AA0172 RESID 14752058 PubMed PMID AA0362 RESID Medzihradszky et al., Mol. Cell. Proteomics 2004, 3, 429-440 Journal SULF FindMod AA0171 RESID AA0361 RESID Global and Site-Specific Analysis Revealing Unexpected and Extensive Protein S‑GlcNAcylation in Human Cells Journal http://dx.doi.org/10.1021/acs.analchem.6b05064 AA0151 RESID GLCN FindMod AA0155 RESID 3086323 PubMed PMID AA0154 RESID Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?hexnac=1&mode=exact The amine derivative of a hexose formed by replacing a hydroxyl group with an amino group.(+acetyl group) 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 histidine oxidation to aspargine Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316. Journal 9252331 PubMed PMID histidine oxidation to aspartic acid Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316. Journal 9252331 PubMed PMID AA0021 RESID 10825024 PubMed PMID 8758896 PubMed PMID AA0211 RESID 15799070 PubMed PMID AA0021 RESID FORM FindMod AA0384 RESID AA0057 RESID AA0384 RESID N-linked glycan core Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?hex=5&hexnac=2&mode=exact Core structure of high-mannose N-linked oligosaccharides 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. Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hexnac=1&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?hexnac=2&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?hex=3&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hexnac=1&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=1&hexnac=1&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hexnac=2&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=2&mode=exact Saito T., Itoh T.; Journal of dairy Science, 75 (1992). p1768. Journal Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=1&neuac=1&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hexnac=2&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?pent=1&hex=1&hexnac=2&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=1&hexnac=2&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?hex=2&hexnac=2&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?pent=1&hex=3&hexnac=1&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?pent=1&dhex=1&hex=1&hexnac=2&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?dhex=2&hex=1&hexnac=2&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?pent=1&hex=2&hexnac=2&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=2&hexnac=2&mode=exact chitobiose core Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?hex=3&hexnac=2&mode=exact Saito T., Itoh T.; Journal of dairy Science, 75 (1992). p1768. Journal Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=1&neuac=2&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?phosphate=1&hex=3&hexnac=2&mode=exact Butylated Hydroxytoluene 9448752 PubMed PMID BHT metabolism has been studied in rats and mice in relation to tumor promotion. 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 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 H2 18O Alkaline Phosphatase 11467524 PubMed PMID heavy lysine 12716131 PubMed PMID Silac introduction Misc. URL http://www.pil.sdu.dk/silac_intro.htm Silac introduction Misc. URL http://www.pil.sdu.dk/silac_intro.htm 12716131 PubMed PMID Silac introduction Misc. URL http://www.pil.sdu.dk/silac_intro.htm 12771378 PubMed PMID NTRY FindMod 10442087 PubMed PMID AA0230 RESID 15688001 PubMed PMID X. Zhan, X. Wang, D.M. Desiderio. Mass Spectrom. Rev., 34 (2015), pp. 423-448 Journal https://onlinelibrary.wiley.com/doi/epdf/10.1002/mas.21413 3-deoxy-D-manno-oct-2-ulosonic acid 2-Keto-3-Deoxy-D-Mannooctanoic Acid Reference for KDO mass, KDO on capsular polysaccharide Book https://books.google.co.in/books?id=IOuPDwAAQBAJ&pg=PA333&lpg=PA333&dq=kdo+220+mass&source=bl&ots=t--BcUkzNH&sig=ACfU3U2lNj05UnTthH1BD6fS0jC6rxYpFw&hl=en&sa=X&ved=2ahUKEwjLmPfoic7nAhWA7XMBHRsiAk4Q6AEwCnoECAoQAQ#v=onepage&q=kdo%20220%20mass&f=false Reference for KDO mass, KDO residue on lipopolysaccharide Book https://books.google.co.in/books?id=webUBwAAQBAJ&pg=PA412&lpg=PA412&dq=kdo+220+mass&source=bl&ots=Qez27T1RJi&sig=ACfU3U1xvo43GBt1sstNunuGfNmQoK2Rmg&hl=en&sa=X&ved=2ahUKEwjLmPfoic7nAhWA7XMBHRsiAk4Q6AEwC3oECAUQAQ#v=onepage&q=kdo%20220%20mass&f=false Reference for KDO mass Book https://books.google.co.in/books?id=HNulYcigSYQC&pg=PA351&lpg=PA351&dq=kdo+220+mass&source=bl&ots=6zTm8qPxlT&sig=ACfU3U3ib4w1BKV-Wz9javn5O9NMLzermw&hl=en&sa=X&ved=2ahUKEwjLmPfoic7nAhWA7XMBHRsiAk4Q6AEwDHoECAgQAQ#v=onepage&q=kdo%20220%20mass&f=false This is the primary reference of KDO modification on protein. PubMed PMID https://pubmed.ncbi.nlm.nih.gov/32886756/ Hydroxy ethyl 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 15351294 PubMed PMID 7730303 PubMed PMID SILAC Introduction Misc. URL http://www.pil.sdu.dk/silac_intro.htm DIMETH FindMod 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 UV induced linkage of Iodo-U-amp with WFY 11567090 PubMed PMID 11112526 PubMed PMID 6540775 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). 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 Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&mode=exact SILAC overview Misc. URL http://www.sigmaaldrich.com/technical-documents/articles/stable-isotopes/stable-isotope-labeling-by-amino-acids.html Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=3&hexnac=4&mode=exact dHex Hex(4) HexNAc(4) ---OR--- Hex(4) HexNAc(4) Pent Me Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=4&hexnac=4&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?dhex=1&hex=5&hexnac=4&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?hex=3&hexnac=4&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?hex=4&hexnac=4&mode=exact Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?hex=5&hexnac=4&mode=exact 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 Thiophos-biotin disulfide AA0153 RESID AA0296 RESID Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?phosphate=1&hexnac=1&mode=exact AA0297 RESID Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?phosphate=1&hex=1&mode=exact J. Mass Spectrom. 2005; 40: 238-249 Journal J. Mass Spectrom. 2005; 40: 238-249 Journal beta-methylaminoethylcysteine Z. A. Knight et al, Nature Biotech., 21(9) 1047-1054 (2003) Journal Modification procedure used for phosphopeptide mapping Berger U, Oehme M, Girardin L., Fresenius J Anal Chem. 2001 Jan 2;369(2):115-23. Journal Found in canned food products lac BIOCHIMECAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 236, 413-417 (1997) Journal ANALYTICAL BIOCHEMISTRY 259, 152-161 (1998) Journal Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?hex=2&mode=exact Lactosylation of bovine Beta-Lactoglobulin fluorescein-NEM 9325338 PubMed PMID 11665566 PubMed PMID Thiol-Reactive Probes Misc. URL http://probes.invitrogen.com/media/pis/mp00003.pdf 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 threo-1,4-dimercaptobutane-2,3-diol Was DTT_ST 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 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 Beta-elimination and Michael addition of dithiothreitol (DTT) to serine and threonine adds a weight of approximately 136.2. Biochemistry 2005 vol 44 pp 1833-1845 Journal http://dx.doi.org/10.1021/bi048228c 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 Acetyl_K4 For SILAC experiments, + PTM Saito T., Itoh T.; Journal of dairy Science, 75 (1992). p1768. Journal Composition search GlyConnect Misc. URL https://glyconnect.expasy.org/browser/global/compositions/search?hex=1&hexnac=1&mode=exact Pierce EZ link biotin hydrazide prod no. 21360 Pierce product page Misc. URL http://www.piercenet.com/products/browse.cfm?fldID=C4FE82D4-DD06-493C-8EC4-9C1D7F83211B 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 Acetyl_heavy lysine Silac introduction Misc. URL http://www.pil.sdu.dk/silac_intro.htm 12716131 PubMed PMID 11945751 PubMed PMID 11698400 PubMed PMID 5723461 PubMed PMID Silac introduction Misc. URL http://www.pil.sdu.dk/silac_intro.htm heavy glygly lysine 12716131 PubMed PMID Silac introduction Misc. URL http://www.pil.sdu.dk/silac_intro.htm 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. GlnGlnGlnThrGlyGly GlnGluGlnThrGlyGly 12595094 PubMed PMID 17873058 PubMed PMID Asn-linked glycan from Gram-negative Bacterium DATDH 12186869 PubMed PMID http://www.jbc.org/cgi/content/full/277/45/42530?view=long&pmid=12186869 heavy glygly lysine 12716131 PubMed PMID Silac introduction Misc. URL http://www.pil.sdu.dk/silac_intro.htm ValPheGlnGlnGlnThrGlyGly 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 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