GIST acetyl light
PT and GIST acetyl light
O-acetyl
14730666
PubMed PMID
15350136
PubMed PMID
AA0055
RESID
IonSource acetylation tutorial
Misc. URL
http://www.ionsource.com/Card/acetylation/acetylation.htm
Chemical Reagents for Protein Modification 3rd edition, pp 215-221, Roger L. Lundblad, CRC Press, New York, N.Y., 2005
Book
11999733
PubMed PMID
AA0043
RESID
AA0044
RESID
AA0354
RESID
AA0045
RESID
AA0056
RESID
AA0046
RESID
AA0051
RESID
AA0052
RESID
AA0364
RESID
AA0041
RESID
AA0049
RESID
AA0048
RESID
AA0047
RESID
12175151
PubMed PMID
11857757
PubMed PMID
AA0042
RESID
AA0050
RESID
AA0053
RESID
AA0054
RESID
ACET
FindMod
PNAS 2006 103: 18574-18579
Journal
http://dx.doi.org/10.1073/pnas.0608995103
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.
Top-Down sequencing c-type fragment ion
AA0088
RESID
AA0087
RESID
AA0086
RESID
AA0085
RESID
AA0084
RESID
AA0083
RESID
AA0082
RESID
AA0081
RESID
AA0089
RESID
AA0090
RESID
AA0091
RESID
AA0092
RESID
AA0093
RESID
AA0094
RESID
AA0095
RESID
AA0096
RESID
AA0097
RESID
AA0098
RESID
AA0099
RESID
AA0100
RESID
AMID
FindMod
14588022
PubMed PMID
AA0117
RESID
BIOT
FindMod
Carboxyamidomethylation
Creasy, D. M., Cottrell, J. S., Proteomics 2 1426-34 (2002)
Journal
11510821
PubMed PMID
Boja, E. S., Fales, H. M., Anal. Chem. 73 3576-82 (2001)
Journal
12422359
PubMed PMID
Smyth; Carbamylation of amino and tyrosine hydroxyl groups. J Biol Chem 242, 1579-1591 (1967)
Journal
10978403
PubMed PMID
AA0332
RESID
AA0343
RESID
Stark; Modification of proteins with cyanate. Meth Enz 25B, 579-584 (1972)
Journal
12203680
PubMed PMID
IonSource carbamylation tutorial
Misc. URL
http://www.ionsource.com/Card/carbam/carbam.htm
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
Hydroxylethanone
Carboxymethylation
Protein which is post-translationally modified by the de-imination of one or more arginine residues; Peptidylarginine deiminase (PAD) converts protein bound to citrulline
Convertion of glycosylated asparagine residues upon deglycosylation with PGNase F in H2O
phenyllactyl from N-term Phe
Citrullination
IonSource tutorial
Misc. URL
http://www.ionsource.com/Card/Deamidation/deamidation.htm
CITR
FindMod
FLAC
FindMod
AA0128
RESID
AA0214
RESID
6838602
PubMed PMID
15700232
PubMed PMID
DEAM
FindMod
10504701
PubMed PMID
Gygi S.P., et. al. Nat Biotechnol. 1999 Oct;17(10):994-9
Journal
10504701
PubMed PMID
Gygi S.P., et. al. Nat Biotechnol. 1999 Oct;17(10):994-9
Journal
Cyanogen bromide (CNBr) cleavage converts the C-term Met to either homoserine or homoserine lactone, depending on pH.
Donald Voet, Judith G. Voet (1995): Biochemistry; p 115
Book
Cyanogen bromide (CNBr) cleavage converts the C-term Met to either homoserine or homoserine lactone, depending on pH.
Structure
Misc. URL
http://www.chemsoc.org/exemplarchem/entries/2002/proteomics/images/icat_reagent.gif
Molecular & Cellular Proteomics 2:428-442, 2003
Journal
http://www.mcponline.org/cgi/content/full/2/7/428
Structure
Misc. URL
http://www.chemsoc.org/exemplarchem/entries/2002/proteomics/images/icat_reagent.gif
Molecular & Cellular Proteomics 2:428-442, 2003
Journal
http://www.mcponline.org/cgi/content/full/2/7/428
Dimethylacrylamide, DMA
Krutzsch and Inman, Analytical Biochemistry, 209, 109-116, (1993)
Journal
Galvani et.al. (2000) Electrophoresis vol 22 p2046-p2074
Journal
8465942
PubMed PMID
11465505
PubMed PMID
Pierce EZ-Link PEO-Iodoacetyl Biotin
12038753
PubMed PMID
J. Biol. Chem., Vol. 278, Issue 7, 4500-4509, February 14, 2003
Journal
http://www.jbc.org/cgi/content/full/278/7/4500#F1
15253424
PubMed PMID
Rare
Rare
Usually don't see beta elimination of phosphate
Rare
IonSource
Misc. URL
http://www.ionsource.com/Card/phos/phos.htm
AA0037
RESID
AA0033
RESID
AA0038
RESID
AA0039
RESID
AA0222
RESID
PHOS
FindMod
AA0034
RESID
AA0036
RESID
AA0035
RESID
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.
beta-elimination
beta-elimination
beta-elimination
Pyro-carboxymethyl as a delta from Carboxymethyl-Cys
didehydroalanine
C-terminal imide
Prompt loss of phosphate from phosphorylated residue
D-Succinimide
DHAS
FindMod
AA0303
RESID
AA0302
RESID
AA0181
RESID
AA0182
RESID
DHB
FindMod
9276974
PubMed PMID
Carboxymethyl-Cys cyclization (N-terminus)
Carbamidomethyl-Cys cyclization (N-terminus)
12643538
PubMed PMID
J. Proteome Res. 1, 181-187 (2002)
Journal
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.
AA0031
RESID
Miller et.al. Arch. Biochem. Biophy. (1993) 301, 41-52.
Journal
8442665
PubMed PMID
PYRE
FindMod
AA0031
RESID
PYRR
FindMod
10446193
PubMed PMID
Sherman, N. E., Yates, N. A., Shabanowitz, J., Hunt, D. F., Jeffery, W. A., Bartlet-Jones, M., and Pappin, D. J. C. (1995) Proceedings of the 43rd ASMS Conference on Mass Spectrometry and Allied Topics, May 21-26, 1995, Atlanta, GA
Journal
Proton replaced by sodium cation
11760118
PubMed PMID
methyl ester
METH
FindMod
AA0318
RESID
AA0338
RESID
AA0064
RESID
AA0061
RESID
AA0063
RESID
AA0065
RESID
AA0069
RESID
AA0336
RESID
AA0305
RESID
AA0272
RESID
AA0076
RESID
AA0071
RESID
AA0070
RESID
AA0073
RESID
AA0234
RESID
AA0273
RESID
AA0317
RESID
AA0337
RESID
AA0299
RESID
AA0072
RESID
11875433
PubMed PMID
AA0105
RESID
Cysteine sulfenic acid
Proline oxidation to glutamic semialdehyde
Hydroxyglycine derivative in amidation pathway
HYDR
FindMod
AA0322
RESID
11212008
PubMed PMID
11120890
PubMed PMID
DOPA
FindMod
CSEA
FindMod
14661084
PubMed PMID
AA0026
RESID
Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.
Journal
15569593
PubMed PMID
AA0205
RESID
AA0215
RESID
Lagerwerf FM, van de Weert M, Heerma W, Haverkamp J, Rapid Commun Mass Spectrom. 1996;10(15):1905-10
Journal
AA0029
RESID
AA0030
RESID
9004526
PubMed PMID
AA0028
RESID
11461766
PubMed PMID
AA0027
RESID
AA0235
RESID
AA0146
RESID
14661085
PubMed PMID
12781462
PubMed PMID
2057999
PubMed PMID
DIMETH
FindMod
AA0311
RESID
AA0068
RESID
14570711
PubMed PMID
AA0067
RESID
12964758
PubMed PMID
AA0075
RESID
AA0066
RESID
J. Hirota et. al., Rapid Commun. Mass Spectrom., 17 371-6 (2003)
Journal
Role of arginine and its methylated derivatives in cancer biology and treatment
Misc. URL
http://www.cancerci.com/content/1/1/3
AA0074
RESID
AA0062
RESID
12590383
PubMed PMID
TRIMETH
FindMod
Explanation of why RESID gives the delta as 43 Da
Misc. URL
http://www.ebi.ac.uk/RESID/faq.html#q12
Methyl methanethiosulfonate
MMTS
J. A. Kowalak and K. A. Walsh, Protein Science (1996) 5: 1625-1632
Journal
AA0232
RESID
TRC data sheet
Misc. URL
http://www.trc-canada.com/white_papers.lasso
Applied Biosystems iTRAQ(TM) Reagents Chemistry Reference Guide Part Number 4351918 Rev. A
Misc. URL
http://docs.appliedbiosystems.com/pebiodocs/04351918.pdf
AA0320
RESID
8844851
PubMed PMID
AA0101
RESID
BMTH
FindMod
Sulfitolysis
AA0362
RESID
AA0361
RESID
SULF
FindMod
AA0171
RESID
Medzihradszky et al., Mol. Cell. Proteomics 2004, 3, 429-440
Journal
14752058
PubMed PMID
AA0172
RESID
glycation
glycation
Fructose
Glucose
Galactose
Mannose
GLUC
FindMod
15279557
PubMed PMID
AA0152
RESID
AA0157
RESID
AA0327
RESID
AA0217
RESID
CMAN
FindMod
PDOC00168
Prosite
AA0118
RESID
LIPY
FindMod
3522581
PubMed PMID
This group is normally a substituent on N6 of a lysine residue of an enzyme or other protein
GLCN
FindMod
AA0151
RESID
AA0154
RESID
3086323
PubMed PMID
AA0155
RESID
The amine derivative of a hexose formed by replacing a hydroxyl group with an amino group.(+acetyl group)
15609361
PubMed PMID
AA0102
RESID
FARN
FindMod
PDOC00008
Prosite
AA0059
RESID
AA0307
RESID
AA0078
RESID
MYRI
FindMod
Biochemistry; D.Voet and J.G.Voet WILEY(p728)
Book
AA0119
RESID
PLP
FindMod
The co-enzyme derivative of vitamin B6. Forms Schiff\'s bases of substrate amino acids during catalysis of transamination, decarboxylation and racemisation reactions.
AA0080
RESID
AA0079
RESID
AA0106
RESID
AA0077
RESID
PALM
FindMod
AA0339
RESID
AA0060
RESID
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.
AA0104
RESID
15609361
PubMed PMID
GERA
FindMod
AA0150
RESID
PPAN
FindMod
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.
AA0143
RESID
Structure
Misc. URL
http://www.aw-bc.com/mathews/EF/FAD.GIF
AA0144
RESID
AA0145
RESID
AA0221
RESID
FAD
FindMod
10356335
PubMed PMID
homoarginine
11078590
PubMed PMID
ASMS 2001 abstract
Misc. URL
http://www.indiana.edu/~reillyjp/ASMS2001posters/beardsley_poster.pdf
11821862
PubMed PMID
11085420
PubMed PMID
Anal. Biochem. 287, p110-117, 2000
Journal
Specific for sidechain of lysine. Does not modify the N-termini except for glycine at a slower rate than the side chain of lysine.
11327326
PubMed PMID
Poli G, Schaur RJ., IUBMB Life 2000 Oct-Nov;50(4-5):315-21
Journal
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.
glucuronosyl
AA0291
RESID
AA0058
RESID
Lin, T.S. Kolattukudy, P.E., Eur. J. Biochem. 106, 341-351, 1980
Journal
7398618
PubMed PMID
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
3083866
PubMed PMID
8344916
PubMed PMID
AA0229
RESID
GLUT
FindMod
N-trideuteriumacetoxy
11857757
PubMed PMID
11999733
PubMed PMID
12175151
PubMed PMID
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
Journal
Global internal standard technology for comparative proteomics. Chakraborty, Asish; Regnier, Fred E.. Department of Chemistry, Purdue University, West Lafayette, IN, USA. Journal of Chromatography, A (2002), 949(1-2), 173-184.
Journal
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
Journal
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
Journal
12175151
PubMed PMID
11999733
PubMed PMID
11857757
PubMed PMID
Global internal standard technology for comparative proteomics. Chakraborty, Asish; Regnier, Fred E.. Department of Chemistry, Purdue University, West Lafayette, IN, USA. Journal of Chromatography, A (2002), 949(1-2), 173-184.
Journal
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
Journal
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
Journal
Global internal standard technology for comparative proteomics. Chakraborty, Asish; Regnier, Fred E.. Department of Chemistry, Purdue University, West Lafayette, IN, USA. Journal of Chromatography, A (2002), 949(1-2), 173-184.
Journal
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
Journal
11857757
PubMed PMID
12175151
PubMed PMID
11999733
PubMed PMID
N-(4-trimethylammoniumbutanoxy)-NHS
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
Journal
11857757
PubMed PMID
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
Journal
11857757
PubMed PMID
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
Journal
11857757
PubMed PMID
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
Journal
11857757
PubMed PMID
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
Journal
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
Journal
12175151
PubMed PMID
11857757
PubMed PMID
AA0130
RESID
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
Journal
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
Journal
11857757
PubMed PMID
12175151
PubMed PMID
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
Journal
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
Journal
11857757
PubMed PMID
12175151
PubMed PMID
http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB
Misc. URL
15174056
PubMed PMID
Yoo, Byoung-Sam; Regnier, Fred E. Electrophoresis (2004), 25(9), 1334-1341
Journal
Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.
Journal
9252331
PubMed PMID
10717661
PubMed PMID
Could also be classed as chemical derivative
Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.
Journal
9252331
PubMed PMID
Could also be classed as chemical derivative
Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.
Journal
9252331
PubMed PMID
Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.
Journal
Degradation of the amino acids Isoleucine, Leucine and Tryptophan
Misc. URL
http://www.lbqp.unb.br/bioq/htm/aulas2D/deg_aa_ile_leu_trp.htm?reload_coolmenus
9252331
PubMed PMID
Reduction of Schiff base formed between K amino group and acetaldehyde
11212008
PubMed PMID
Arginine oxidation to gamma-glutamyl semialdehyde
Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.
Journal
Jesus Requena, Chien-Chung Chao, Rodney L. Levine, and Earl R. Stadtman, Glutamic and aminoadipic semialdehydes are the main carbonyl products of metal-catalyzed oxidation of proteins, PNAS 98 69-74 (2001)
Journal
http://www.pnas.org/cgi/content/full/98/1/69
9252331
PubMed PMID
1680314
PubMed PMID
14678012
PubMed PMID
Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.
Journal
9252331
PubMed PMID
9750125
PubMed PMID
Poster abstract P-48
Misc. URL
http://www.wzw.tum.de/proteomik/forum2003/Posters-Abstracts.pdf
Poster abstract P-48
Misc. URL
http://www.wzw.tum.de/proteomik/forum2003/Posters-Abstracts.pdf
Introduction to Protein Labeling
Misc. URL
http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB
EZ-Link Sulfo-NHS-Biotin Reagents
Misc. URL
http://www.piercenet.com/Products/Browse.cfm?fldID=8D38BA83-EFDC-421A-853F-E96EBA380612
EZ-Link Maleimide PEOn-Biotin (n = 2 and 11)
Misc. URL
http://www.piercenet.com/Products/Browse.cfm?fldID=01031005
2-methoxy-4,5-dihydro-1H-imidazole derivative
Lys imidazole
11746907
PubMed PMID
Rapid Communications in Mass Spectrometry, Volume 15, Issue 24 , Pages 2387 - 2392
Journal
http://dx.doi.org/10.1002/rcm.517
Agilent Lys Tag 4H Reagent Kit
Misc. URL
http://www.chem.agilent.com/cag/lystag.asp
Poster: Kelly Zhang, Gordon Nicol, Nina Zolotarjova, Cory Szafranski, Jerome Bailey, Liang-Sheng Yang, and Barry Boyes
Misc. URL
http://www.chem.agilent.com/cag/other/IMTHUPO2003.pdf
2-methoxy-4,5-dihydro-1H-imidazole derivative
Rapid Communications in Mass Spectrometry, Volume 15, Issue 24 , Pages 2387 - 2392
Journal
http://dx.doi.org/10.1002/rcm.517
Agilent Lys Tag 4H Reagent Kit
Misc. URL
http://www.chem.agilent.com/cag/lystag.asp
11746907
PubMed PMID
Poster: Kelly Zhang, Gordon Nicol, Nina Zolotarjova, Cory Szafranski, Jerome Bailey, Liang-Sheng Yang, and Barry Boyes
Misc. URL
http://www.chem.agilent.com/cag/other/IMTHUPO2003.pdf
http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB
Misc. URL
Yoo, Byoung-Sam; Regnier, Fred E. Electrophoresis (2004), 25(9), 1334-1341
Journal
8839040
PubMed PMID
9252331
PubMed PMID
Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.
Journal
ICAT page from the Royal Society of Chemistry
Misc. URL
http://www.chemsoc.org/exemplarchem/entries/2002/proteomics/icat.htm
Applied Biosystems product page
Misc. URL
https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600902
Cleavable ICAT Reagent Kit for Protein Labeling
Misc. URL
http://docs.appliedbiosystems.com/pebiodocs/04333373.pdf
7744761
PubMed PMID
Lys modification is formation of Schiff base.
Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.
Journal
9252331
PubMed PMID
AA0121
RESID
ALLYS
FindMod
9252331
PubMed PMID
11120890
PubMed PMID
Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.
Journal
Cleavable ICAT Reagent Kit for Protein Labeling
Misc. URL
http://docs.appliedbiosystems.com/pebiodocs/04333373.pdf
Applied Biosystems product page
Misc. URL
https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600902
ICAT page from the Royal Society of Chemistry
Misc. URL
http://www.chemsoc.org/exemplarchem/entries/2002/proteomics/icat.htm
only with Listeria monocytogenes (gram-positive bacteria)
AA0021
RESID
10825024
PubMed PMID
8758896
PubMed PMID
CysNEM
reaction
Misc. URL
http://www.chemistry.ucsc.edu/~fink/231/Image118.gif
12777388
PubMed PMID
11813307
PubMed PMID
J. Biol. Chem 2002 vol277 pp17048-17056
Journal
11861642
PubMed PMID
Reference http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB
Misc. URL
http://web.indstate.edu/thcme/mwking/nitrogen-metabolism.html#urea
Misc. URL
http://web.indstate.edu/thcme/mwking/nitrogen-metabolism.html#urea
Misc. URL
http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB
Misc. URL
glycineglycine
Grou et al., J Biol Chem. 2008 Mar 22; Epub
Journal
http://www.jbc.org/cgi/content/abstract/M800402200v1
Wang et al., J Cell Biol. 2007 May 21;177(4):613-24
Journal
http://www.ncbi.nlm.nih.gov/pubmed/17502423
12872131
PubMed PMID
The Ubiquitin System for Protein Modification and Degradation
Misc. URL
http://www.nottingham.ac.uk/biochemcourses/students/ub/ubindex.html
The two glycine residues left on ubiquitinylated lysine after tryptic digestion
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)
Can occur under CNBr cleavage conditions (70% HCOOH)
Can occur under CNBr cleavage conditions (70% HCOOH)
Can occur under CNBr cleavage conditions (70% HCOOH)
AA0211
RESID
15799070
PubMed PMID
AA0021
RESID
FORM
FindMod
AA0384
RESID
AA0057
RESID
AA0384
RESID
Harbury glyco-ICAT C12
Silverman, Harbury, J. Biol. Chem. 2002, 277, 34, pp. 30968-30975
Journal
12185208
PubMed PMID
Harbury glyco-ICAT C13
Silverman, Harbury, J. Biol. Chem. 2002, 277, 34, pp. 30968-30975
Journal
12185208
PubMed PMID
11710128
PubMed PMID
3155470
PubMed PMID
Lomant, A.J. and Fairbanks, G., J.Mol. Biol. 104, 243-261 (1976)
Journal
Lee,W.T. and Conrad, D.H. 1985, J. Immunol. 134:518
Journal
957432
PubMed PMID
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.
1093385
PubMed PMID
5-iodoacetamidofluorescein, [63368-54-7]
CAS Registry
3578767
PubMed PMID
Gorman, J. J., Eur. J. Biochem 1987, 168-9
Journal
Gorman, J. J., Anal Biochem 1984, 160, 376
Journal
3311742
PubMed PMID
2026710
PubMed PMID
15627961
PubMed PMID
15627961
PubMed PMID
2026710
PubMed PMID
15627961
PubMed PMID
myristoyl with one double bond
C14:1 acylation
Neubert TA, Johnson RS, Hurley JB, Walsh KA (1992). The rod transducin alpha subunit amino terminus is heterogeneously fatty acylated. J Biol Chem. 267(26):18274-7.
Journal
1326520
PubMed PMID
Found on vision signal transduction proteins
9252331
PubMed PMID
Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.
Journal
myristoyl with 2 double bonds
C14:2 fatty acylation
Neubert TA, Johnson RS, Hurley JB, Walsh KA (1992). The rod transducin alpha subunit amino terminus is heterogeneously fatty acylated. J Biol Chem. 267(26):18274-7.
Journal
1326520
PubMed PMID
Found on vision signal transduction proteins
Julka,S.Regnier,F.E Anal Chem. 2004 Oct 1;76(19):5799-806.
Journal
15456300
PubMed PMID
Man5
Core structure of high-mannose N-linked oligosaccharides
dansyl chloride [605-65-2]
CAS Registry
Virtual Modification for MS/MS of a-type ions
corrected by subtraction of a further -O at 8.6.2010
Decarboxylation of C-terminus as reaction inside the mass spectrometer
D. Suckau, A. Resemann, Anal. Chem., 75(21):5817-24 (2003)
Journal
14588022
PubMed PMID
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.
ASMS 2004 abstract
Misc. URL
http://www.indiana.edu/~reillyjp/ASMS2004/janecki_Ext-Abs%20Amidination.pdf
12643539
PubMed PMID
6273432
PubMed PMID
Saito T., Itoh T.; Journal of dairy Science, 75 (1992). p1768.
Journal
chitobiose core
Saito T., Itoh T.; Journal of dairy Science, 75 (1992). p1768.
Journal
Selenocysteine conventionally represented by 1 letter code U
12148805
PubMed PMID
AA0022
RESID
NBS reagent heavy
Rapid Communications in Mass Spectrometry, 17, 1642-1650 (2003)
Journal
12845591
PubMed PMID
Identifying and quantifying in vivo methylation sites by heavy methyl SILAC, Shao-En Ong et al., Nature methods 1(2) 2004, 1-8
Journal
Identifying and quantifying in vivo methylation sites by heavy methyl SILAC, Shao-En Ong et al., Nature Methods 1(2) 1-8
PubMed PMID
Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates. Boersema PJ, Aye TT, van Veen TA, Heck AJ, Mohammed S. Proteomics. 2008 Nov;8(22):4624-32
Journal
2-nitrobenzenesulfenyl
12845591
PubMed PMID
Rapid Communications in Mass Spectrometry, 17, 1642-1650 (2003)
Journal
Anal. Biochem. 1992, 205:151-158
Journal
1443554
PubMed PMID
Conversion of glycosylated asparagine residues upon deglycosylation with PGNase F in 18O labelled water.
(3-acrylamidopropyl)trimethylammonium
15283597
PubMed PMID
Secondary adduct - much less common as C
Secondary adduct - much less common as C
Primary adduct formed
Butylated Hydroxytoluene
9448752
PubMed PMID
BHT metabolism has been studied in rats and mice in relation to tumor promotion.
2005 ASMS poster Presentation TP 527
Other
Phosphoserine to S-ethylcystine\r\nvia Beta elimination/Michael addition of ethylthiol
b-elimination thiol derivatization
12216740
PubMed PMID
DAET = 2-(dimethylamino)ethanethiol; The phosphorylation to amine is the beta elimination of phosphate and Michael addition of 2-(dimethylamino)ethanethiol to the site.
Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.
Journal
9252331
PubMed PMID
Used in SILAC experiment
heavy tyrosine
Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181
Journal
Silac introduction
Misc. URL
http://www.pil.sdu.dk/silac_intro.htm
12716131
PubMed PMID
Used in SILAC experiment
heavy phosphotyrosine
12716131
PubMed PMID
Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181
Journal
Silac introduction
Misc. URL
http://www.pil.sdu.dk/silac_intro.htm
Used in SILAC experiment
Used in SILAC experiment
Used in SILAC experiment
Used in SILAC experiment
Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181
Journal
Silac introduction
Misc. URL
http://www.pil.sdu.dk/silac_intro.htm
12716131
PubMed PMID
HPG arginine
11698400
PubMed PMID
11914093
PubMed PMID
11698400
PubMed PMID
OH-PGO and PGO react with arginine at a stoichiometry of 2:1
(3-acrylamidopropyl)trimethylammonium
15283597
PubMed PMID
Double O18 (C-term)
11467524
PubMed PMID
Waters Application Note 930494
Misc. URL
http://www2.waters.com/watprod.nsf/newdocs/930494
14997490
PubMed PMID
Hochleitner, E. O. et al, Proteomics 2004, 4, 669-676,
Journal
reductive amination
Anal Chem 2003. 75, 6843
Journal
14670044
PubMed PMID
Jue-Liang Hsu, Sheng-Yu Huang, and Shu-Hui Chen. Stable-Isotope based Multiplex Labeling Coupled with LC-MS/MS, HUPO 3rd ANNUAL WORLD CONGRESS, Bejing (China) 2004
Book
11507762
PubMed PMID
12766232
PubMed PMID
Acrolein94, FDP
Acrolein56
10825247
PubMed PMID
15541752
PubMed PMID
Acrolein38
Acrolein76
Acrolein112
AA0237
RESID
AA0169
RESID
Structure
Misc. URL
http://betelgeuse.u-strasbg.fr/DocPARP/DocPARG/images/Structure-pADPR.jpg
AA0168
RESID
AA0231
RESID
15842200
PubMed PMID
AA0295
RESID
ADP
FindMod
12766232
PubMed PMID
Low abundance
AKA iTRAQ4plex116/7
Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry
Applied Biosystems Chemistry Reference Guide
Misc. URL
http://docs.appliedbiosystems.com/pebiodocs/04351918.pdf
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
11283024
PubMed PMID
BROM
FindMod
AA0179
RESID
AA0180
RESID
AA0173
RESID
AA0176
RESID
AA0175
RESID
AA0174
RESID
9033387
PubMed PMID
9252331
PubMed PMID
Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.
Journal
Yoo, Byoung-Sam; Regnier, Fred E. Electrophoresis (2004), 25(9), 1334-1341.
Journal
15828771
PubMed PMID
alkaline phosphatase to dephosphorylate
alkaline phosphatase to dephosphorylate
alkaline phosphatase to dephosphorylate
digesting in labelled water
H2 18O Alkaline Phosphatase
11467524
PubMed PMID
Used in SILAC experiment
heavy lysine
Silac introduction
Misc. URL
http://www.pil.sdu.dk/silac_intro.htm
12716131
PubMed PMID
12110917
PubMed PMID
N-terminal / lysine sulfonation
Wang et al. 2004. Rapid Commun Mass Spectrom. 18(1):96-102
Journal
Chen et. al. Rapid Commun Mass Spectrom. 2004;18(2):191-8.
Journal
Shimadzu application note
Misc. URL
http://www.shimadzu-biotech.net/literature/application_note/202_1.pdf
14745769
PubMed PMID
14689565
PubMed PMID
16526082
PubMed PMID
Under construction
Misc. URL
http://www.targetdiscovery.com/index.php?topic=prod.idbe
Target discovery , Inc. IDBEST IGBP user manual
Other
15549660
PubMed PMID
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.
15549660
PubMed PMID
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.
Used in SILAC experiment
Silac introduction
Misc. URL
http://www.pil.sdu.dk/silac_intro.htm
12716131
PubMed PMID
Used in AQUA experiment
Silac introduction
Misc. URL
http://www.pil.sdu.dk/silac_intro.htm
12771378
PubMed PMID
for SILAC expt
Trideuteration
Silac introduction
Misc. URL
http://www.pil.sdu.dk/silac_intro.htm
Used in AQUA experiment
Result of conversion of 13C6, 15N4 arginine to 13C5, 15N1 proline
SILAC label used in COFRADIC
12771378
PubMed PMID
b-elimination PET derivatisation
Manfredo Quadroni in: ''Proteome Research: Mass Spectrometry (ed. P.James)'' pp 187-206
Book
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.
Ettan CAF MALDI
Anal.Chem 75(7):156A-165A
Journal
15732931
PubMed PMID
16046801
PubMed PMID
N-terminal sulfonation of diglycine to detect ubiquitination sites
Partis MD et al. 1983 J Prot Chem 2 263-277
Journal
AA0230
RESID
10442087
PubMed PMID
NTRY
FindMod
15688001
PubMed PMID
Protein which is posttranslationally modified by the attachment of a nitric oxide group on the sulfur atom of one or more cysteine residues.
Primary site of modification
Biochim Biophys Acta. 1996 Feb 16; 1299(3):353-7
Journal
8597590
PubMed PMID
Potential protein modification when using AEBSF (Pefabloc) as a serine protease inhibitor.
reduced form of oxidation product
from reaction of SH group with iodoethanol
reduced form of oxidation product
Hydroxy ethyl
15351294
PubMed PMID
J Biol Chem. 1995 Apr 28;270(17):10017-26.
Journal
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. Anal Biochem. 2004 Oct 1;333(1):174-81
Journal
7730303
PubMed PMID
SILAC+PTM
SILAC Introduction
Misc. URL
http://www.pil.sdu.dk/silac_intro.htm
DIMETH
FindMod
hydroxymethylvinyl ketone
11743741
PubMed PMID
9629898
PubMed PMID
Effects of tryptic peptide esterification in MALDI mass spectrometry Anal. Chem. 2005, 77, 4185-4193
Journal
http://pubs.acs.org/doi/abs/10.1021/ac0481250
Structure
Misc. URL
http://commons.wikimedia.org/wiki/Image:Coenzyme_a.png
AA0306
RESID
Glutamate methyl ester
P02942
Swiss-Prot
DEAME
FindMod
Anal Chem. 2007 Jan 15;79(2):673-81.
Journal
DIMETP
FindMod
Nature. 2004 Nov 18;432(7015):353-60. Epub 2004 Nov 03
Journal
15525938
PubMed PMID
C-Terminal/Glutamate/Aspartate sulfonation
ASMS 2005: Panchaud et al. (Poster ThP 509) ''Combining protein identification and quantitation: C-terminal isotope-coded tagging''
Other
C-Terminal/Glutamate/Aspartate sulfonation
ASMS 2005: Panchaud et al. (Poster ThP 509) ''Combining protein identification and quantitation: C-terminal isotope-coded tagging''
Other
9254591
PubMed PMID
EDC-coupled modification of D, E and C-terminus
EDC-coupled modification of D, E and C-terminus
EDC-coupled modification of D, E and C-terminus
Introduction to Protein Labeling
Misc. URL
http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB
EDC crosslinker is used to couple biotin PEO-amine to carboxyl groups or 5\' phosphate groups
7949339
PubMed PMID
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.
EZ-Link Biotin-HPDP (N-(6-(Biotinamido)hexyl)-3'-(2'-pyridyldithio)-propionamide
Misc. URL
http://www.piercenet.com/Products/Browse.cfm?fldID=01031002
10695144
PubMed PMID
Used in base/residue interactions (in principle?)
Used in base/residue interactions (observed)
Used in base/residue interactions (in principle?)
UV induced cross-link product of Iodo-U-amp with WFY
6540775
PubMed PMID
11112526
PubMed PMID
11567090
PubMed PMID
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).
3-thiopropanoyl moiety from reduced DSP crosslinker or NHS-SS-biotin, modified with Iodoacetamide
Peirce MJ, Wait R, Begum S, Saklatvala J, Cope AP (2004) Mol Cell Proteomics 3: 56-65
Journal
Swaim CL, Smith JB, Smith DL (2004) J Am Soc Mass Spectrom 15:736-749
Journal
15121203
PubMed PMID
10906242
PubMed PMID
deoxyhexose
15189151
PubMed PMID
Mormann, M., Macek, B., Gonzalez de Peredo, A., Hofsteenge, J., Peter-Katalinic, J. (2004). ''Structural studies on protein O-fucosylation by electron capture dissoziation.'' International Journal of Mass Spectrometry 234:11-21
Journal
11344537
PubMed PMID
esterification of carboxylic acids using D3-Methanolic HCl
Gamma-carboxylation
Gamma-carboxylation
AA0114
RESID
GGLU
FindMod
AA0363
RESID
AA0032
RESID
3802193
PubMed PMID
AA0304
RESID
mBromobimane
7856876
PubMed PMID
Vitamin k3 (Q)
15939799
PubMed PMID
12442261
PubMed PMID
AA0025
RESID
16078144
PubMed PMID
Amersham (GE Healthcare) instruction leaflet 25800983PL Rev-B, 2003
Other
12872219
PubMed PMID
MDA62
usually major adduct formed from malondialdehyde (MDA) with the amino group of lysine residues
Malondialdehyde (MDA) adduct
5-hydro-5-methylimidazol-4-one, Methylglyoxal adduct
MDA54
Uchida K, Sakai K, Itakura K, Osawa T, Toyokuni S. 1977. Protein modification by lipid peroxidation products: formation of malondialdehyde-derived N(epsilon)-(2-propenol)lysine in proteins. Arch Biochem Biophys. 346(1):45-52
Journal
Chemistry of Protein Conjugation and Crosslinking by Shan S. Wong, 1991, pg.32
Book
Invitrogen X-link reagent
Pierce data sheet
Misc. URL
http://www.piercenet.com/files/0668ss5.pdf
770170
PubMed PMID
imidoester cross-linker
O-ethyl-N-(biotinamidopentyl)decanamido phosphonate
Liu, Patricelli and Cravatt; Activity-based protein profiling: The serine hydrolases. Proc Natl Acad Sci USA 96, 14694-14699 (1999)
Journal
Schopfer, Champion, Tamblyn, Thompson and Lockridge; Characteristic mass spectral fragments of the organophosphorus agent FP-biotin and FP-biotinylated peptides from trypsin and bovine albumin (Tyr410). Anal Biochem 345, 122-132 (2005)
Journal
10611275
PubMed PMID
Grigoryan, Li, Xue, Grigoryan, Schopfer and Lockridge; Mass spectral characterization of organophosphate-labeled lysine in peptides. Analytical Biochemistry 394, 92-100 (2009)
Journal
FP-biotin was designed to label the active site serine of serine esterases/proteases.
Thiophos-biotin disulfide
O-isopropyl-N-biotinylaminohexyl phosphonate
Higson, Ferguson and Nikolaev; Synthesis of 6-N-biotinylaminohexyl isopropyl phosphorofluoridate: A potent tool for the inhibition/isolation of serine esterases and proteases. Synthesis 3, 407-409 (1999)
Journal
Commercially available from Toronto Research Chemicals Inc, as of 2005. Designed to label the active site serine of serine esterases/proteases.
Crabb JW et al, Protein Sci. 2002;11: 831
PubMed PMID
Michael addition adduct of 4-hydroxynonenal with histidine, cystein and lysine residues stabilized by reduction with NaBH4
http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB
Misc. URL
Yoo, Byoung-Sam; Regnier, Fred E. Electrophoresis (2004), 25(9), 1334-1341
Journal
Rapid Commun. Mass Spectrom. 2002; 16: 999-1001
Journal
Main; Mode of action of anticholinesterases. Pharmac Ther 6, 579-628 (1979)
Journal
Grigoryan, Li, Xue, Grigoryan, Schopfer and Lockridge; Mass spectral characterization of organophosphate-labeled lysine in peptides. Analytical Biochemistry 394, 92-100 (2009)
Journal
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.
Main; Mode of action of anticholnesterases. Pharmac Ther 6, 579-628 (1979)
Journal
Created by auto-catalytic dealkylation of the O-Diisopropylphosphate adduct.
Use when labelling post-digest
Use when labelling pre-digest
Bruker Daltonics order reference
Misc. URL
http://www.bdal.de/life-science-tools/care-consumables-more/icpl-kit.html
Schmidt A, Kellermann J, Lottspeich F (2005): A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5: 4-15
Journal
Attention: As the digest is typically applied AFTER ICPL_light/heavy labeling, only ProteinN-term labeling and Lys-specific labeling is applied.
18653769
PubMed PMID
http://www.ncbi.nlm.nih.gov/pubmed/18653769
Use when labelling pre-digest
Use when labelling post-digest
Bruker Daltonics order reference
Misc. URL
http://www.bdal.de/life-science-tools/care-consumables-more/icpl-kit.html
Schmidt A, Kellermann J, Lottspeich F (2005): A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5: 4-15.
Journal
Attention: As the digest is typically applied AFTER ICPL_light/heavy labeling, only ProteinN-term labeling and Lys-specific labeling is applied.
Observed
15489230
PubMed PMID
AA0025
RESID
AA0040
RESID
DIPH
FindMod
AA0103
RESID
FAR0
FindMod
AA0107
RESID
DIAC
FindMod
AA0115
RESID
CETH
FindMod
AA0116
RESID
HYPU
FindMod
AA0120
RESID
AA0122
RESID
AA0127
RESID
PYRUC
FindMod
Pyro-carbamidomethyl as a delta from Carbamidomethyl-Cys
N-Succinimide
oxobutanoic acid from N term Thr
pyruvic acid from N-term ser
AA0127
RESID
PYRUS
FindMod
AA0129
RESID
OXOB
FindMod
phycobiliviolin
AA0258
RESID
AA0131
RESID
phycocyanobilin and phycobiliviolin have different structures but the same empirical formula
AA0132
RESID
AA0133
RESID
AA0329
RESID
AA0135
RESID
AA0276
RESID
AA0142
RESID
AA0147
RESID
AA0148
RESID
TOPA
FindMod
AA0153
RESID
AA0158
RESID
AA0159
RESID
AA0160
RESID
AA0161
RESID
AA0162
RESID
AA0163
RESID
AA0164
RESID
AA0165
RESID
AA0166
RESID
AA0167
RESID
AA0170
RESID
AA0177
RESID
THRN
FindMod
AA0178
RESID
THRX
FindMod
AA0181
RESID
oxoalanine formylglycine
Lactone formation from C-terminal hydroxylysine
oxoalanine
AA0183
RESID
Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.
Journal
AA0185
RESID
9252331
PubMed PMID
AA0365
RESID
OXOAS
FindMod
DHY
FindMod
15705169
PubMed PMID
formylglycine
AA0185
RESID
OXOAC
FindMod
Dierks T, Miech C, Hummerjohann J, Schmidt B, Kertesz MA, von Figura K. Posttranslational formation of formylglycine in prokaryotic sulfatases by modification of either cysteine or serine. J. Biol. Chem. 1998; 273: 25 560
Journal
18722427
PubMed PMID
17450134
PubMed PMID
AA0186
RESID
J. Biol. Chem., Vol. 277, Issue 48, 46140-46144, November 29, 2002
Journal
12356754
PubMed PMID
AA0371
RESID
AA0227
RESID
AA0203
RESID
AA0267
RESID
12356754
PubMed PMID
J. Biol. Chem., Vol. 277, Issue 48, 46140-46144, November 29, 2002
Journal
AA0207
RESID
AA0212
RESID
AA0353
RESID
AA0220
RESID
AA0352
RESID
FMNH
FindMod
AA0223
RESID
ARCH
FindMod
AA0325
RESID
AA0228
RESID
AA0236
RESID
AA0248
RESID
AA0252
RESID
AA0256
RESID
AA0264
RESID
THIOG
FindMod
AA0265
RESID
beta-thiolation
AA0269
RESID
CYSP
FindMod
AA0287
RESID
AA0274
RESID
AA0275
RESID
AA0277
RESID
AA0281
RESID
AA0375
RESID
trihydroxyphenylalanine
tryptophan oxidation to formylkynurenin
phenylalanine oxidation to dihydroxyphenylalanine
Sulphone
sulfinic acid
12686488
PubMed PMID
AA0262
RESID
CSIA
FindMod
MSONE
FindMod
DIHYDR
FindMod
9252331
PubMed PMID
AA0251
RESID
AA0370
RESID
Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.
Journal
AA0282
RESID
AA0369
RESID
AA0263
RESID
Hyun Ae Woo, et. al., Science Vol. 300. no. 5619, pp. 653 - 656
Journal
AA0386
RESID
AA0290
RESID
OCTA
FindMod
AA0296
RESID
AA0297
RESID
AA0308
RESID
PALE
FindMod
17141155
PubMed PMID
AA0309
RESID
CHOL
FindMod
AA0312
RESID
AA0316
RESID
CHDH
FindMod
AA0321
RESID
PYRK
FindMod
AA0324
RESID
AA0328
RESID
AA0333
RESID
AA0334
RESID
AA0335
RESID
AA0350
RESID
AA0349
RESID
FMN
FindMod
AA0351
RESID
FMNC
FindMod
AA0355
RESID
AA0359
RESID
TRIMETK
FindMod
Beta elimination of O-glycosylation under alkaline conditions followed by reduction
Beta elimination of O-glycosylation under alkaline conditions followed by reduction
Serine to Alanine
Threonine to a-aminobutyrate
AA0191
RESID
14235557
PubMed PMID
AA0373
RESID
AA0374
RESID
AA0387
RESID
AA0385
RESID
DECA
FindMod
12356754
PubMed PMID
J. Biol. Chem., Vol. 277, Issue 48, 46140-46144, November 29, 2002
Journal
J. Biol. Chem., Vol. 277, Issue 48, 46140-46144, November 29, 2002
Journal
12356754
PubMed PMID
Galactosamine
Glucosamine
Dimethyl pimelimidate
Imidoester Cross-linkers
Misc. URL
http://www.piercenet.com/files/0668ss5.pdf
Packman, L.C. and Perhan, R.N. (1982). Quaternary Structures the Pyruvate Dehydrogenase Multienzyme Complex of Bacillus Stearothermophilus Studies by a New Reversible Crosslinking Procedure with Bis(imidoesters). Biochem. 21, 5171-5175.
Journal
Hand, E.S., and Jencks, W.P. (1962). Mechanism of the reaction of imidoesters with amines. J. Am. Chem. Soc. 84, 3505-3514.
Journal
Dimethyl pimelimidate, reaction with both ends
Dimethyl pimelimidate, reaction with both ends
Dimethyl pimelimidate
Imidoester Cross-linkers
Misc. URL
http://www.piercenet.com/files/0668ss5.pdf
Hand, E.S., and Jencks, W.P. (1962). Mechanism of the reaction of imidoesters with amines. J. Am. Chem. Soc. 84, 3505-3514.
Journal
Packman, L.C. and Perhan, R.N. (1982). Quaternary Structures the Pyruvate Dehydrogenase Multienzyme Complex of Bacillus StearothermophilusStudies by a New Reversible Crosslinking Procedure with Bis(imidoesters). Biochem. 21, 5171-5175.
Journal
2081203
PubMed PMID
fluorescent derivative
N-terminal / lysine sulfonation
16526082
PubMed PMID
Lee et al, Rapid Commun Mass Spetrom 2004, 18, 3019-3027
Journal
J. Mass Spectrom. 2005; 40: 238-249
Journal
J. Mass Spectrom. 2005; 40: 238-249
Journal
Ahn, B., Rhee, S.G., and Stadtmann, E. R. (1987) Anal. Biochem.
Journal
pT gives beta-methylaminoethylcysteine
pS gives aminoethylcysteine
beta-methylaminoethylcysteine
Z. A. Knight et al, Nature Biotech., 21(9) 1047-1054 (2003)
Journal
Modification procedure used for phosphopeptide mapping
found in canned food products
Berger U, Oehme M, Girardin L., Fresenius J Anal Chem. 2001 Jan 2;369(2):115-23.
Journal
Found in canned food products
Cambridge Labs DLM-451
K4
For SILAC experiments
Amersham (GE Healthcare) instruction leaflet 25800983PL Rev-B, 2003
Other
12872219
PubMed PMID
Dehydroretronecine
16222722
PubMed PMID
primary adduct
t-butyl hydroxylated BHT
16533022
PubMed PMID
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
Under construction
Misc. URL
http://www.targetdiscovery.com/index.php?topic=prod.idbe
Target discovery , Inc. IDBEST IGBP user manual
Other
Chemistry of Protein Conjugation and Crosslinking by Shan S. Wong, 1991, pg.32
Book
Salomon RG. Antioxid Redox Signal. 2005 Jan-Feb;7(1-2):185-201.
Journal
Salomon RG. Chem Phys Lipids. 2005 Mar;134(1):1-20.
Journal
15650407
PubMed PMID
15752459
PubMed PMID
Pierce, A., Dewaal, E., Vanremmen, H., Richardson, A. & Chaudhuri, A. (2006). A Novel Approach for Screening the Proteome for Changes in Protein Conformation. Biochemistry 45, 3077-3085.
Journal
Jue-Liang Hsu, Sheng-Yu Huang, and Shu-Hui Chen. Stable-Isotope based Multiplex Labeling Coupled with LC-MS/MS, HUPO 3rd ANNUAL WORLD CONGRESS, Bejing (China) 2004
Other
J. Proteome Res. 2005, 4, 101-108.
Journal
Salomon RG. Antioxid Redox Signal. 2005 Jan-Feb;7(1-2):185-201.
Journal
Salomon RG. Chem Phys Lipids. 2005 Mar;134(1):1-20.
Journal
15650407
PubMed PMID
15752459
PubMed PMID
16335955
PubMed PMID
J Proteome Res. 2005 Nov-Dec;4(6):2099-108
Journal
16771548
PubMed PMID
Maillard reaction (first event)
Maillard reaction (first event)
lac
ANALYTICAL BIOCHEMISTRY 259, 152-161 (1998)
Journal
BIOCHIMECAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 236, 413-417 (1997)
Journal
Lactosylation of bovine Beta-Lactoglobulin
15650407
PubMed PMID
15752459
PubMed PMID
Salomon RG. Chem Phys Lipids. 2005 Mar;134(1):1-20.
Journal
Salomon RG. Antioxid Redox Signal. 2005 Jan-Feb;7(1-2):185-201.
Journal
Side reaction, low abundance
CLIP_TRAQ_single
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).
Side reaction, low abundance
CLIP_TRAQ_double
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).
15650407
PubMed PMID
15752459
PubMed PMID
Salomon RG. Chem Phys Lipids. 2005 Mar;134(1):1-20.
Journal
Salomon RG. Antioxid Redox Signal. 2005 Jan-Feb;7(1-2):185-201.
Journal
Maleimide-PEG-Biotin
EZ-Link Maleimide PEOn-Biotin
Misc. URL
http://www.piercenet.com/Products/Browse.cfm?fldID=01031005
EZ-Link Sulfo-NHS-Biotin Reagents
Misc. URL
http://www.piercenet.com/Products/Browse.cfm?fldID=8D38BA83-EFDC-421A-853F-E96EBA380612
photosensitive
fluorescein-NEM
9325338
PubMed PMID
11665566
PubMed PMID
Thiol-Reactive Probes
Misc. URL
http://probes.invitrogen.com/media/pis/mp00003.pdf
15795231
PubMed PMID
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.
9004526
PubMed PMID
More commonly seen as a neutral loss
Low abundance
Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry
Applied Biosystems Chemistry Reference Guide
Misc. URL
http://docs.appliedbiosystems.com/pebiodocs/04351918.pdf
Different channels have the same nominal mass but slightly different exact masses.
Low abundance
Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry
Applied Biosystems Chemistry Reference Guide
Misc. URL
http://docs.appliedbiosystems.com/pebiodocs/04351918.pdf
Different channels have the same nominal mass but slightly different exact masses.
Addition of LRGG
Low abundance
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).
Low abundance
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).
Cayman Chemical data sheet
Misc. URL
http://www.caymanchem.com/pdfs/10141.pdf
Cayman Chemical data sheet
Misc. URL
http://www.caymanchem.com/pdfs/10013.pdf
Nature Biotechnology 22, 450 - 454 (2004)
Journal
http://www.nature.com/nbt/journal/v22/n4/abs/nbt947.html
15004565
PubMed PMID
Nature Biotechnology 22, 450 - 454 (2004)
Journal
http://www.nature.com/nbt/journal/v22/n4/abs/nbt947.html
15004565
PubMed PMID
Low efficiency
Low efficiency
Low efficiency
Isotope-differentiated binding energy shift tags
Misc. URL
http://www.targetdiscovery.com/article.php?topic=crpc.prst&story=20060321132643690
Michael addition of nitro-linoleic acid to Cys and His
JBC 281(29):20450-63; 2006
Journal
Reversible post-translational modification of proteins by nitrated fatty acids
Michael addition of nitro-oleic acid to Cys and His
JBC 281(29):20450-63; 2006
Journal
Reversible post-translational modification of proteins by nitrated fatty acids
Use when labelling post-digest
Use when labelling pre-digest
Bruker Daltonics order reference
Misc. URL
http://www.bdal.de/life-science-tools/care-consumables-more/icpl-kit.html
Schmidt A, Kellermann J, Lottspeich F (2005): A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5: 4-15
Journal
15602776
PubMed PMID
Attention: As the digest is typically applied AFTER ICPL_light/heavy labeling, only ProteinN-term labeling and Lys-specific labeling is applied.
18653769
PubMed PMID
http://www.ncbi.nlm.nih.gov/pubmed/18653769
Low abundance
AKA iTRAQ8plex:13C(7)15N(1)
Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry
Other 4 channels have the same nominal mass but slightly different exact mass. For quantitation purposes, use this entry for all channels
Silac introduction
Misc. URL
http://www.pil.sdu.dk/silac_intro.htm
Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181
Journal
Used in SILAC experiment
heavy D9 lysine
Silac introduction
Misc. URL
http://www.pil.sdu.dk/silac_intro.htm
CDNLM-6810
Misc. URL
http://www.isotope.com/cil/products/displayproduct.cfm?prod_id=8635
Liu Z, Minkler P, and Sayre L. Chem. Res. Toxicology 2003 16 901-911
Journal
Mass Spectroscopic Characterization of Protein Modification by 4-Hydroxy-2-(E)-nonenal and 4-Oxo-2-(E)-nonenal.
Chemico-Biological Interactions 143-144(2003) 93-100.
Journal
Covalent adduction of nucleophilic amino acids by 4-hydroxynonenal and 4-oxononenal
Fidder, Hulst, Noort, Ruiter, van der Schans, Benschop and Langenberg; Retrospective detection of exposure to organophosphorus anti-cholinesterases: Mass spectrometric analysis of phosphylated human butyrylcholinestease. Chem. Res. Toxicol. 15, 582-590 (2002)
Journal
Main; Mode of action of anticholnesterases. Pharmac Ther 6, 579-628 (1979)
Journal
Created by auto-catalytic dealkylation of the O-Dimethylphosphate adduct.
Grigoryan, Li, Xue, Grigoryan, Schopfer and Lockridge; Mass spectral characterization of organophosphate-labeled lysine in peptides. Analytical Biochemistry 394, 92-100 (2009)
Journal
Fidder, Hulst, Noort, Ruiter, van der Schans, Benschop and Langenberg; Retrospective detection of exposure to organophosphorus anti-cholinesterases: Mass spectrometric analysis of phosphylated human butyrylcholinestease. Chem. Res. Toxicol. 15, 582-590 (2002)
Journal
Main; Mode of action of anticholnesterases. Pharmac Ther 6, 579-628 (1979)
Journal
Created by auto-catalytic dealkylation of the O-Diethylphosphate adduct.
Fidder, Hulst, Noort, Ruiter, van der Schans, Benschop and Langenberg; Retrospective detection of exposure to organophosphorus anti-cholinesterases: Mass spectrometric analysis of phosphylated human butyrylcholinestease. Chem. Res. Toxicol. 15, 582-590 (2002)
Journal
Main; Mode of action of anticholnesterases. Pharmac Ther 6, 579-628 (1979)
Journal
Created by auto-catalytic dealkylation of either the O-pinacolylmethylphosphonate adduct, or the O-isopropylmethylphosphonate adduct.
Fidder, Hulst, Noort, Ruiter, van der Schans, Benschop and Langenberg; Retrospective detection of exposure to organophosphorus anti-cholinesterases: Mass spectrometric analysis of phosphylated human butyrylcholinestease. Chem. Res. Toxicol. 15, 582-590 (2002)
Journal
Low abundance
Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry
Other 4 channels have the same nominal mass but slightly different exact mass. For quantitation purposes, use iTRAQ8plex for all channels
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
threo-1,4-dimercaptobutane-2,3-diol
Cleland's reagent
Methods Enzymol. 2006;415:113-33. Links rnIdentification of O-GlcNAc sites on proteins.Whelan SA, Hart GW.
PubMed PMID
17116471
Mol Cell Proteomics. 2002 Oct;1(10):791-804. rnMapping sites of O-GlcNAc modification using affinity tags for serine and threonine post-translational modifications.Wells L, Vosseller K, Cole RN, Cronshaw JM, Matunis MJ, Hart GW.
PubMed PMID
12438562
Proteomics. 2005 Feb;5(2):388-98. Links rnQuantitative analysis of both protein expression and serine / threonine post-translational modifications through stable isotope labeling with dithiothreitol.Vosseller K, Hansen KC, Chalkley RJ, Trinidad JC, Wells L, Hart GW, Burlingame AL.
PubMed PMID
15648052
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.
Tandem Mass Tag sixplex labelling kit Proteome Sciences
Tandem Mass Tag® and TMT® are registered Trademarks of Proteome Sciences plc.
Juergen.Schaefer@Proteomics.com
Other
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
Cleland's reagent
Methods Enzymol. 2006;415:113-33. Links rnIdentification of O-GlcNAc sites on proteins.Whelan SA, Hart GW.
PubMed PMID
17116471
Mol Cell Proteomics. 2006 May;5(5):923-34. Epub 2006 Feb 1. Links rnO-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry.Vosseller K, Trinidad JC, Chalkley RJ, Specht CG, Thalhammer A, Lynn AJ, Snedecor JO, Guan S, Medzihradszky KF, Maltby DA, Schoepfer R, Burlingame AL.
PubMed PMID
16452088
Mol Cell Proteomics. 2002 Oct;1(10):791-804. Mapping sites of O-GlcNAc modification using affinity tags for serine and threonine post-translational modifications.Wells L, Vosseller K, Cole RN, Cronshaw JM, Matunis MJ, Hart GW.
PubMed PMID
12438562
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.
Tandem Mass Tag Duplex labelling kit Proteome Sciences
Juergen.Schaefer@Proteomics.com
Other
Duplex-TMT® reagents 2TMT-126, 2TMT-127 Masses of the TMT® fragment ions to be quantified: 126.1283 127.1316
Tandem Mass Tag® and TMT® are registered Trademarks of Proteome Sciences plc.
Juergen.Schaefer@Proteomics.com
Other
This modification describes the \"native\" TMT Reagent without isotopic label.
PerkinElmer ExacTag Thiol kit
PerkinElmer ExacTag product page
Misc. URL
http://www.perkinelmer.com/exactag
Accurate mass for Exactag Thiol labels
PerkinElmer ExacTag Amine kit
PerkinElmer ExacTag product page
Misc. URL
http://www.perkinelmer.com/exactag
Accurate mass for Exactag Amine labels. Includes the mass of the conjugation reagent
Naisbitt, D. J., O'Neill, P. M., Pirohamed, M., and Park, B. K. 1996. Bioorganic and Medicinal Chemistry Letters 6(13):1511-1516.
Journal
Synthesis and Reactions of Nitroso Sulphamethoxazole with Biological Nucleophiles: Implications for Immune Mediated Toxicity.
Liu. Z., Minkler, P. E., and Sayre, L. M. Chem. Res. Toxico. 2003, 16, 901-911.
Journal
Mass Spectorscopic Characterization of Protein Modification by 4-hydroxy-2-(E)-nonenal and 4-oxo-2-(E)-nonenal
Naisbitt, D. J., O'Neill, P. M., Pirohamed, M., and Park, B. K. 1996. Bioorganic and Medicinal Chemistry Letters 6(13):1511-1516.
Journal
Synthesis and Reactions of Nitroso Sulphamethoxazole with Biological Nucleophiles: Implications for Immune Mediated Toxicity.
Naisbitt, D. J., O'Neill, P. M., Pirohamed, M., and Park, B. K. 1996. Bioorganic and Medicinal Chemistry Letters 6(13):1511-1516.
Journal
Synthesis and Reactions of Nitroso Sulphamethoxazole with Biological Nucleophiles: Implications for Immune Mediated Toxicity.
4-bromophenacyl bromide [99-73-0]
CAS Registry
428399
PubMed PMID
phenacyl bromide conjugated with a linker and biotin tag, details not published yet
Cleland's reagent
Vosseller K, Hansen KC, Chalkley RJ, Trinidad JC, Wells L, Hart GW, Burlingame AL. Proteomics. 2005 5(2):388-98. Quantitative analysis of both protein expression and serine / threonine post-translational modifications through stable isotope labeling with dithiothreitol.
Journal
15648052
PubMed PMID
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.
Simple cyclic compound C16H16O2 adds to cysteine forming fluorescent derivative.
Biochemistry 2005 vol 44 pp 1833-1845
Journal
http://dx.doi.org/10.1021/bi048228c
Result of Arg to Pro conversion of 13C(6) labelled Arg
Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181
Journal
Silac introduction
Misc. URL
http://www.pil.sdu.dk/silac_intro.htm
12716131
PubMed PMID
2,4-dichlorobenzylcarbamidomethyl
Analytical Chemistry (2000) 72 6 1112-1118
Journal
10740847
PubMed PMID
Modified peptides identified by isotope pattern. Restriction to cysteine-containing peptides combined with high mass accuracy allows peptide identification.
Cleland's reagent
15648052
PubMed PMID
Vosseller K, Hansen KC, Chalkley RJ, Trinidad JC, Wells L, Hart GW, Burlingame AL. Proteomics. 2005 5(2):388-98. Quantitative analysis of both protein expression and serine / threonine post-translational modifications through stable isotope labeling with dithiothreitol.
Journal
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.
Biochemistry (1987) 26 8242-8246
Journal
3327521
PubMed PMID
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.
3327521
PubMed PMID
Biochemistry (1987) 26 8242-8246
Journal
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.
15939799
PubMed PMID
Carboxymethylation w/ 13C label
B. Schilling, C.B. Yoo, C.J. Collins, B.W. Gibson, Determining Cysteine Oxidation Status Using Differential Alkylation, Int. J. Mass Spectrom., 2004, 236 (1-3), 117-121
Journal
http://dx.doi.org/10.1016/j.ijms.2004.06.004
CysNEM D5
reaction
Misc. URL
http://www.chemistry.ucsc.edu/~fink/231/Image118.gif
12777388
PubMed PMID
11813307
PubMed PMID
Amidation requires presence of glycine at peptide terminus
Richmond, T., Baggerman, G., Vandekerckhove, T., Menschaert, G., Husson, S., Verleyen, P., Schoofs, L., Van Criekinge, W. (2008). Bioinformatic Strategies for More Complete and Accurate Identification of Neuropeptides. . ASMS Conference on Mass Spectrometry. Denver, Colorado, USA, June 1-5 2008.
Other
Bradbury, A.F. and D.G. Smyth, Peptide amidation. Trends Biochem Sci, 1991. 16(3): p. 112-5.
Journal
Weibin Chen et. al., Anal. Chem.2007, 79,1583-1590
Journal
http://dx.doi.org/10.1021/ac061670b
Sadagopan, N. and Watson, J. T., Journal of the American Society For Mass Spectrometry 11 107-119 (2000)
Journal
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
Peng J, Schwartz D, Elias JE, Thoreen CC, Cheng D, Marsischky G, Roelofs J, Finley D, Gygi SP.
Nat Biotechnol. 2003 Aug;21(8):921-6
Journal
http://dx.doi.org/10.1038/nbt849
Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181
Journal
http://dx.doi.org/10.1021/pr0255708
The two glycine residues left on SILAC labeled ubiquitinylated lysine after tryptic digestion
JBC 258(1) 203-207 1983
Journal
http://www.jbc.org/cgi/reprint/258/1/203.pdf
Both isotopiclabel and post translational mod
Acetyl_K4
For SILAC experiments, + PTM
Pierce EZ-Link Pentylamine-Biotin
Misc. URL
http://www.piercenet.com/Products/Browse.cfm?fldID=01031206
J. Mass. Spectrom. 2007; 42:89-100.
Journal
http://dx.doi.org/10.1002/jms.1144
Chen, X., et al. (1999). Anal. Biochem. 273, 192-203.
Other
http://www.piercenet.com/products/browse.cfm?fldID=02030220
Kornblatt, J.A. and Lake, D.F. (1980). Crosslinking of cytochrome oxidase subunits with difluorodinitrobenzene. Can J. Biochem. 58, 219-224.
Other
http://www.piercenet.com/products/browse.cfm?fldID=02030220
Cy3b meleimide reacted with Cysteine
Article describing design of Cy3B
Journal
http://www.springerlink.com/content/q3u3271467573733/
Amersham website for chemical
Other
http://www1.gelifesciences.com/APTRIX/upp01077.nsf/Content/Products?OpenDocument&parentid=658513&moduleid=166300
Saito T., Itoh T.; Journal of dairy Science, 75 (1992). p1768.
Journal
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
Other
http://www.piercenet.com/Products/Browse.cfm?fldID=02030208
hydrazide reacts at any activated carboxyl group
Pierce product page
Misc. URL
http://www.piercenet.com/products/browse.cfm?fldID=C4FE82D4-DD06-493C-8EC4-9C1D7F83211B
SILAC and PTM
Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181
Journal
Silac introduction
Misc. URL
http://www.pil.sdu.dk/silac_intro.htm
12716131
PubMed PMID
Used in SILAC experiment
Acetyl_heavy lysine
Silac introduction
Misc. URL
http://www.pil.sdu.dk/silac_intro.htm
12716131
PubMed PMID
Sumoylation
Wohlschlegel, J. A. et al., J Proteome Res. 5 761 2006
Journal
http://dx.doi.org/10.1021/pr050451o
Nat Chem Biol. 3: 727-735, 2007
Journal
17906641
PubMed PMID
15063129
PubMed PMID
Protein which is posttranslationally modified by the attachment of cGMP on the sulfur atom of Cys or hydroxyl group of Ser residues.
Nat Chem Biol. 3: 727-735, 2007
Journal
17906641
PubMed PMID
15063129
PubMed PMID
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.
Low abundance
Applied Biosystems mTRAQ(TM) reagent
Applied Biosystems mTRAQ(TM) Reagents
Misc. URL
http://www3.appliedbiosystems.com/cms/groups/psm_support/documents/generaldocuments/cms_054141.pdf
The reaction product of Arg with phenylglyoxal has been shown to be a 2:1 adduct
11945751
PubMed PMID
11698400
PubMed PMID
5723461
PubMed PMID
Isotopic labeled methionine SILAC
Silac introduction
Misc. URL
http://www.pil.sdu.dk/silac_intro.htm
Created for Commercial use by ZDye. Being utilized in proteomic and peptidomic research soon to be published
Misc. URL
http://www.zdye.com/
15377717
PubMed PMID
17143934
PubMed PMID
Used in SILAC PTM (glygly) experiment
heavy glygly lysine
12716131
PubMed PMID
Silac introduction
Misc. URL
http://www.pil.sdu.dk/silac_intro.htm
Use when labelling post-digest
Use when labelling pre-digest
ICPL_10
Schmidt A, Kellermann J, Lottspeich F (2005): A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5: 4-15.
Journal
Bruker Daltonics order reference
Misc. URL
http://www.bdal.de/life-science-tools/care-consumables-more/icpl-kit.html
Attention: As the digest is typically applied AFTER ICPL labeling, only ProteinN-term labeling and Lys-specific labeling is applied.
Pierce data sheet
Misc. URL
http://www.piercenet.com/files/1964as4.pdf
Low abundance
Applied Biosystems mTRAQ(TM) reagent
mTRAQ heavy is identical to iTRAQ4plex 117
Applied Biosystems mTRAQ(TM) Reagents
Misc. URL
http://www3.appliedbiosystems.com/cms/groups/psm_support/documents/generaldocuments/cms_054141.pdf
Pierce data sheet
Misc. URL
http://www.piercenet.com/files/1768dh5.pdf
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.
CAS 156571-46-9
7-diethylamino-3-((((2-maleimidyl)ethyl)amino)carbonyl)coumarin
technical resources at Molecular Probes
Other
http://products.invitrogen.com/ivgn/en/US/adirect/invitrogen?cmd=catProductDetail&entryPoint=adirect&productID=D10253&messageType=catProductDetail&showAddButton=true
MDCC is used extensively as a fluorescent probe to report changes in protein conformation.
This peptide is generated from a trypsin/chymotrypsin dual digest
GlnGlnGlnThrGlyGly
This peptide is generated from a trypsin/chymotrypsin dual digest.
GlnGluGlnThrGlyGly
Advanced Glycation Endproduct
12595094
PubMed PMID
Thermo Scientific (Pierce) Product 21325
Misc. URL
http://www.piercenet.com/Products/Browse.cfm?fldID=44B1F9DF-B306-4278-B292-6CDB5B3B9D53
Which one?
Invitrogen BODIPY Handbook
Misc. URL
http://probes.invitrogen.com/handbook/sections/0104.html
Page 12 Scheme 1: (1) Structure of azidohomoalanine (2) Biotin-PEO-alkyne in our case PEO n=3 as in this publication
Misc. URL
http://etd.caltech.edu/etd/available/etd-09132005-120123/unrestricted/Chapter2.pdf
Drug Discovery Today Volume 8, Issue 24, 15 December 2003, Pages 1128-1137 Figure 4 page 1335
Journal
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T64-4B6C6T5-D&_user=616146&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000032323&_version=1&_urlVersion=0&_userid=616146&md5=b526a97bcf2d86ccddd5f602e2bcb53a
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.
16281315
PubMed PMID
11752401
PubMed PMID
Silac introduction
Misc. URL
http://www.pil.sdu.dk/silac_intro.htm
17873058
PubMed PMID
DOI: 10.1021/ja992749j
Efficient incorporation of unsaturated methionine analogues into proteins in vivo
Journal
http://pubs.acs.org/doi/pdf/10.1021/ja992749j
19798718
PubMed PMID
18275052
PubMed PMID
Protein from animals exposed to organoarsenicals
for Brad Strader
for Brad Strader
for Brad Strader
for Brad Strader
743239
PubMed PMID
http://www.ncbi.nlm.nih.gov/pubmed/743239?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum
http://www.piercenet.com/files/0581dh5.pdf
Other
http://www.piercenet.com/files/0581dh5.pdf
Asn-linked glycan from Gram-negative Bacterium
12186869
PubMed PMID
http://www.jbc.org/cgi/content/full/277/45/42530?view=long&pmid=12186869
9335564
PubMed PMID
12441112
PubMed PMID
19054759
PubMed PMID
http://www.ncbi.nlm.nih.gov/pubmed/19054759?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum
for Bindu Abraham
Journal
http://pubs.acs.org/doi/abs/10.1021/bi00804a010
Journal
http://pubs.acs.org/doi/abs/10.1021/ja9012134
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.
Used in SILAC PTM (glygly) experiment
heavy glygly lysine
12716131
PubMed PMID
Silac introduction
Misc. URL
http://www.pil.sdu.dk/silac_intro.htm
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
Sigma datasheet
Other
http://www.sigmaaldrich.com/etc/medialib/docs/Sigma/Datasheet/6/41022dat.Par.0001.File.tmp/41022dat.pdf
Fluorescence depletion mechanisms in super-resolving STED microscopy
Journal
http://dx.doi.org/10.1016/j.cplett.2007.06.017
Enrichment and site-mapping of O-Linked N-Acetylglucosamine by a combination of chemical/enzymatic tagging, photochemical cleavage, and electron transfer dissociation (ETD) mass spectrometry
Journal
http://dx.doi.org/10.1074/mcp.M900268-MCP200
Effects of Tryptic peptide esterification in MALDI mass spectrometry Anal. Chem. 2005, 77, 4185-4193
Journal
http://pubs.acs.org/doi/abs/10.1021/ac0481250
This peptide is generated from a formic acid digest
ValPheGlnGlnGlnThrGlyGly
ValIleGluValTyrGlnGluGlnThrGlyGly
14660678
PubMed PMID
11733505
PubMed PMID
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.
Trp modification with 2,4-Dinitrobenzenesulfenyl
Fontana A. Methods Enzymol 25 482-494 (1972)
Journal
Fontana A. Biochemistry. vol 7. 971-979 and 980-986 (1968)
Journal
Fontana A. Biochemical and biophysical research communications. vol. 25 (2). 170-174 (1966)
Journal
Pierce data sheet
Misc. URL
http://www.piercenet.com/files/1763dh4.pdf
Pierce data sheet
Misc. URL
http://www.piercenet.com/files/1763dh4.pdf
Label:15N(2)2H(9)
Boutaud O, Brame CJ, Salomon RG, Roberts LJ 2nd, Oates JA. Characterization of the lysyl adducts formed from prostaglandin H2 via the levuglandin pathway.
Biochemistry. 1999 Jul 20;38(29):9389-96.
PubMed PMID
10413514
Boutaud O, Brame CJ, Salomon RG, Roberts LJ 2nd, Oates JA. Characterization of the lysyl adducts formed from prostaglandin H2 via the levuglandin pathway.
Biochemistry. 1999 Jul 20;38(29):9389-96.
PubMed PMID
10413514
Boutaud O, Brame CJ, Salomon RG, Roberts LJ 2nd, Oates JA., Characterization of the lysyl adducts formed from prostaglandin H2 via the levuglandin pathway.
Biochemistry. 1999 Jul 20;38(29):9389-96.
PubMed PMID
10413514
Journal
http://www.biochemj.org/bj/344/0109/bj3440109.htm
18448829
PubMed PMID
ELGMEEEDVIEVYQEQTGG
FDGQPINETDTPAQLEMEDEDTIDVFQQQTGG
Li, Ricordel, Tong, Schopfer, Baud, Megarbane, Maury, Masson and Lockridge; Carbofuran poisoning detected by mass spectrometry of butyrylcholinesterase adduct in human serum. J Applied Toxicol 29, 149-155 (2009)
Journal
18925771
PubMed PMID
Created for Bindu Abraham 12/22/09
18925771
PubMed PMID
Created for Bindu Abraham 12/22/09
10666460
PubMed PMID
Created for Michael (Brad) Strader 2/12/10
glucosone
Journal
http://pubs.acs.org/doi/full/10.1021/jf9019085
SILAC+PTM
DIMETH
FindMod
SILAC introduction
Misc. URL
http://www.pil.sdu.dk/silac_intro.htm
Stable-isotope dimethyl labeling for quantitative proteomics
PubMed PMID
http://www.ncbi.nlm.nih.gov/pubmed/14670044?dopt=AbstractPlus
Tandem Mass Tag® and TMT® are registered Trademarks of Proteome Sciences plc.
John.C.Rogers@thermo.com
Other
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).
Tandem Mass Tag® and TMT® are registered Trademarks of Proteome Sciences plc.
John.C.Rogers@thermo.com
Other
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).
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
sometimes observed after elution of phosphopeptides from TiO2 with ammonium hydroxide
Patricelli et al. (2007). Functional Interrogation of the Kinome Using Nucleotide Acyl Phosphates. Biochemistry, 46, 350-358.
Journal
http://pubs.acs.org/doi/abs/10.1021/bi062142x
Datasheet for Sigma Aldrich product.
Other
http://www.sigmaaldrich.com/catalog/DataSheetPage.do?brandKey=SIGMA&symbol=B1267
15449375
PubMed PMID
Metabolic labeling with ammonium sulfate (15N)
19664813
PubMed PMID
Metabolic labeling with ammonium sulfate (15N)
19664813
PubMed PMID
Metabolic labeling with ammonium sulfate (15N)
19664813
PubMed PMID
amino_sulfate
Observed
alkaline phosphatase to dephosphorylate
alkaline phosphatase to dephosphorylate
alkaline phosphatase to dephosphorylate
digesting in labelled water
H2 18O Alkaline Phosphatase
11467524
PubMed PMID
Double O18 (C-term)
11467524
PubMed PMID
Double O18 (C-term)
11467524
PubMed PMID