Post-translational modifications (PTMs) are very important to biological function, however their identification and characterization is technically challenging. In this study, we have identified glycation modifications by nano LC-MSE, a data independent acquisition work flow, followed by database search using the Protein Lynx Global Server (PLGS). PLGS search with a complete human protein database hardly identified glycation modifications in a glycated human serum albumin (HSA), which was detected to be glycated by western blotting with advanced glycation end products (AGE) antibody and fluorescence spectroscopy. To overcome this difficulty, “Zoom-In” approach, a targeted database search was used to identify glycation modifications in a glycated HSA, which were further manually validated. This approach was useful for identification of glycation modifications from untargeted tandem mass spectrometry workflow such as MSE, but may require the development of a new algorithm or an upgrade of the existing software.
BrownleeM., “Biochemistry and molecular cell biology of diabetic complications”, Nature414, 813 (2001). doi: 10.1038/414813a
2.
GrilloM.A.ColombattoS., “Advanced glycation end-products (AGEs): Involvement in aging and in neurodegenerative diseases”, Amino Acids35, 29 (2008). doi: 10.1007/s00726-007-0606-0
3.
ZhangQ.TangN.SchepmoesA.A.PhillipsL.S.SmithR.D.MetzT.O., “Proteomic profiling of nonenzymatically glycated proteins in human plasma and erythrocyte membranes”, J. Proteome Res.7, 2025 (2008). doi: 10.1021/pr700763r
4.
ZhangQ.MonroeM.E.SchepmoesA.A.ClaussT.R.W.GritsenkoM.A.MengD.PetyukV.A.SmithR.D.MetzT.O., “Comprehensive identification of glycated peptides and their glycation motifs in plasma and erythrocytes of control and diabetic subjects”, J. Proteome Res.10, 3076 (2011). doi: 10.1021/pr200040j
5.
LangerK.A.PoonF.H.MunchG.LynnC.B.ArendtT.ButterfieldA.D., “Identification of AGE-modified proteins in SH-SY5Y and OLN-93 cells”, Neurotox. Res.9, 255 (2006). doi: 10.1007/s12640-011-9239-x
6.
ChougaleA.D.BhatS.P.BhujbalS.V.ZambareM.PuntambekarS.SomaniR.BoppanaR.GiriA.P.KulkarniM.J., “Proteomic analysis of glycated proteins from streptozotocin-induced diabetic rat kidney”, Mol. Biotechnol.50, 28 (2012). doi: 10.1007/s12033-011-9409-3
7.
MoriyamaT.KemiM.OkumuraC.YoshiharaK.HorieT., “Involvement of advanced glycation end-products, pentosidine and N(epsilon)-(carboxymethyl)lysine, in doxorubicin-induced cardiomyopathy in rats”, Toxicology268, 89 (2010). doi: 10.1016/j.tox.2009.12.004
8.
ZhaoH.R.NagarajH.R.AbrahamE.C., “The role of α-and ε-amino groups in the glycation-mediated cross-linking of γ-crystallin”, J. Biol. Chem.272, 14465 (1997). doi: 10.1074/jbc.272.22.14465
9.
KueperT.GruneT.PrahlS.LenzH.WelgeV.BiernothT.VogtY.MuhrM.GaemlichA.JungT.BoemkeG.ElsasserH.WitternK.WenckH.StabF.BlattT., “Vimentin is the specific target in skin glycation”, J. Biol. Chem.282, 23427 (2007). doi: 10.1074/jbc.M701586200
10.
LapollaA.FedeleD.SeragliaR.TraldiP., “The role of mass spectrometry in the study of non-enzymatic protein glycation in diabetes: An update”, Mass Spectrom. Rev.25, 775 (2006). doi: 10.1074/jbc.M701586200
11.
CapoteF.P.SanchezJ.C., “Strategies for proteomic analysis of non-enzymatically glycated proteins”, Mass Spectrom. Rev.28, 135 (2009). doi: 10.1002/mas.20187
12.
FrolovA.HoffmannP.HoffmannR., “Fragmentation behavior of glycated peptides derived from d-glucose, d-fructose and d-ribose in tandem mass spectrometry”, J. Mass Spectrom.41, 1459 (2006). doi: 10.1002/jms.1117
13.
StefanowiczP.KapczynskaK.JaremkoM.JaremkobL.SzewczukaZ., “A mechanistic study on the fragmentation of peptide-derived Amadori products”, J. Mass Spectrom.44, 1500 (2009). doi: 10.1002/jms.1639
14.
GadgilH.S.BondarenkoPV.TreuheitM.J.RenD., “Screening and sequencing of glycated proteins by neutral loss scan LC/MS/MS method”, Anal. Chem.79, 5991 (2007). doi: 10.1021/ac070619k
15.
ZhangQ.VladislavA.P.AthenaPA.SchepmoesA.A.OrtonD.MonroeM.E.YangF.SmithD.MetzT.O., Analysis of non-enzymatically glycated peptides: Neutral-loss-triggered MS3 versus multi-stage activation tandem mass spectrometry”, Rapid Commun. Mass Spectrom.22, 3027 (2008). doi: 10.1002/rcm.3703
16.
CapoteF.P.ScherlA.MullerM.WaridelP.LisacekF.SanchezJ.C., “Glycation isotopic labeling with 13C-reducing sugars for quantitative analysis of glycated proteins in human plasma”, Mol. Cell Proteomics.9, 579 (2010). doi: 10.1074/mcp.M900439-
17.
MereishK.A.RosenbergH.CobbyJ., “Glucosylated albumin and its influence on salicylate binding”, J. Pharm. Sci.71, 235 (1982).
18.
SilvaJ.C.DennyR.DorschelC.GorensteinM.V.LiG.Z.RichardsonK.WallD.GeromanosS.J., “Simultaneous qualitative and quantitative analysis of the escherichia coli proteome”, Mol Cell Proteomics.5, 589 (2006). doi: 10.1074/mcp.M500321-MCP200
19.
NakayamaM.YoshimuraK.MaruyamaY.NumataM.HosoyaT.IzumiG., “Possible involvement of cross-linking advanced glycation endproducts in long-term CAPD peritoneal degeneration”, Nephrol. Dial. Transplant.19, 1664 (2004). doi: 10.1093/ndt/gfh198
20.
WaC.CernyR.L.ClarkeW.A.HageD.S., “Characterization of glycation adducts on human serum albumin by matrix assisted laser desorption/ionization time-of-flight mass spectrometry”, Clin. Chim. Acta.385, 48 (2004). doi: 10.1016/j.cca.2007.06.011
TannerS.ShuH.FrankH.WangL.ZandiE.MumbyM.PevznerP.A.BafnaV., “InsPect: Identification of post translationally modified peptides from tandem mass spectra”, Anal. Chem.77, 4626 (2005). doi: 10.1021/ac050102d
23.
ChamradD.C.KörtingG.StühlerK.MeyerH.E.KloseJ.BlüggelM., “Evaluation of algorithms for protein identification from sequence databases using mass spectrometry data”, Proteomics4, 619 (2004). doi: 10.1002/pmic.200300612
24.
McHughL.ArthurJ.W., “Computational methods for protein identification from mass spectrometry data”, PLOS Comput. Biol.4, 1 (2008). doi: 10.1371/journal.pcbi.0040012
25.
ChenY.ChenW.CobbM.H.ZhaoY., “PTMap- A sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites,”Proc. Natl. Acad. Sci. USA106, 761 (2009). doi: 10.1073/pnas.0811739106
26.
WilmarthP.A.TannerS.DasariS.NagallaS.R.RiviereM.A.BafnaV.PevznerP.A.DavidL.L., “Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: Does deamidation contribute to crystallin insolubility?”J. Proteome Res.10, 2554 (2006). doi: 10.1021/pr050473a
27.
XieH.GilarM.GeblerJ.C., “Characterization of protein impurities and site-specific modifications using peptide mapping with liquid chromatography and data independent acquisition mass spectrometry”, Anal Chem.81, 5699 (2009). doi: 10.1021/ac900468j
28.
BhonsleH.S.KorwarA.M.KoteS.S.GolegaonkarS.B.ChougaleA.D.ShaikM.L.DhandeN.L.GiriA.P.ShelgikarK.M.BoppanaR.KulkarniM.J., “Low plasma albumin levels are associated with increased plasma protein glycation and HbA1c in diabetes”, J. Proteome Res.11, 1391 (2012). doi: 10.1021/pr201030m
29.
BlackburnK.GosheM.B., “Challenges and strategies for targeted phosphorylation site identification and quantification using mass spectrometry analysis”, Brief. Funct. Genomic Proteomic8, 90 (2008). doi: 10.1093/bfgp/eln051
