Common PT-mod, see RESID entries from AA0081 - AA0100
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.
RESID AA0041 to AA0054
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.
Labelling of C-terminus by digesting in labelled water
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.
The standard Phospho entry has a neutral loss of 98 for S and T. This entry is for cases where beta elimination is not observed
Cyclisation of N-term carbamidomethyl-Cys
Proton replaced by sodium cation
sulfinic acid has same mass, different structure
Protein which is post-translationally modified by the de-imination of one or more arginine residues; Peptidylarginine deiminase (PAD) converts protein bound to citrulline
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.
Convertion of glycosylated asparagine residues upon deglycosylation with PGNase F in H2O.
The two glycine residues left on ubiquitinylated lysine after tryptic digestion
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
via 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.
Beta elimination of O-glycosylation under alkaline conditions followed by reduction
Beta elimination of O-glycosylation under alkaline conditions followed by reduction
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. The values used here are for iTRAQ116/7. iTRAQ114 is 0.0038 Da heavier, iTRAQ115 is 0.0025 Da lighter
18O incorporation to serine, threonine, and tyrosine by using alkaline phosphatase to dephosphorylate
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.
A simplified procedure for the reduction and alkylation of cysteine residues in proteins prior to proteolytic digestion and mass spectral analysis. Hale JE, Butler JP, Gelfanova V, You JS, Knierman MD.
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).
esterification of carboxylic acids using D3-Methanolic HCl
usually major adduct formed from malondialdehyde (MDA) with the amino group of lysine residues
Malondialdehyde (MDA) adduct
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.
ICPL method description found in:
Schmidt A, Kellermann J, Lottspeich F (2005): A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5: 4-15.
Attention: The paper describes an H/D labeling strategy whereas the commercial product follows a C/13C labeling strategy!
As the digest is typically applied AFTER ICPL_light/heavy labeling, only ProteinN-term labeling and Lys-specific labeling is applied.
ICPL method description found in: Schmidt A, Kellermann J, Lottspeich F (2005): A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5: 4-15. Attention: The paper describes an H/D labeling strategy whereas the commercial product follows a C/13C labeling strategy! As the digest is typically applied AFTER ICPL_light/heavy labeling, only ProteinN-term labeling and Lys-specific labeling is applied.
Selenocysteine conventionally represented by 1 letter code U
phycocyanobilin and phycobiliviolin have different structures but the same empirical formula
RESID AA0158 to AA0166
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
CLIP-TRAQ-1
H(17) C(11) N(3) O(4) is an in-house made compound that reacts with primary amines through a N-hydroxysuccinimide group leading to a 140.0949 Da mass shift (monoisotopic) in MS mode. The reporter ion in MS/MS mode is 113 m/z. (See also CLIP-TRAQ-2).
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.
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).
ICPL method description found in: Schmidt A, Kellermann J, Lottspeich F (2005): A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5: 4-15. Attention: The paper describes an H/D labeling strategy whereas the commercial duplex product follows a C/13C labeling strategy! As the digest is typically applied AFTER ICPL_light/heavy labeling, only ProteinN-term labeling and Lys-specific labeling is applied.
Reversible post-translational modification of proteins by nitrated fatty acids
Reversible post-translational modification of proteins by nitrated fatty acids
beta-elimination
Usually don't see beta elimination of phosphate
Rare
Rare
only with Listeria monocytogenes (gram-positive bacteria)
Can occur under CNBr cleavage conditions (70% HCOOH)
Virtual Modification for MS/MS of a-type ions
Rare
Secondary adduct - much less common as C
Primary adduct formed
Secondary adduct - much less common as C
Used in AQUA experiment
Used in SILAC experiment
Used in SILAC experiment
Used in AQUA experiment
Used in SILAC experiment
Low abundance
Used in SILAC experiment
for SILAC expt
Used in SILAC experiment
Used in SILAC experiment
Primary site of modification
from reaction of SH group with iodoethanol
EDC-coupled modification of D, E and C-terminus
EDC-coupled modification of D, E and C-terminus
Used in base/residue interactions (observed)
Used in base/residue interactions (in principle?)
EDC-coupled modification of D, E and C-terminus
Used in base/residue interactions (in principle?)
Used in SILAC experiment
proteins are treated with DSP followed by DTT and iodoacetimide
Used in SILAC experiment
Used in SILAC experiment
13C6-nicotinic acid-amide
13C6-nicotinic acid-amide
nicotinic acid-amide
nicotinic acid-amide
beta-elimination
beta-elimination
Can occur under CNBr cleavage conditions (70% HCOOH)
Can occur under CNBr cleavage conditions (70% HCOOH)
Can occur under CNBr cleavage conditions (70% HCOOH)
glycation
oxoalanine
glycation
Dimethyl pimelimidate, reaction with both ends
Dimethyl pimelimidate, reaction with both ends
pS gives aminoethylcysteine
pT gives beta-methylaminoethylcysteine
found in canned food products
primary adduct
Maillard reaction (first event)
Maillard reaction (first event)
photosensitive
Side reaction, low abundance
Side reaction, low abundance
Low abundance
Low abundance
Low efficiency labeling of Trp residues by BDMAPP-NHS ester
Low efficiency labeling of Tyr residues by BDMAPP-NHS ester
Mass Defect Tag on protein N-terminus
Low efficiency labeling of His residues by BDMAPP-NHS ester
Expected labeling of Lys residues by BDMAPP-NHS ester
2H4-nicotinic acid-amide
2H4-nicotinic acid-amide
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Comparative proteomics based on stable isotope labeling and affinity selection. Regnier, Fred E.; Riggs, Larry; Zhang, Roujian; Xiong, Li; Liu, Peiran; Chakraborty, Asish; Seeley, Erin; Sioma, Cathy; Thompson, Robert A. Department of Chemistry, Pu
Comparative proteomics based on stable isotope labeling and affinity selection. Regnier, Fred E.; Riggs, Larry; Zhang, Roujian; Xiong, Li; Liu, Peiran; Chakraborty, Asish; Seeley, Erin; Sioma, Cathy; Thompson, Robert A. Department of Chemistry, Pu
Comparative proteomics based on stable isotope labeling and affinity selection. Regnier, Fred E.; Riggs, Larry; Zhang, Roujian; Xiong, Li; Liu, Peiran; Chakraborty, Asish; Seeley, Erin; Sioma, Cathy; Thompson, Robert A. Department of Chemistry, Pu
Comparative proteomics based on stable isotope labeling and affinity selection. Regnier, Fred E.; Riggs, Larry; Zhang, Roujian; Xiong, Li; Liu, Peiran; Chakraborty, Asish; Seeley, Erin; Sioma, Cathy; Thompson, Robert A. Department of Chemistry, Pu
Controlling Deuterium isotope effects in comparative proteomics. Zhang, Roujian; Sioma, Cathy S.; Thompson, Robert A.; Xiong, Li; Regnier, Fred E.. Department of Chemistry, Purdue University, West Lafayette, IN, USA. Analytical Chemistry (2
Comparative proteomics based on stable isotope labeling and affinity selection. Regnier, Fred E.; Riggs, Larry; Zhang, Roujian; Xiong, Li; Liu, Peiran; Chakraborty, Asish; Seeley, Erin; Sioma, Cathy; Thompson, Robert A. Department of Chemistry, Pu
Controlling Deuterium isotope effects in comparative proteomics. Zhang, Roujian; Sioma, Cathy S.; Thompson, Robert A.; Xiong, Li; Regnier, Fred E.. Department of Chemistry, Purdue University, West Lafayette, IN, USA. Analytical Chemistry (2
Comparative proteomics based on stable isotope labeling and affinity selection. Regnier, Fred E.; Riggs, Larry; Zhang, Roujian; Xiong, Li; Liu, Peiran; Chakraborty, Asish; Seeley, Erin; Sioma, Cathy; Thompson, Robert A. Department of Chemistry, Pu
Controlling Deuterium isotope effects in comparative proteomics. Zhang, Roujian; Sioma, Cathy S.; Thompson, Robert A.; Xiong, Li; Regnier, Fred E.. Department of Chemistry, Purdue University, West Lafayette, IN, USA. Analytical Chemistry (2
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