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.
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.
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.
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
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
Discontinued 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.
m/z values of the TMT® fragment ions to be quantified for 6plex and 10plex: 126.12773 127.12476 128.13443 129.13147 130.14114 131.13818. Additional m/z values for 10plex: 127.13108 128.12811 129.13779 130.13482
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. m/z values of the TMT® fragment ions to be quantified: 126.12773 127.13108
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
Methionine is substituted in culture with azidohomoalanine. The azide group reacts with the alkyne group of DADPS Biotin Alkyne.
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.
This modification describes the Super Heavy TMTpro Reagent. Upon HCD, this reagent releases a reporter ion of 135.151600 (monoisotopic mass)
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
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.
Occasionally used as chemical tag. In most cases, +57 is actually over-alkylation with iodoacetamide
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
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).
For SILAC experiments
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
Different tags have the same nominal mass but slightly different exact masses.
Different tags have the same nominal mass but slightly different exact masses.
Different tags have the same nominal mass but slightly different exact masses.
Different tags have the same nominal mass but slightly different exact masses.
Addition of gram negative peptidoglycan amino acid (DAP) plus monolinked DSP
Gram negative peptidoglycan saccharide amide bonded to Alanine
For SILAC experiments
For SILAC experiments
also available as 21329, 21362, 21363
Covalently bound structure in Manglik et al., Fig. 1b-Fig1c. Chemical formula % Sigma catalog entry.
LRGG remnant of ubiquitin remaining attached to lysine with missed cleavage due to dimethylation of arginine
LRGG remnant of ubiquitin remaining attached to lysine with missed cleavage due to methylation of arginine
By analogy with AMP
imidoester cross-linker
imidoester cross-linker
Created by auto-catalytic dealkylation of the O-dimethylphosphothione adduct.
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
Glutamine-donor substrate for transglutaminase
This modification describes the Super Heavy TMT Reagent. Upon HCD, this reagent releases a reporter ion of 132.14153 (monoisotopic mass)
This modification describes the isotope-labeled TMTpro Reagent with m/z values of the TMTpro fragment ions to be quantified for 16plex: 126.127726,127. 124761, 127.131081, 128.128116, 128.134436, 129.131471, 129.13779, 130.134825, 130.141145, 131.13818, 131.1445, 132.141535, 132.147855, 133.14489, 133.15121, and 134.148245rnAdditional reporter ions for 18plex: 134.154565 and 135.151600
This modification describes the native TMTpro Reagent without isotopic label with reporter mass m/z 126.127726
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 hydrolysis of the product of the reaction of 2-(o-cresyl)-4H-1,3,2-benzodioxaphosphorane-2-one with amino acids residues in proteins.
Methionine is substituted in culture with azidohomoalanine. The azide group reacts with the alkyne group of PC Biotin Alkyne.
- desthiobiotin-azide to enrich L-Gln-propargyl modified peptides
- desthiobiotin-azide to enrich L-Gln-propargyl modified peptides
- desthiobiotin-azide to enrich L-Gln-propargyl modified peptides
The lysis buffer in the iST-NHS kit, called LYSE-NHS, does not contain primary amines and therefore does not interfere with chemical labeling. The LYSE-NHS contains a distinct alkylation agent. Please consider the following as fixed modification in your database search: Specific cysteine modification (C6H11NO), specificity [C], mass shift +113.084 Da
Tandem Mass Tag and TMT are registered Trademarks of Proteome Sciences plc.
Tandem Mass Tag and TMT are registered Trademarks of Proteome Sciences plc.
The valine glycine residues left on ufmylated lysine after tryptic digestion.
Search engines that analyze MS3 spectra derived from b-ions from the MS2 stage must recognize this virtual modification for this purpose.
Serine/Threonine/Tyrosine of a protein becomes posttranslationally modified with a phosphocholine moiety. Phosphocholine itself has a molecular weight of 183,1426 Da for (C5H14NO4P), but in classic LC-MS it would be protonated due to the acidic environment (C5H15NO4P) and would have a molecular weight of 184,1205 Da. Since the modification is attached to the protein in an enzymatic process the actual mass gain of a phosphocholination to a peptide is: 166,1357 Da if no acidic environment is present and 167,1436 Da for evironments that are acidic.
Search engines that analyze MS3 spectra derived from c-ions from the MS2 stage must recognize this virtual modification for this purpose.
Search engines that analyze MS3 spectra derived from x-ions from the MS2 stage must recognize this virtual modification for this purpose.
Search engines that analyze MS3 spectra derived from z-ions from the MS2 stage must recognize this virtual modification for this purpose.
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.
When dimethyl labelling is pre-digest
When dimethyl labelling is pre-digest
only with Listeria monocytogenes (gram-positive bacteria)
Secondary adduct - much less common as C
Secondary adduct - much less common as C
Used in AQUA experiment
Used in SILAC experiment
Used in SILAC experiment
for SILAC expt
Used in SILAC experiment
Used in SILAC experiment
S-nitrosylation
Primary site of modification
Selenocysteine conventionally represented by 1 letter code U
hydroxyglutamic acid
Used in base/residue interactions (in principle?)
Used in base/residue interactions (observed)
EDC-coupled modification of D, E and C-terminus
Used in base/residue interactions (in principle?)
Not reported for human proteins
esterification of carboxylic acids using D3-Methanolic HCl
Error in peptide synthesis
Used in SILAC experiment
Beta elimination of O-glycosylation under alkaline conditions followed by reduction
Used in SILAC experiment
Used in SILAC experiment
Could also be classed as chemical derivative
Could also be classed as chemical derivative
Use when labelling post-digest
Use when labelling pre-digest
beta-elimination
beta-elimination
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.
Can occur under CNBr cleavage conditions (70% HCOOH)
Labeling with diethylpyrocarbonate (DEPC)
Pyro-carbamidomethyl as a delta from Carbamidomethyl-Cys
oxoalanine formylglycine
Rare
beta-thiolation
Gamma-carboxylation
sulfinic acid
glycation
pT gives beta-methylaminoethylcysteine
pS gives aminoethylcysteine
485845 Aldrich
found in canned food products
primary adduct
Maillard reaction (first event)
photosensitive
beta-elimination
Beta elimination of O-glycosylation under alkaline conditions followed by reduction
alkaline phosphatase to dephosphorylate
Protein which is post-translationally modified by the de-imination of one or more arginine residues; Peptidylarginine deiminase (PAD) converts protein bound to citrulline
alkaline phosphatase to dephosphorylate
alkaline phosphatase to dephosphorylate
digesting in labelled water
Hydroxyglycine derivative in amidation pathway
Can occur under CNBr cleavage conditions (70% HCOOH)
Can occur under CNBr cleavage conditions (70% HCOOH)
Can occur under CNBr cleavage conditions (70% HCOOH)
tryptophan oxidation to formylkynurenin
trihydroxyphenylalanine
Gamma-carboxylation
Malondialdehyde (MDA) adduct
5-hydro-5-methylimidazol-4-one, Methylglyoxal adduct
Because the modification is quantitatively lost on CID, site assigment is not possible when there is a choice of sites
Low abundance
Low abundance
Primary adduct formed
EDC-coupled modification of D, E and C-terminus
Side reaction, low abundance
Low abundance
Low abundance
Low efficiency
Low efficiency
Low efficiency
Use when labelling post-digest
Use when labelling pre-digest
Use when labelling pre-digest
Pyro-carboxymethyl as a delta from Carboxymethyl-Cys
EDC-coupled modification of D, E and C-terminus
Used in SILAC experiment
Low abundance
Very low abundance
The addition of DTT adds 136.2 not 154.2 to Threonine due to loss of water in reaction
The addition of DTT adds 136.2 not 154.2 to Serine due to loss of water in reaction
N-Succinimide
Simple cyclic compound C16H16O2 adds to cysteine forming fluorescent derivative.
Result of Arg to Pro conversion of 13C(6) labelled Arg
Not reported for human proteins
hydrazide reacts at any activated carboxyl group
GIST acetyl light
PT and GIST acetyl light
Both isotopiclabel and post translational mod
SILAC and PTM
Used in SILAC experiment
The reaction product of Arg with phenylglyoxal has been shown to be a 2:1 adduct
putrescine Q-PUT
Lactone formation from C-terminal hydroxylysine
Isotopic labeled methionine SILAC
Use when labelling post-digest
Used in SILAC PTM (glygly) experiment
Use when labelling post-digest
Use when labelling pre-digest
Advanced Glycation Endproduct
Very low abundance
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.
SILAC label used in COFRADIC
Result of conversion of 13C6, 15N4 arginine to 13C5, 15N1 proline
Used in AQUA experiment
Very low abundance
Low abundance
This peptide is generated from a trypsin/chymotrypsin dual digest.
This peptide is generated from a trypsin/chymotrypsin dual digest
When dimethyl labelling is pre-digest
15-deoxy-PGJ2 (15d-PGJ2) influences multiple signaling pathways by covalently binding with key signaling molecules
Used in SILAC PTM (glygly) experiment
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.
This peptide is generated from a formic acid digest
SILAC+PTM
reduced form of oxidation product
from reaction of SH group with iodoethanol
SILAC+PTM
Cambridge Labs DLM-451
Virtual Modification for MS/MS of a-type ions
corrected by subtraction of a further -O at 8.6.2010
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
Low abundance
Convertion of glycosylated asparagine residues upon deglycosylation with PNGase F in H2O
Sulfo-SBED Label Transfer ReagentrnReaction path that does not remove one Hidrogen atom from the target peptide
Sulfo-SBED Label Transfer Reagent. Reaction path that removes one Hydrogen atom from the target peptide
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
This peptide is generated from a trypsin/chymotrypsin dual digest.
This peptide is generated from a trypsin/chymotrypsin dual digest.
Very low abundance
Very low abundance
Very low abundance
Low abundance
Very low abundance
Very low abundance
Low abundance
Used in SILAC experiment
Very low abundance
Very low abundance
Very low abundance
Very low abundance
Low abundance
Low abundance
Very low abundance
Very low abundance
Very low abundance
Rare
Rare
Because the modification is quantitatively lost on CID, site assigment is not possible when there is a choice of sites
Because the modification is quantitatively lost on CID, site assigment is not possible when there is a choice of sites
Sulfitolysis
Low abundance
Low abundance
Low abundance
Addition of a single sulfur atom by Pi3-Tryptophan reagent to create thiol
esterification of carboxylic acids using D3-Methanolic HCl
esterification of carboxylic acids using D3-Methanolic HCl
SILAC labelling with L-Methionine-(methyl-d3)
SILAC labelling with L-Methionine-(methyl-d3)
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
From exposure to hydroxylamine (used with TMT)
From exposure to hydroxylamine (used with TMT)
Low abundance
Low abundance
Low abundance
Low abundance
The cleavage products of SUMO-2 and SUMO-3 are indistinguishable
Not reported for human proteins
When dimethyl labelling is pre-digest
propyl ester
propyl ester
propyl ester
propyl ester
Pyro-carbamidomethyl as a delta from Carbamidomethyl-Cys
Not reported for human proteins
Hydroxylethanone
sulfenic acid
2-oxohistidine
phenylalanine oxidation to dihydroxyphenylalanine
observed in monoclonal antibodies
Triton X-114
Triton X-100
GEE (glycine ethyl ester) is a substrate for the enzyme Factor XIII for cross-linking to fibrinogen
NG sequence specifically after deamidation - Deamidated Asparagine with adjacent glycine are prone for this modification.
-SOH
methionine sulfoxide
dihydroxyphenylalanine (DOPA)
glutamic semialdehyde
3-hydroxyasparagine
3-hydroxyaspartic acid
reduced form of oxidation product
Sulphone
O-acetyl
glyoxal-derived hydroimidazolone
Note that Table 3 in the reference has the delta as H(3) C(3) O(2) = 71 Da
Maillard reaction (first event)
Not reported for human proteins
possible side chain reaction when labeling N-term
possible side chain reaction when labeling N-term
glycation
photochemical decomposition
Loss of MBS, peptide from KLH after trypsin digestion
Oxidative cross-link of free methionine to histidine residue in protein.
Only observed on a small fraction of residues (~2%). See doi: 10.1038/nmeth.4465
Only observed on a small fraction of residues (~2%). See doi: 10.1038/nmeth.4465
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)
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)
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)
GFAP from human brain tissues
GFAP from human brain tissues
side reaction
side reaction
side reaction
side reaction
side reaction
Low abundance
Virtual modification for MS/MS of b-type ions
glycation
Virtual modification for MS/MS of c-type ions
Virtual modification for MS/MS of x-type ions
Virtual modification for MS/MS of z-type ions. This is for the Biemann z-type ion, but the most common ETD z-dot ion has one more hydrogen.
Krutzsch and Inman, Analytical Biochemistry, 209, 109-116, (1993)
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25197743
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34673284
AA0114
GGLU
AA0363
21942216
31980631
32233093
dabcyl-c2-maleimide
Reference for KDO mass, KDO on capsular polysaccharide
Isotopically Labeled Desthiobiotin Azide (isoDTB) Tags Enable Global Profiling of the Bacterial Cysteinome
Thermo Scientific DSPP (Disuccinimidyl Phenyl Phosphonic Acid, PhoX) Data Sheet
Thermo Scientific DSPP (Disuccinimidyl Phenyl Phosphonic Acid, PhoX) Data Sheet
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AA0021
dansyl chloride [605-65-2]
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2005 ASMS poster Presentation TP 527
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11212008
9252331
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AA0211
15799070
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AA0031
9252331
11120890
6838602
AA0214
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AA0087
AA0183
Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.
11467524
12771378
Silac introduction
Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.
7949339
THIOG
AA0021
FORM
AA0384
1093385
7744761
DIMETH
AA0311
NTRY
14670044
AA0049
AA0041
ASMS 2004 abstract
12643539
6273432
TRIMETH
11821862
ASMS 2001 abstract
11078590
8839040
9252331
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29048423
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11999733
12175151
28112733
28112733
25218447
14678012
AA0022
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15541752
10825247
20513473
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Agilent Lys Tag 4H Reagent Kit
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31572778
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2026710
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Thermo Scientific DSPP (tert-Butyl Disuccinimidyl Phenyl Phosphonate, tBu-PhoX) Data Sheet
Thermo Scientific DSPP (tert-Butyl Disuccinimidyl Phenyl Phosphonate, tBu-PhoX) Data Sheet
31572778
11698400
11914093
Thermo Scientific DSPP (Disuccinimidyl Phenyl Phosphonic Acid, PhoX) Data Sheet
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PDOC00008
AA0059
AA0307
AA0078
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9448752
9750125
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AA0350
AA0080
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8344916
AA0229
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Pierce introduction to biotin
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10504701
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10825024
DIMETP
9252331
AA0025
AA0025
AA0031
Miller et.al. Arch. Biochem. Biophy. (1993) 301, 41-52.
AA0036
IonSource
AA0037
AA0052
AA0364
10442087
9252331
P02942
AA0068
14570711
DEAME
AA0105
11875433
AA0072
AA0299
AA0067
AA0337
12148805
AA0102
AA0103
AA0107
AA0032
AA0116
LIPY
Biochemistry; D.Voet and J.G.Voet WILEY(p728)
AA0120
Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.
AA0122
AA0127
12643538
15456300
AA0258
AA0132
AA0133
AA0329
AA0142
AA0143
Structure
AA0144
AA0147
AA0148
AA0150
AA0152
AA0153
GLCN
AA0155
3086323
AA0154
AA0217
AA0167
AA0170
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9033387
AA0174
AA0175
AA0176
AA0173
AA0177
AA0178
AA0180
AA0179
AA0181
BROM
8442665
AA0185
AA0186
15650407
Degradation of the amino acids Isoleucine, Leucine and Tryptophan
AA0207
AA0057
AA0212
AA0157
AA0353
AA0145
AA0223
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AA0325
AA0230
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AA0317
AA0236
AA0248
AA0252
AA0256
AA0131
AA0264
AA0265
AA0267
AA0269
AA0273
AA0234
AA0287
AA0274
AA0135
AA0277
AA0375
9252331
AA0275
AA0290
8597590
AA0296
AA0297
DHAS
PYRUC
3802193
AA0073
Structure
AA0309
12964758
AA0312
AA0316
AA0070
TOPA
AA0324
AA0228
CMAN
AA0328
AA0276
AA0333
AA0334
AA0335
AA0071
AA0076
CHDH
GERA
AA0349
AA0351
AA0220
AA0352
AA0320
8844851
AA0355
AA0359
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AA0172
14752058
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AA0303
AA0302
AA0181
AA0127
PYRUS
AA0182
DHB
PYRR
14235557
AA0373
AA0086
AA0085
AA0084
AA0083
AA0082
AA0081
AA0089
AA0090
AA0091
AA0092
AA0093
AA0094
AA0095
AA0096
AA0097
AA0098
AA0099
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AA0100
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AA0272
AA0305
AA0336
AA0069
AA0065
AA0063
AA0061
AA0064
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AA0318
METH
AA0027
11461766
AA0029
AA0028
AA0030
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AA0205
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AA0282
AA0370
DIHYDR
MSONE
CSIA
12686488
AA0262
AA0056
AA0046
AA0051
AA0045
AA0354
AA0044
AA0043
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TRC data sheet
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AA0033
AA0038
HYPU
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8465942
11465505
AA0130
11857757
12175151
12175151
11857757
12175151
11857757
Bruker Daltonics order reference
Bruker Daltonics order reference
AA0158
12777388
11813307
AA0321
PYRK
AA0386
11857757
11857757
11857757
11857757
AA0040
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15121203
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DECA
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1326520
1326520
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14745769
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FAR0
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AA0117
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AA0119
PLP
AA0308
AA0077
PALM
AA0339
AA0060
AA0159
AA0160
AA0161
AA0162
AA0163
AA0164
AA0165
AA0166
GLUT
11861642
PPAN
12185208
12185208
CHOL
3578767
5-iodoacetamidofluorescein, [63368-54-7]
FMN
FMNH
FMNC
THRN
DIAC
THRX
ARCH
AA0306
AA0221
FAD
12356754
12872219
12872219
Cayman Chemical data sheet
Cayman Chemical data sheet
AA0185
OXOAC
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AA0129
AA0304
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AA0146
DOPA
9252331
15253424
AA0232
AA0384
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15828771
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9252331
1680314
AA0215
CSEA
AA0026
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Juergen.Schaefer@Proteomics.com
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John.C.Rogers@thermo.com
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John.C.Rogers@thermo.com
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Uncovering protein polyamination by the spermine-specific
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Uncovering protein polyamination by the spermine-specific
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GlycomeDB Entry 13,423
ACS Book series: "State-of-the-Art and Emerging Technologies for Therapeutic Monoclonal Antibody Characterization"rnVolume 1 - Monoclonal Antibody Therapeutics: Structure, and Regulatory Space
PMID:23924801 rnCorrect primary structure assessment and extensive glyco-profiling of cetuximab by a combination of intact, middle-up, middle-down and bottom-up ESI and MALDI mass spectrometry techniques.
Thermo data sheet
Thermo Fisher data sheet
Kao et. al, Development of a Novel Cross-linking Strategy for Fast and Accurate Identification of Cross-linked Peptides of Protein Complexes, MCP
Mapping PARP-1 auto-ADP-ribosylation sites by liquid chromatography-tandem mass spectrometry
Chen, L.L., Rosa, J.J., Turner, S. and Pepinsky, R.B. (1991). Production of multimeric forms of CD4 through a sugar-based crosslinking strategy. J. Biol. Chem. 266(27), 18237-18243
Cross-linking of the proteins in the outer membrane of Escherichia coli
770170
Nature Chemical Biology 5, 378 - 379 (2009)
Pierce data sheet
Pierce data sheet
Pierce data sheet
36892
26597962
12872131
AA0151
20373501
Mass spectrometric identification of formaldehyde-induced
peptide modifications under in vivo protein
cross-linking conditions
Identification of Formaldehyde-induced Modifications in Proteins
Dai, L., et al. (2014). "Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark." Nat Chem Biol 10(5): 365-370.
Tan, M., et al. (2014). "Lysine glutarylation is a protein posttranslational modification regulated by SIRT5." Cell Metab 19(4): 605-617.
Lysine succinylation and lysine malonylation in histones
24703693
Barakat, Zheng, Gilley, MacDonald, Okolotowicz, Cashman, Vyas, Beck, Hadad, Zhang; Chemical synthesis of two series of nerve agent model compounds and their stereoselective interaction with human acetylcholinesterase and human butyrylcholinesterase; Chemical Research in Toxicology 22, 1669-1679 (2009)
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics
15648052
18653769
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics
DYn-2 Based Identification of Arabidopsis Sulfenomes
Mass Spectrometry of Intact Proteins Reveals +98 u Chemical Artifacts Following Precipitation in Acetone
Kao et. al, Development of a Novel Cross-linking Strategy
Thermo Fisher data sheet
Kao et. al, Development of a Novel Cross-linking Strategy
ThermoFisher data sheet
8326953
Bioconjug Chem. 2006 May-Jun;17(3):815-22.rnIdentification of formaldehyde-induced modifications in proteins: reactions with insulin.rnMetz B1, Kersten GF, Baart GJ, de Jong A, Meiring H, ten Hove J, van Steenbergen MJ, Hennink WE, Crommelin DJ, Jiskoot W.
J Biol Chem. 2004 Feb 20;279(8):6235-43. Epub 2003 Nov 24.rnIdentification of formaldehyde-induced modifications in proteins: reactions with model peptides.rnMetz B1, Kersten GF, Hoogerhout P, Brugghe HF, Timmermans HA, de Jong A, Meiring H, ten Hove J, Hennink WE, Crommelin DJ, Jiskoot W.
Thermo Fisher data sheet
Kao et. al, Development of a Novel Cross-linking Strategy
Thermo Fisher data sheet
Thermo Fisher data sheet
Kao et. al, Development of a Novel Cross-linking Strategy
Thermo Fisher data sheet
Kao et. al, Development of a Novel Cross-linking Strategy
Thermo Fisher data sheet
Kao et. al, Development of a Novel Cross-linking Strategy
Thermo Fisher data sheet
Anal. Chem. 2016, 88, 7930-7937, Integrated Workflow for Structural Proteomics Studies
Thermo Fisher data sheet
Anal. Chem. 2016, 88, 7930-7937, Integrated Workflow for Structural Proteomics Studies
Thermo Fisher data sheet
Anal. Chem. 2016, 88, 7930-7937, Integrated Workflow for Structural Proteomics Studies
Thermo Fisher data sheet
Thermo Fisher data sheet
Thermo Fisher data sheet
Hand, E.S., and Jencks, W.P. (1962). Mechanism of the reaction of imidoesters with amines. J. Am. Chem. Soc. 84, 3505-3514.
Pierce data sheet
Pierce data sheet
3001048
ThermoFisher data sheet
ThermoFisher data sheet
212103
3001048
8457554
322714
8457554
322714
1262347
ThermoFisher data sheet
Thermo Fisher data sheet
36892
1262347
Kao et. al, Development of a Novel Cross-linking Strategy
ThermoFisher data sheet
Lee,W.T. and Conrad, D.H. 1985, J. Immunol. 134:518
Lomant, A.J. and Fairbanks, G., J.Mol. Biol. 104, 243-261 (1976)
Pierce data sheet
8326953
Thermo Fisher data sheet
770170
Pierce data sheet
212103
ThermoFisher data sheet
3001048
ThermoFisher data sheet
1262347
8457554
322714
ThermoFisher data sheet
Biophys J (2001) 81:2851-2863
Thermo datasheet
Thermo datasheet
Thermo datasheet
Thermo datasheet
ThermoFisher data sheet
Trying to illuminate proteomics 'dark matter'
2144419
14696200
2144419
14696200
Study of an Unusual Advanced Glycation End-Product (AGE) Derived from Glyoxal Using Mass Spectrometry
Bachi et al., Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises
Bachi et al., Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises
Bachi et al., Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises
Bachi et al., Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises
Havelund et al., A biotin enrichment strategy identifies novel carbonylated amino acids in proteins from human plasma
AA0235
HYDR
14661085
12781462
2057999
BIOT
7730303
F. P. Guengerich, K. O. Arneson, K. M. Williams, Z. Deng, T. M. Harris, Reaction of aflatoxin B1 oxidation products with lysine, Chem. Res. Toxicol. 2002, 15, 780-792.
Quantification of hydroxyl radical-derived oxidation products in peptides containing glycine, alanine, valine, and proline
Gorman, J. J., Anal Biochem 1984, 160, 376
3311742
Bachi et al., Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises
AA0251
Bachi et al., Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises
Bachi et al., Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises
AA0047
12175151
11857757
AA0042
AA0050
AA0053
AA0054
ACET
PNAS 2006 103: 18574-18579
Bachi et al., Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises
Bachi et al., Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises
Bachi et al., Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises
Bachi et al., Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises
Bachi et al., Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises
Bachi et al., Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises
Bachi et al., Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises
Bachi et al., Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises
Bachi et al., Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises
Applied Biosystems Chemistry Reference Guide
Anal Chem. 2011 Feb 1; 83(3): 701-707
Applied Biosystems Chemistry Reference Guide
Anal Chem. 2011 Feb 1; 83(3): 701-707
Anal Chem. 2011 Feb 1; 83(3): 701-707
Trying to illuminate proteomics 'dark matter'
Trying to illuminate proteomics 'dark matter'
Trying to illuminate proteomics 'dark matter'
Trying to illuminate proteomics 'dark matter'
Trying to illuminate proteomics 'dark matter'
Trying to illuminate proteomics 'dark matter'
Trying to illuminate proteomics 'dark matter'
Trying to illuminate proteomics 'dark matter'
Trying to illuminate proteomics 'dark matter'
Results round-up for the 'dark matter' challenge
Product of a reaction with chlorpyrifos with human serum albumin. Li, Eyer, Eddleston, Jiang, Schopfer & Lockridge; Protein tyrosine adduct in humans self-poisoned by chlorpyrifos; Tox Appl Pharmacol 269, 215 (2013)
O15205
O15205
Composition search GlyConnect
7947762
11067851
AA0327
Global and Site-Specific Analysis Revealing Unexpected and
Extensive Protein S-GlcNAcylation in Human Cells
Composition search GlyConnect
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UniCarbKB 1187
Composition search GlyConnect
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AA0528
Bertaccini et. al., J Proteome Res. 2013, 12,3063-3070
AA0222
PHOS
AA0034
AA0035
ThermoFisher data sheet
212103
3001048
Anal. Chem., 2016, 88 (16), pp 8239-8247
770170
15700232
DEAM
4677141
Tacal & Lockridge; Methamidophos, dichlorvos, O-methoate and diazinon pesticides used in Turkey make a covalent bond with butyrylcholinesterase detected by mass spectrometry; J Appl Toxicol 30, 469-475 (2010)
Tacal & Lockridge; Methamidophos, dichlorvos, O-methoate and diazinon pesticides used in Turkey make a covalent bond with butyrylcholinesterase detected by mass spectrometry; J Appl Toxicol 30, 469-475 (2010)
Trying to illuminate proteomics 'dark matter'
X. Zhan, X. Wang, D.M. Desiderio. Mass Spectrom. Rev., 34 (2015), pp. 423-448
https://www.thermofisher.com/order/catalog/product/A43073
24681537
ryan.bomgarden@thermofisher.com
TMTpro Zero Label Reagent
TMTpro 16plex Label Reagent Set
ryan.bomgarden@thermofisher.com
15688001
X. Zhan, X. Wang, D.M. Desiderio. Mass Spectrom. Rev., 34 (2015), pp. 423-448
Thermo data sheet
Pierce LC-MS/MS System Suitability Standard
Thioredoxin as a Molecular Target of CyclopentenonernProstaglandins
HMDB
Reference for KDO mass
This is the primary reference of KDO modification on protein.
Reference for KDO mass, KDO residue on lipopolysaccharide
Site-specific characterization of the Asp- and Glu-ADP-ribosylated proteome
24445406
Nutrients 2019, 11(10), 2263
Discovery of a Photoinduced Histidine-Histidine Cross-Link in an IgG4 Antibody
Composition search GlyConnect
Composition search GlyConnect
Photoinduced cross-linking of formulation buffer amino acids to monoclonal antibodies
Photoinduced cross-linking of formulation buffer amino acids to monoclonal antibodies
Photoinduced cross-linking of formulation buffer amino acids to monoclonal antibodies
European Journal of Pharmaceutics and Biopharmaceutics
Photoinduced cross-linking of formulation buffer amino acids to monoclonal antibodies
S. N. Abramson, J. A. Trischman, D. M. Tapiolas, E. E. Harold, W. Fenical, P. Taylor, Structure/activity and molecular modeling studies of the lophotoxin family of irreversible nicotinic receptor antagonists, J Med Chem. 1991, 34, 1798-804.
AA0115
CETH
Biochemistry, 1970, 9 (2), pp 251-258 DOI: 10.1021/bi00804a010
UniProtKB - Q10583 (HCY1_MEGCR)
MBS (m-maleimidobenzoyl-N-hydroxysuccinimide ester)
Keyhole limpet hemocyanin: structural and functional characterization of two different subunits and multimers PMID:8829804
Schopfer, Furlong and Lockridge; Development of diagnostics in the search for an explanation of aerotoxic syndrome; Anal Biochem 404, 64-74 (2010)
Schopfer, Furlong and Lockridge; Development of diagnostics in the search for an explanation of aerotoxic syndrome; Anal Biochem 404, 64-74 (2010)
AA0371
AA0227
1443554
Photoactivatable ribonucleosides mark base-specific RNA-binding sites
DADPS Biotin Alkyne
Photocleavable Biotin Alkyne
Photoactivatable ribonucleosides mark base-specific RNA-binding sites
Photoactivatable ribonucleosides mark base-specific RNA-binding sites
Chemical RNA digestion enables robust RNA-binding site mapping at single amino acid resolution
Required fixed modification when using PreOmics iST-NHS Kit
This is available for synthetic SIL peptides
Anal. Chem. 2016, 88, 7930-7937, Integrated Workflow for Structural Proteomics Studies
Anal. Chem. 2016, 88, 7930-7937, Integrated Workflow for Structural Proteomics Studies
Anal. Chem. 2016, 88, 7930-7937, Integrated Workflow for Structural Proteomics Studies
Anal. Chem. 2016, 88, 7930-7937, Integrated Workflow for Structural Proteomics Studies
Modification of Cytochrome c by 4-hydroxy- 2-nonenal: evidence for histidine, lysine, and arginine-aldehyde adducts
Pentanoyl-CoA from KEGG
Isovaleryl-CoA from KEGG
2-Methylbutanoyl-CoA from KEGG
11327326
Poli G, Schaur RJ., IUBMB Life 2000 Oct-Nov;50(4-5):315-21
15276160
Tiglyl-CoA from KEGG
Acetoacetyl-CoA from KEGG
Bridge et al., Cell Chem Biol. 2024, 31(3):534-549.e8
iST NHS Application Note
31645732
Desthiobiotin polyethyleneoxide iodoacetamide is useful for cysteine labeling in chemoproteomic experiments. Cat. No.: HY-143205
Baldensperger et. al., Anal. Chem. 2019, 91, 19, 12336
Baldensperger et. al., Anal. Chem. 2019, 91, 19, 12336
Baldensperger et. al., Anal. Chem. 2019, 91, 19, 12336
Baldensperger et. al., Anal. Chem. 2019, 91, 19, 12336
Wagner et al. (2017). "A Class of Reactive Acyl-CoA Species Reveals the Non-enzymatic Origins of Protein Acylation." Cell Metab 25, 823
Wagner et al. (2017). "A Class of Reactive Acyl-CoA Species Reveals the Non-enzymatic Origins of Protein Acylation." Cell Metab 25, 823
Wagner et al. (2017). "A Class of Reactive Acyl-CoA Species Reveals the Non-enzymatic Origins of Protein Acylation." Cell Metab 25, 823
Baldensperger et at. J. Agric. Food Chem. 2018, 66, 1898
Baldensperger et at. J. Agric. Food Chem. 2018, 66, 1898
Cifani et at. J. Proteome Res. 2021, 20, 1835
Liu et at. J. Am. Chem. Soc. 2023, 145, 12673
Makhlouf, L. et al., Nature. 2024 627, 437–444
8383789
Banerjee S. et al., Biomolecules. 2020 Oct; 10(10): 1442
33066455
Tolmachova K.A. et al., ACS Cent. Sci. 2022 Jun 22;8(6):756-762.
35756382
Fu et. al., Front. Microbiol. 2022
Fu et. al., Front. Microbiol. 2022
34847359
34847359
Composition search GlyConnect
15842200
AA0231
AA0237
AA0295
ADP
AA0168
AA0169
TMT Mass Tagging Kits and Reagents
Glushchenko A. V., Jacobsen D. W. Antioxid. Redox Signal. 2007. V. 9. P. 1883–1898.
38724559
9497327
25514000
9497327
Biemann, K. Appendix 5. Nomenclature for Peptide Fragment Ions (Positive Ions). In Methods in Enzymology; Elsevier, 1990; Vol. 193, pp 886–887.
2074849
9497327
L-Serine-O-sulfate
25514000
Streamlined isolation of the n-terminome via phosphonate tagging and coordination-based depletion
Desthiobiotin-Phenol
Streamlined isolation of the n-terminome via phosphonate tagging and coordination-based depletion
Composition search GlyConnect
GLUC
15279557
ryan.bomgarden@thermofisher.com
17591739
Lascoux D, Paramelle D, Subra G, Heymann M, Geourjon C, Martinez J, Forest E., Angew Chem Int Ed Engl 2007;46(29):5594-7
Biemann, K. Appendix 5. Nomenclature for Peptide Fragment Ions (Positive Ions). In Methods in Enzymology; Elsevier, 1990; Vol. 193, pp 886–887.
Biemann, K. Appendix 5. Nomenclature for Peptide Fragment Ions (Positive Ions). In Methods in Enzymology; Elsevier, 1990; Vol. 193, pp 886–887.
2074849
Biemann, K. Appendix 5. Nomenclature for Peptide Fragment Ions (Positive Ions). In Methods in Enzymology; Elsevier, 1990; Vol. 193, pp 886–887.
2074849
2074849
Oxidation of Methionine to Dehydromethionine by Reactive Halogen Species Generated by Neutrophils
Dehydromethionine is a common product of methionine oxidation by singlet molecular oxygen and hypohalous acids
L-Lysine·2HCl
Niwa et al., Imidazolone, a novel advanced glycation end product, is present at highlevels in kidneys of rats with streptozotocin-induced diabetes, FEBS, 1997
27644970
16335955
This publication describes the enzymatic modification of the Rab1b by AnkX.
Detection and Site Localization of Phosphorylcholine-Modified Peptides by NanoLC-ESI-MS/MS Using Precursor Ion Scanning and Multiple Reaction Monitoring Experiments