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Table 2 Identification of glycosylated proteins, peptides and their glycosylation sites in royal jelly proteins

From: Comprehensive identification of novel proteins and N-glycosylation sites in royal jelly

Accession Glycoprotein and glycopeptide -10lgP Mass(Da) Charge No. of spectra Amino acid residue no. Glycosylation site (N-type) Enrichment method
Lectin Hydrazide
         Orbitrap Triple TOF Orbitrap Triple TOF
gi|58585098 Major royal jelly protein 1 precursor 442.09 48886         
  R.GESLN(+2.99)KSLPILHEWK.Fb 57.82 585.32 3 8 24-38 28   
gi|58585108 Major royal jelly protein 2 precursor 398.06 51074         
  K.TSNHLKQIEIPHDIAVN(+2.99)ATTGK.Ga 67.92 797.42 3 15 162-183 178
  K.IAIDKFDRLWVLDSGLVN(+2.99)R.Ta 57.57 1117.1 2 9 128-146 145
gi|284182838 Major royal jelly protein 4 298.73 53015         
  R.KN(+2.99)LTNTLNVIHEWK.Yb 57.71 856.97 2 5 30-41 31   
  K.M(+15.99)SNQQEN(+2.99)LTLKEVDNK.Vb 47.23 637.31 3 2 236-251 242   
gi|58585188 Major royal jelly protein 6 precursor 203.5 49786         
  K.NYPFDVDQWHN(+2.99)K.Td 47.63 783.35 2 4 68-79 78   
  K.LLAFDLN(+2.99)TSKLLK.Qd 47 739.94 2 2 158-170 164    
gi|62198227 Major royal jelly protein 7 precursor 312.92 50541         
  K.QVDIPHEIAVN(+2.99)TTTEQGR.Ld 54.49 1006 2 11 168-185 178
  R.LWVLDSGLVN(+2.99)NTQPM(+15.99)C(+57.02)FPK.Ld 45.55 1112 2 8 136-154 145  
  K.NGILFFGLVN(+2.99)NTAVGC(+57.02)WNEHQ(+0.98)TLQ(+0.98)R.Ed 57.66 1447.2 2 2 312-316 321    
gi|67010041 Major royal jelly protein 9 precursor 107.71 48688         
  K.IPHDIAIN(+2.99)STTGK.Rd 40.14 685.37 2 2 170-182 177    
gi|148277624 Yellow-e3 precursor 89 48235         
  K.YM(+15.99)SGTLNSN(+2.99)ETNFR.Ie 50.32 826.86 2 2 384-397 392    
gi|328787887 Lysosomal alpha-mannosidase 165.89 188194         
  R.LTQSFHYYEGM(+15.99)EGNNM(+15.99)EFKN(+2.99)R.Sd 53.93 877.38 3 4 538-558 557   
  R.LLKDDAFGVGEALN(+2.99)ESAYGEGLVVR.Gd 50.85 1313.2 2 2 722-746 735    
gi|89885579 Alpha-glucosidase 193.65 65565         
  K.N(+2.99)VSRDSN(+2.99)SSDFKK.Lb 39.74 497.24 3 2 313-325 313 319    
  K.HM(+15.99)LIEAYTN(+2.99)LSM(+15.99)TM(+15.99)K.Yb 38.65 917.42 2 2 282-296 290    
gi|66564326 Plasma glutamate carboxypeptidase isoform 1 178.08 52947         
  K.ESADYGLENVHGEN(+2.99)VTVPFWVR.Gd 63.89 1261.1 2 2 99-120 112    
  R.SVTPYSLYTPHTGHQSYGEN(+2.99)VTK.Id 55.98 643.06 4 5 212-234 231   
  R.IM(+15.99)TLLSPM(+15.99)GN(+2.99)LTVR.Sd 42.7 790.92 2 3 394-407 403   
  R.AIM(+15.99)NEALN(+2.99)GSFK.Gd 34.47 657.33 2 2 54-65 61    
gi|328778095 Lysosomal Pro-X carboxypeptidase 71.61 56432         
  R.YYGESM(+15.99)PYNN(+2.99)K.Se 35.71 692.79 2 1 124-134 133    
gi|66560290 Lysosomal aspartic protease 62.1 42222         
  K.N(+2.99)GTDFAIR.Ye 35.21 448.72 2 1 120-127 120    
gi|328782027 Membrane metallo-endopeptidase 1 89.03 88720         
  K.HNPIPDN(+.98)KVEWSEDEIKAN(+2.99)K.Te 50.01 592.55 4 2 92-111 110    
  K.WYDN(+.98)SGVN(+2.99)TSTAK.Ie 37.35 723.83 2 1 311-323 318    
  R.IVNTN(+2.99)DTETR.Le 36.04 583.28 2 1 31-40 35    
gi|48118838 Glucosylceramidase 142.8 58571         
  K.QFDNN(+2.99)ITYLKEEHYETYVNYLIK.Fd 54.42 735.86 4 3 211-233 215   
  K.N(+2.99)FSLAPEDYNYK.Id 46.71 732.33 2 2 171-182 171    
  K.TQANWIANYFGPILASSPFN(+2.99)K.Td 30.3 781.41 3 1 273-293 292    
  R.M(+15.99)N(+2.99)VSEVKFDR.Cd 40.85 622.3 2 3 72-81 73  
gi|58585090 Glucose oxidase 277.69 67938         
  R.SNLHVIVN(+2.99)ATVTK.Vd 54.93 699.9 2 8 277-289 284
  K.LVN(+2.99)TTVM(+15.99)RDLGVEFQK.Id 52.05 934.99 2 7 499-514 501
  R.WVQQGAFGWSWDEVM(+15.99)PYYLKSEN(+2.99)NTELSR.Vd 40.6 1180.9 3 4 172-200 194   
  R.AFITPFEN(+2.99)R.Sd 41.19 549.28 2 3 268-276 275   
  K.YYTTN(+2.99)ESHACLSTGGSCYWPR.Gd 41.83 800.34 3 2 126-146 130    
gi|166795901 Apolipophorin-III-like protein precursor 226.7 21348         
  K.DQSANFVNNIQDYIKN(+2.99)VTEEVK.Td 62.84 857.76 3 6 71-92 86  
gi|328782084 Antithrombin-III 97.9 59502         
  K.ISN(+2.99)DSAQNGERDSIYHLIER.Ld 48.05 580.78 4 2 362-381 364    
gi|187281543 Venom dipeptidyl peptidase 4 precursor 80.93 87937         
  R.HLAFATFN(+2.99)DTNVR.Dc 47.19 503.59 3 2 232-244 239    
  R.ANSFN(+2.99)GTWK.Tc 39.89 514.24 2 2 64-72 68    
  K.YSWIDSN(+2.99)R.Tc 34.35 522.24 2 2 625-632 631    
gi|110755367 Toll-like receptor 13 isoform 1 127.33 75706         
  R.M(+15.99)LEHLDLSN(+2.99)NSLSTVNR.Rd 55.39 981.48 2 2 547-563 555    
  R.HLNTQFFHN(+2.99)TTNLNK.Ld 54.76 611.31 3 2 166-180 174    
  K.LHTLEEGLFAN(+2.99)LTR.Ld 50.96 539.62 3 2 432-445 442    
  R.LSEEAFKN(+2.99)ASK.Ld 39.92 613.81 2 1 315-325 322    
gi|328790726 Venom acid phosphatase Acph-1 142.25 42665         
  K.M(+15.99)PSTINFYPNDPYIN(+2.99)YTYEPAGK.Gd 57.47 1357.6 2 2 38-60 52    
gi|328792524 Hypothetical protein LOC408570 89.27 90763         
  R.WSLTPVNSN(+2.99)TTVVVK.Qe 43.11 824.45 2 2 539-553 547    
  R.QN(+2.99)YTDAPPAK.Le 41.13 554.27 2 2 590-599 591    
  R.IDPN(+2.99)SSFTQSNPIR.Fe 38.14 789.89 2 2 284-297 287   
gi|66514614 Idgf4 135.8 48741         
  R.LKDLTIGVLPHVN(+2.99)STVYYDAR.Ld 57.43 595.07 4 2 216-236 228    
gi|110766389 Protein takeout 90.9 30201         
  R.ALFSN(+2.99)ITVIGAGN(+2.99)YSLTK.Sd 56.15 938 3 2 105-122 109 117   
gi|48094573 Hypothetical protein LOC408608 292.9 19434         
  K.GNLGTVN(+2.99)LTKVLKSVEDR.Ld 53.12 641.34 4 5 61-78 67
gi|110763647 Hypothetical protein LOC726323 109.47 18478         
  R.IYDPITN(+2.99)TSK.Md 35.5 577.8 2 1 133-142 139    
  1. Note: All of the identified proteins are from Apis mellifera. Accession is the unique number given to mark the entry of a protein in the database of Apis (downloaded April 2012, version 4.5 of the honeybee genome). “-10logP” is the score calculated by PEAKS software (version 6.0, Bioinformatics Solutions Inc.). Charge is the number of the carrying charge of the peptide. No. of spectra is the number of the spectrum of the peptide generated by mass spectrometry. Amino acid residue No. corresponds to the position of the N-terminal and C-terminal amino acid of the peptide in the protein sequence. Glycosylation site indicates the position of the N-glycosylated amino acids of the peptide in the protein sequence. Orbitrap refers the peptides analyzed by the Q-Exactive mass spectrometry (Thermo Fisher Scientific). Triple TOF refers the peptides analyzed by Triple TOF 5600 (AB SCIEX). Lectin denotes N-glycopeptides enriched by the lectin method. Hydrazide represents N-glycopeptides enriched by hydrazide chemistry. “√” indicates that peptide is identified by the corresponding enrichment method and mass spectrometer. “a” is the known site in the known protein. “b” is the potential site (bioinformatics has predicted these potential sites in UniProt Database (updated April 2013), and it is experimentally confirmed in this study) in the known protein. “c” is the potential site in the novel protein. “d” denotes the novel site in the known protein. “e” is the novel site in the novel protein.