by Marshall Bern For SILAC experiments Different channels have the same nominal mass but slightly different exact masses. Different channels have the same nominal mass but slightly different exact masses. Different channels have the same nominal mass but slightly different exact masses. Different channels have the same nominal mass but slightly different exact masses. Chemical reaction with 2,4-dinitro-1-chloro benzene (DNCB) by nucleophilic attack on electrophilic amino acid side chains post-translational enzymatic myristoylation of glycine with a synthetic alkynyl-analogue of myristic acid followed by in vitro CuAAC reaction to an azido-enrichment reagent (manuscript in preparation) Lab based observation that D5 NEM hydrolyses in an analogous way to NEM 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. This modification describes the native iodoTMT Reagent without isotopic label. Upon CID, this reagent releases a reporter ion of 126.127725(monoisotopic mass). 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).