Supplemental Figure 1. TEM of Zr4+-PO3-Modified Magnetic Fe3o4/Sio2 Nanoparticles

Supplemental Figure 1. TEM of Zr4+-PO3-modified magnetic Fe3O4/SiO2 nanoparticles.

Supplemental Figure 2. A tryptic digest of -casein in deionized water (1pmol, 2 l) treated by Zr4+-PO3-magnetic Fe3O4/SiO2 nanoparticles and the nanoparticles were subsequently rinsed by (a) a solution containing 0.1% TFA and 80% ACN;(b) a solution containing 0.5% TFA and 80% ACN;(c) a solution containing 1.5% TFA and 80% ACN;(d) a solution containing 6.0% TFA and 80% ACN. Then the eluents was respectively collected, lyophilized and re-dissolved for the MALDI-TOF MS analysis. MALDI-TOF mass spectra were as followings. The peaks marked as“*” were phosphopeptides.

Supplemental Table 1. The identification of the phosphorylated peptides in mouse liver derived from MS2 and MS3.

IPI number / Prontein / Peptide sequence* / charge / Xcorr / Eluting step** / Ref.***
MS2 / MS3
00109311.2
/ Ezrin-radixin-moesin binding phosphoprotein / [pS]ASSDTSEELNSQDSPKR / 2 / 2.706 / 3.559 / A / M(4)
00109311.2 / Ezrin-radixin-moesin binding phosphoprotein / [pS]ASSDTSEELNSQDSPK / 2 / 5.614 / 2.963 / A / M(4)
00109311.2 / Ezrin-radixin-moesin binding phosphoprotein / SASSDTSEELN[pS]QD[pS]PKR / 2 / 3.568 / 3.987 / B / M(3,4)
00111740.1 / hypothetical protein / KSPVF[pS]DED[pS]DLDFDIGKLEQQTK / 3 / 4.063 / 2.908 / B / M(3)
00112963.1 / Alpha-1 catenin / TPEELDD[pS]DFETEDFDVR / 2 / 6.693 / 5.937 / A / M(1,10)
00112963.1 / Alpha-1 catenin / [pS]RT[pS]VQTEDDQLIAGQSAR / 2 / 4.109 / 4.869 / B / M(3,10)
00112963.1 / Alpha-1 catenin / [pS]R[pT]SVQTEDDQLIAGQSAR / 2 / 4.45 / 4.239 / B / M(3,10)
00113377.1 / acidic ribosomal protein P1 / KEESEE[pS]EDDMGFGLFD / 2 / 3.983 / 4.165 / A / M(3,9)
00113377.1 / acidic ribosomal protein P1 / KEE[pS]EE[pS]EDDMGFGLFD / 2 / 5.582 / 4.257 / B / M(3,9)
00113377.1 / acidic ribosomal protein P1 / KEE[pS]EESEDDMGFGLFD / 2 / 4.493 / 3.542 / B / M(3,9)
00113539.2 / Fibronectin precursor / TNTNVNCPIECFMPLDVQADRDD[pS]RE / 3 / 4.708 / 2.28 / B / M(3)
00113584.2
/ Isoform PNS-Tau of Microtubule-associated protein tau / AKTDHGAEIVYK[pS]PVVSGD[pS][pS]PR / 3 / 2.953 / 4.01 / B / M(1,3,10)
00113635.6 / Nucleolar protein / KRD[pS]E[pS]E[pS]DETPTVPQLK / 2 / 4.309 / 4.037 / B / M(3)
00113635.6 / Nucleolar protein / KRD[pS]E[pS]ESDETPTVPQLK / 2 / 3.712 / 3.008 / B / M(3)
00114232.1 / Histone deacetylase 1 / IACEEEF[pS]D[pS]DEEGEGGRK / 2 / 4.936 / 4.001 / B / M(3)
00114862.1 / THUMP domain-containing protein 1 / FIDKDQQP[pS]G[pS]EGEDDDAEAALKK / 3 / 4.512 / 4.12 / B / M(3)
00114918.1 / 5830416A07Rik protein / ESG[pS]EQDLDGAGERA[pS]DLEEEENATR / 3 / 3.386 / 2.78 / B / M(3)
00114945.1 / Septin-2 / IYHLPDAE[pS]DEDEDFKEQTR / 3 / 4.23 / 2.674 / A / M(3,10)
00115040.1 / BCL2/adenovirus E1B 19-kDa protein-interacting protein 3 / AEIDSH[pS]FGEKNSTL[pS]EED[pY]IER / 3 / 4.63 / 4.315 / B / M(1,3,10)
00115040.1 / BCL2/adenovirus E1B 19-kDa protein-interacting protein 3 / AEIDSHSFGEKNS[pT]L[pS]EEDYIER / 3 / 4.223 / 3.95 / B / M(1,3,10)
00115040.1 / BCL2/adenovirus E1B 19-kDa protein-interacting protein 3 / AEIDSHSFGEKN[pS]TL[pS]EEDYIER / 3 / 4.279 / 3.287 / B / M(1,3,10)
00115040.1 / BCL2/adenovirus E1B 19-kDa protein-interacting protein 3 / AEID[pS]H[pS]FGEKN[pS]TLSEEDYIER / 3 / 4.577 / 2.628 / B / M(1,3,10)
00115257.1
/ Isoform 1 of PC4 and SFRS1-interacting protein / NLAKPGVTS[pT][pS]DSEDEDDQEGEK / 3 / 4.275 / 2.922 / B / M(2,3)
00116442.1 / Hdgfrp2 protein / GG[pS][pS]GEELEDEEPVK / 2 / 4.558 / 4.594 / B / M(3,12)
00117811.2 / AP-3 complex subunit delta-1 / KVPVPEGLDLDAWINEPP[pS]D[pS]ESEDEKPK / 3 / 5.596 / 5.529 / B / M(3)
00117811.2 / AP-3 complex subunit delta-1 / KVPVPEGLDLDAWINEP[pS]D[pS]E[pS]EDEKPK / 3 / 5.644 / 2.986 / B / M(3)
00118143.1 / Src substrate cortactin / KQ[pT]PPA[pS]P[pS]PQPIEDRP[pS]SPIYEDAAPFK / 3 / 4.932 / 2.393 / B / M(3,10)
00118231.1 / Isoform 1 of Williams-Beuren syndrome chromosome region 14 protein / VV[pS]PD[pS]D[pS]DTDLED[pS]PR / 2 / 3.404 / 2.506 / B / M(3)
00118438.4 / Isoform 2 of Serine/arginine repetitive matrix protein 1 / HRP[pS]SPA[pT]PPPK / 3 / 2.793 / 2.95 / A / M(3,6,12)
00118438.4 / Isoform 2 of Serine/arginine repetitive matrix protein 1 / HRPpS[pS]PATPPPK / 2 / 2.768 / 1.645 / A / M(6,12)
00118438.4 / Isoform 2 of Serine/arginine repetitive matrix protein 1 / RR[pS]P[pS]PAPPPPPPPPPPR / 3 / 3.684 / 2.695 / B / M(3,9)
00118438.4 / Isoform 2 of Serine/arginine repetitive matrix protein 1 / KPPAPP[pS]PVQ[pS]Q[pS][pS]TNWSPAVPAK / 3 / 4.076 / 3.582 / B / M(3,6)
00118438.4 / Isoform 2 of Serine/arginine repetitive matrix protein 1 / KPPAPP[pS]PVQ[pS]QS[pS]TNW[pS]PAVPAK / 3 / 4.555 / 2.554 / B / M(3,6)
00118438.4 / Isoform 2 of Serine/arginine repetitive matrix protein 1 / KPPAPP[pS]PVQ[pS]QS[pS]TNW[pS]PAVPAKK / 3 / 3.148 / 2.886 / B / M(3,6)
00118438.4 / Isoform 2 of Serine/arginine repetitive matrix protein 1 / RY[pS]P[pS]PPPK / 2 / 2.444 / 2.691 / A / M(3)
00118438.4 / Isoform 2 of Serine/arginine repetitive matrix protein 1 / SRV[pS]V[pS]PGR / 2 / 3.019 / 2.411 / B / M(3)
00118438.4 / Isoform 2 of Serine/arginine repetitive matrix protein 1 / KVEL[pS]E[pS]EEDKGSK / 2 / 3.761 / 3.498 / B / M(3)
00118438.4 / Isoform 2 of Serine/arginine repetitive matrix protein 1 / RE[pS]P[pS]PAPKPR / 2 / 2.645 / 3.099 / B / M(6,12)
00118438.4 / Isoform 2 of Serine/arginine repetitive matrix protein 1 / RL[pS]P[pS]A[pS]PPR / 2 / 1.796 / 2.62 / B / M(3)
00118438.4 / Isoform 2 of Serine/arginine repetitive matrix protein 1 / KPPAPP[pS]PVQSQ[pS][pS]TNW[pS]PAVPAKK / 3 / 3.859 / 2.24 / B / M(3)
00118875.3
/ Guanine nucleotide exchange protein / GATPAEDDEDKDIDLFG[[pS]]DEEEEDKEAAR / 3 / 6.66 / 5.708 / B / M(3)
00119695.1 / Signal recognition particle receptor subunit alpha / GTGPGGQLQDLDC[pS][pS][pS]DDEGATQNTKPSATK / 3 / 4.961 / 3.348 / B
00120046.1 / Isoform 1 of 5'-3' exoribonuclease 2 / KAED[pS]D[pS]EPEPEDNVR / 2 / 5.369 / 4.57 / B / M(3)
00120095.2 / SAM domain and HD domain-containing protein 1 / CDG[pS]PR[pT]P[pS][pT]PPATANLSADDDFQNTDLR / 3 / 7.156 / 3.228 / B / M(3)
00120095.2 / SAM domain and HD domain-containing protein 1 / CDG[pS]PR[pT]PP[pS]TPPATANLSADDDFQNTDLR / 3 / 5.436 / 3.228 / B / M(3)
00120529.2 / SAM domain and HD domain-containing protein 1 / IIND[pS]D[pS]ESEETVQVK / 2 / 3.735 / 3.492 / B
00120761.3 / Splice Isoform Erythrocyte of Band 3 anion transport protein / DHEEVLEIPDRD[pS]EEELENIIGQIAYR / 3 / 7.605 / 6.724 / B / M(3,5)
00121135.4 / Splicing factor, arginine/serine-rich 2 / SKSPPK[pS]PEEEGAV[pS][pS] / 2 / 3.28 / 3.47 / B / M(3,6)
00121136.6 / Isoform 1 of Apoptotic chromatin condensation / SQ[pS]P[pS]PPPLPEDLEK / 2 / 4.632 / 3.002 / B / M(3,9)
00121136.6 / Isoform 1 of Apoptotic chromatin condensation / [pS]QSP[pS]PPPLPEDLEK / 2 / 4.668 / 2.83 / B / M(3,9)
00121962.2
/ Thioredoxin domain-containing protein 1 precursor / KVEEEQEADEEDV[pS]EEEAEDR / 3 / 5.816 / 6.123 / A / M(1,10)
00121962.2 / Adult male aorta and vein cDNA / [pS]LSVT[pS]LGGLPVWEAER / 2 / 5.692 / 5.024 / B / M(3)
00122858.1 / Adult male aorta and vein cDNA / SLSV[pT][pS]LGGLPVWEAER / 2 / 5.966 / 4.545 / B / M(3)
00122858.1 / Isoform 1 of Solute carrier organic anion transporter family member 1B2 / KN[pS]A[pS]LHVLK / 2 / 5.172 / 3.778 / B / M(3)
00123181.2 / Isoform 1 of SAPS domain family member 3 / IQQFDDGG[pS]DEEDIWEEK / 2 / 4.542 / 3.726 / B / M(12)
00123181.2 / Myosin-9 / KGTGDC[pS]DEEVDGK / 2 / 4.28 / 3.186 / A / M(2,3)
00123624.8 / Myosin-9 / KGTGDC[pS]DEEVDGKADGADAK / 3 / 4.798 / 3.356 / A / M(2,3)
00123624.8 / Protein KIAA1967 homolog / [pS]VA[pS]NQSEMEYSSLQDMPK / 2 / 6.564 / 3.923 / B / M(3,12)
00124248.1 / Protein KIAA1967 homolog / [pS]VA[pS]NQ[pS]EMEYSSLQDMPK / 2 / 5.215 / 3.066 / B / M(3,12)
00125515.3 / Chloride channel, nucleotide-sensitive, 1A / LGEESKEPL[pS]DEDEEDNDDVEPISEFR / 3 / 5.68 / 3.429 / A / M(3,12)
00126317.1 / PCTP-like protein / AGGAGGEG[pS]DDDTSLT / 1 / 2.651 / 2.008 / A / M(3)
00126338.4 / MIDA1 / KEL[pS]EE[pS]EDEELQLEEFPMLK / 2 / 5.167 / 4.25 / B / M(3,6)
00127271.1 / thymopoietin / GPPDF[pS][pS]DEEREPTPVLGSGASVGR / 3 / 6.055 / 3.34 / B / M(3)
00127415.1 / Isoform 1 of WD repeat protein 23 / GAANLQLIQALpSD[pS]EEEHDSAWDGR / 3 / 3.683 / 3.258 / B / M(3)
00127493.1 / Nucleophosmin / CGSGPVHISGQHLVAVEEDAE[pS]EDEDEEDVK / 3 / 7.131 / 6.384 / A / M(2,3)
00127941.1 / Anaphase-promoting complex subunit 4 / IKEEVL[pS]ESE[pS]EAHQDAAALDPDVVIK / 3 / 3.175 / 3.529 / B
00127989.1 / Sid2057p / [pS]ASPDDDLGSSNWEAADLGNEER / 2 / 6.099 / 2.983 / B / M(6,12)
00128249.1
/ Telomerase-binding protein p23 / DWEDD[pS]DEDMSNFDR / 2 / 6.274 / 5.223 / B / M(1,3)
00128249.1 / Alpha-2-HS-glycoprotein precursor / VMHTQCHSTPD[pS]AEDVR / 3 / 4.647 / 2.403 / A / M(3)
00128249.1 / Alpha-2-HS-glycoprotein precursor / HAFSPVASVE[pS]A[pS]GETLHSPK / 2 / 6.045 / 5.583 / B / M(3)
00128249.1 / Alpha-2-HS-glycoprotein precursor / HAFSPVA[pS]VE[pS]A[pS]GETLHSPK / 2 / 5.328 / 5.099 / B / M(3)
00128975.2 / Death-associated protein 1 / DKDDQEWEST[pS]PPKPTVFISGVIAR / 3 / 4.913 / 3.467 / A / M(8)
00128975.2 / Death-associated protein 1 / DKDDQEWE[pS]TSPPKPTVFISGVIAR / 3 / 4.338 / 3.723 / B
00129319.3 / Protein phosphatase 1 regulatory subunit 7 / RVE[pS]EE[pS]GDEEGKK / 2 / 1.929 / 3.061 / B / M(6)
00131125.1 / BCL2/adenovirus E1B 19 kDa protein-interacting protein 3-like / DH[pS][pS]Q[pS]EEEVVEGEKEVEALKK / 3 / 3.94 / 1.798 / B / M(3)
00132134.2 / 12 days pregnant adult female placenta cDNA / RLEI[pS]PD[pS]SPER / 2 / 3.882 / 2.937 / B / M(3,10)
00132134.2 / 12 days pregnant adult female placenta cDNA / RLEI[pS]PDS[pS]PER / 2 / 3.541 / 2.574 / B / M(3,10)
00133174.3 / Adult male corpora quadrigemina cDNA / GQTPL[pT]EG[pS]EDLDGHSDPEE[pS]FAR / 3 / 3.901 / 3.124 / B / M(3)
00133349.1
/ Calcium-regulated heat stable protein / DR[pS]P[pS]PLRGNVVP[pS]PLPTR / 3 / 4.825 / 3.576 / B / M(3,8)
00134398.6 / Translocation protein SEC62 / EELEQQ[pT]DGDCDEEDDDKDGEVPK / 3 / 5.081 / 1.826 / A / M(3)
00135190.3 / Ran-binding protein 3 / SAGS[pS][pS]PEAGED[pS]DHEDGNYCPPVKR / 3 / 5.731 / 3.108 / B / M(3)
00135443.2 / DNA topoisomerase 2-beta / IVETIN[pS]DSD[pS]EFGIPK / 2 / 3.113 / 2.77 / B / M(3)
00135660.4 / Serum deprivation-response protein / SLEETLHNVDL[pS][pS]DDELPR / 2 / 5.793 / 2.95 / B / M(3,6)
00135971.1 / Tight junction protein ZO-1 / DDISEIQSLApSDH[pS]GR / 2 / 4.413 / 3.559 / B / M(10)
00135971.1 / Tight junction protein ZO-1 / VQIPVSHPDPEPV[pS]DNEDDSpYDEEVHDPR / 3 / 5.394 / 3.799 / B / M(3,10)
00136134.1 / Isoform 1 of Protein NDRG2 / [pS]R[pT]L[pS]QSSESGTL[pS]GPPGHTMEVSC / 2 / 5.131 / 3.641 / B / M(3,6,7)
00136134.1 / Isoform 1 of Protein NDRG2 / [pS]RTLSQ[pS]SESGTL[pS]GPPGHTMEVSC / 2 / 5.023 / 3.306 / B / M(6,7)
00136134.1 / Isoform 1 of Protein NDRG2 / TASLTSAA[pS]IDG[pS]R[pS]R / 2 / 4.368 / 3.132 / B / M(3,10)
00136134.1 / Isoform 1 of Protein NDRG2 / [pS]RTL[pS]QSSESGTL[pS]GPPGHTMEVSC / 3 / 4.263 / 4.259 / B / M(3,6,7)
00136134.1 / Isoform 1 of Protein NDRG2 / SR[pT]A[pS]LTSAASIDGSR / 2 / 5.001 / 5.21 / B / M(6,7)
00136134.1 / Isoform 1 of Protein NDRG2 / TA[pS]LTSAA[pS]IDGSR / 2 / 5.273 / 4.24 / B / M(6,7)
00136134.1 / Isoform 1 of Protein NDRG2 / [pS]R[pT]A[pS]LTSAASIDGSR / 2 / 4.825 / 4.759 / B / M(3)
00136134.1 / Isoform 1 of Protein NDRG2 / [pS]R[pT]LSQSSESGTL[pS]GPPGHTMEVSC / 2 / 5.488 / 3.829 / B / M(3,6,7)
00136134.1 / Isoform 1 of Protein NDRG2 / [pT]L[pS]QSSESGTL[pS]GPPGHTMEVSC / 2 / 5.367 / 3.224 / B / M(3,6,7)
00136134.1 / Isoform 1 of Protein NDRG2 / SRTL[pS]QS[pS]ESGTL[pS]GPPGHTMEVSC / 3 / 5.179 / 4.259 / B / M(6,7)
00136134.1 / Isoform 1 of Protein NDRG2 / L[pS]RpSR[pT]ASLTSAASIDGSR / 3 / 3.97 / 3.732 / B / M(3)
00137459.4
/ PREDICTED: HIV-1 induced protein / LQRPKEE[pS][pS]EDENEVSNILR / 3 / 3.005 / 3.019 / B / M(3)
00137668.1 / Histone deacetylase 2 / IACDEEF[pS]D[pS]EDEGEGGRR / 2 / 4.718 / 3.119 / B / M(3)
00137802.2 / PREDICTED: hypothetical protein LOC69638 / KDGRVPPQS[pT]TNGAG[pT]WPGQPIER / 2 / 3.075 / 2.649 / A
00138209.1 / Isoform 2A of Desmocollin-2 precursor / GSAAG[pS]VGCC[pS]DLQEEDGLEFLDHLEPK / 3 / 4.087 / 2.944 / B
00138209.1 / Isoform 2A of Desmocollin-2 precursor / G[pS]AAGSVGCC[pS]DLQEEDGLEFLDHLEPK / 3 / 4.173 / 2.983 / B
00138343.7 / PREDICTED: oxysterol binding protein isoform 1 / MLAE[pS]DD[pS]GDEESVSQTDKTELQSTLR / 3 / 5.616 / 3.487 / B / M(3)
00139259.1 / Isoform 1 of Arginine/serine-rich-splicing factor 10 / RH[pS]H[pS]H[pS]PMSTR / 2 / 3.193 / 2.867 / B / M(2,6)
00139259.1 / Isoform 1 of Arginine/serine-rich-splicing factor 10 / RR[pS]P[pS]PYYSR / 3 / 2.463 / 3.22 / A / M(2,3)
00139795.2 / 60S acidic ribosomal protein P2 / KEE[pS]EE[pS]DDDMGFGLFD / 2 / 5.039 / 3.901 / B / M(3,8)
00139795.2 / 60S acidic ribosomal protein P2 / KEESEE[pS]DDDMGFGLFD / 2 / 4.891 / 3.922 / B / M(3,8)
00139795.2 / 60S acidic ribosomal protein P2 / KEE[pS]EESDDDMGFGLFD / 2 / 4.667 / 3.026 / B / M(3,8)
00139795.2 / 60S acidic ribosomal protein P2 / DSGTMG[pS]D[pS]DESVIQTK / 2 / 2.733 / 2.248 / B / M(3,6)
00187443.1 / Eukaryotic translation initiation factor 5 / EAEEE[pS][pS]GGEEEDEDENIEVVYSK / 2 / 5.221 / 2.973 / B / M(3,12)
00223738.2 / Serine/threonine-protein kinase OSR1 / TEDGGWEW[pS]DDEFDEESEEGR / 2 / 5.184 / 4.005 / B / M(3,12)
00223738.2 / Serine/threonine-protein kinase OSR1 / SL[pS]Y[pS]PVER / 2 / 3.333 / 2.662 / B / M(3)
00223738.2 / Serine/threonine-protein kinase OSR1 / R[pS][pS]SEL[pS]PEVVEK / 2 / 4.892 / 4.626 / B / M(3,12)
00223738.2 / Serine/threonine-protein kinase OSR1 / NH[pS]G[pS]R[pT]PPVALSSSR / 2 / 4.751 / 3.45 / B / M(3)
00223738.2 / Serine/threonine-protein kinase OSR1 / AQ[pS]GTD[pS][pS]PEHKIPAPR / 2 / 3.95 / 2.737 / B / M(1,6,12)
00226282.3
/ Cobll1 protein / ITVEKDPDSALGI[pS]DGET[pS][pS]SK / 3 / 3.042 / 2.921 / B / M(3)
00229080.5 / 17 days embryo kidney cDNA / IEDVG[pS]DEEDDSGKDK / 2 / 5.828 / 4.437 / A / M(1,8)
00229080.5 / 17 days embryo kidney cDNA / IEDVG[pS]DEEDDSGKDKK / 2 / 4.437 / 3.94 / A / M(1,8)
00229080.5 / 17 days embryo kidney cDNA / IEDVG[pS]DEEDDSGK / 2 / 5.018 / 3.916 / B / M(1,8)
00229784.2 / Transcriptional repressor p66 alpha / RPP[pS]PDVIVL[pS]DSEQ[pS][pS]PR / 3 / 4.24 / 5.079 / B / M(3)
00229804.4 / Adult male liver cDNA / AE[pS][pS]D[pS]GAESEEEEAQEELKGAEQSGSDDKK / 3 / 5.127 / 3.55 / B / M(3)
00229804.4 / Adult male liver cDNA / AESSD[pS]GAE[pS]EEEEAQEELK / 2 / 6.93 / 5.622 / B / M(3)
00229804.4 / Adult male liver cDNA / AESSD[pS]GAE[pS]EEEEAQEELKGAEQSGSDDKK / 3 / 5.981 / 4.409 / B / M(3)
00229856.1
/ CDNA fis, clone TRACH2007688 / GHGH[pS]DEEDEEQPR / 3 / 3.764 / 2.112 / A
00229859.1 / Eif3s9 protein / AKPAAQSEEETATSPAA[pS]P[pT]PQSAER / 3 / 5.553 / 3.667 / A / M(2,3)
00229859.1 / Eif3s9 protein / GH[pS]AGAEEEGG[pS]DG[pS]AAEAEPR / 2 / 5.837 / 5.603 / B / M(2,3)
00313817.1 / Hepatoma-derived growth factor / SCAAEPEVEPEAHEGDGDKKGSAEG[pS][pS]DEEGK / 3 / 5.213 / 4.864 / B / M(3,9)
00313817.1 / Hepatoma-derived growth factor / GSAEG[pS][pS]DEEGKLVIDEPAK / 2 / 5.823 / 4.503 / B / M(3,9)
00313817.1 / Hepatoma-derived growth factor / G[pS]AEG[pS]SDEEGKLVIDEPAK / 2 / 5.525 / 4.792 / B / M(3,9)
00313817.1 / Hepatoma-derived growth factor / G[pS]AEGS[pS]DEEGKLVIDEPAKEK / 2 / 4.122 / 1.949 / B / M(3,9)
00313817.1 / Hepatoma-derived growth factor / GSAEG[pS][pS]DEEGKLVIDEPAKEK / 3 / 3.906 / 3.757 / B / M(3,9)
00314240.5
/ high mobility group AT-hook 1 / KLEKEEEEGISQE[pS][pS]EEEQ / 2 / 4.552 / 4.186 / B / M(2,3)
00314240.5 / Isoform 1 of Electrogenic sodium bicarbonate cotransporter 1 / NL[pT][pS]SSLNDISDKPEKDQLK / 2 / 4.919 / 2.921 / B / M(3)
00314950.2 / 60S acidic ribosomal protein P0 / AEAKEE[pS]EE[pS]DEDMGFGLFD / 2 / 4.557 / 3.594 / B / M(10,12)
00316623.2 / 13 days embryo male testis cDNA / G[pS]LASLD[pS]LR / 2 / 2.65 / 3.236 / B / M(3)
00316623.2 / 13 days embryo male testis cDNA / GSLA[pS]LD[pS]LR / 2 / 3.488 / 3.236 / B / M(1,3)
00319830.7 / Spectrin beta chain, brain 1 / TSSKE[pS][pS]PVP[pS]PTLDRK / 2 / 4.801 / 3.436 / B / M(2,10)
00319973.2 / Membrane associated progesterone receptor component 1 / EGEEPTVY[pS]DDEEPK / 2 / 4.041 / 3.243 / A / M(3,4)
00320208.2 / Elongation factor 1-beta / DDDDIDLFG[pS]DDEEESEEAK / 2 / 5.877 / 5.329 / B / M(9,10)
00320208.2 / Elongation factor 1-beta / DDDDIDLFG[pS]DDEEESEEAKK / 2 / 4.533 / 4.204 / B / M(9,10)
00320690.1 / Serine/threonine-protein kinase PRP4 homolog / [pS]R[pS]PLLNDR / 2 / 1.328 / 2.969 / B / M(3,6)
00320690.1 / Serine/threonine-protein kinase PRP4 homolog / AD[pS]DGDL[pS]ENDDGAGDLR / 2 / 4.565 / 4.268 / B / M(3)
00322145.9
/ Protein tyrosine phosphatase-like A domain containing 1 / WLDE[pS]DAEMELR / 2 / 4.747 / 4.178 / A / M(1,10)
00323349.2 / Tight junction protein ZO-2 / SR[pS]P[pS]PESR / 2 / 3.474 / 2.771 / B / M(2,3)
00330804.3 / Heat shock protein HSP 90-alpha / DKEV[pS]DDEAEEKEEK / 2 / 4.362 / 4.604 / A / M(12)
00330804.3 / Heat shock protein HSP 90-alpha / ERDKEV[pS]DDEAEEK / 2 / 2.277 / 4.223 / A / 1,10
00330804.3 / Heat shock protein HSP 90-alpha / ESDDKPEIEDVG[pS]DEEEEEK / 3 / 5.151 / 3.075 / A / 3,8
00330804.3 / Heat shock protein HSP 90-alpha / ESDDKPEIEDVG[pS]DEEEEEKK / 2 / 3.663 / 3.943 / B / M(3,8)
00330804.3 / Heat shock protein HSP 90-alpha / DKEV[pS]DDEAEEK / 2 / 4.802 / 3.922 / A / M(12)
00331644.4 / Proteasome subunit alpha type 3 / ESLKEEDE[pS]DDDNM / 2 / 4.926 / 3.899 / B / M(3)
00337893.2 / Pyruvate dehydrogenase E1 component alpha subunit, somatic form, mitochondrial precursor / pYHGHSMSDPGV[pS]YR / 3 / 4.12 / 3.35 / B / M(3,12)
00337893.2 / Pyruvate dehydrogenase E1 component alpha subunit, somatic form, mitochondrial precursor / YHGHSM[pS]DPGV[pS]YR / 2 / 3.524 / 3.356 / A / M(3)
00337893.2 / Pyruvate dehydrogenase E1 component alpha subunit, somatic form, mitochondrial precursor / YHGH[pS]MSDPGV[pS]YR / 2 / 4.255 / 3.944 / A / M(3,11)
00337893.2 / Pyruvate dehydrogenase E1 component alpha subunit, somatic form, mitochondrial precursor / YHGH[pS]M[pS]DPGVSYR / 2 / 3.763 / 3.687 / A / M(3,11)
00341869.5
/ Nuclear ubiquitous casein and cyclin-dependent kinases substrate / NSQEDSED[pS]EEKDVK / 2 / 3.582 / 3.931 / B / M(3)
00341869.5 / Nuclear ubiquitous casein and cyclin-dependent kinases substrate / D[pS]G[pS]DEDFLMEDDDDSDYGSSK / 2 / 6.251 / 5.637 / A
00341869.5 / Nuclear ubiquitous casein and cyclin-dependent kinases substrate / KVVDYSQFQE[pS]DDADEDYGR / 2 / 5.238 / 5.767 / B / M(10,12)
00341869.5 / Nuclear ubiquitous casein and cyclin-dependent kinases substrate / DSGSDEDFLMEDDDD[pS]DYGSSK / 2 / 5.517 / 3.164 / B / M(6,9)
00341869.5 / Nuclear ubiquitous casein and cyclin-dependent kinases substrate / NSQED[pS]ED[pS]EEKDVK / 2 / 4.937 / 3.5 / A / M(3)
00342158.4
/ Nuclear pore membrane glycoprotein 210 precursor / APIVH[pT]DEK / 2 / 1.535 / 2.112 / B
00344088.5 / la related protein / VEPAWHDQDE[pT]S[pS]VKSDGAGGAR / 3 / 3.952 / 3.327 / B
00344088.5 / la related protein / KNTFTAW[pS]EED[pS]DYEIDDRDVNK / 3 / 4.822 / 4.527 / B / M(3,9)
00344088.5 / la related protein / ESPRPPAAAEAPAG[pS]DGEDGGRR / 3 / 3.347 / 2.89 / B
00344088.5 / la related protein / KNTFTAW[pS]EED[pS]DYEIDDR / 2 / 5.786 / 4.516 / A / M(3,9)
00344626.2
/ Glycerol-3-phosphate acyltransferase, mitochondrial precursor / SDEEDED[pS]DFGEEQR / 2 / 4.716 / 3.836 / B / M(3)
00344626.2 / Glycerol-3-phosphate acyltransferase, mitochondrial precursor / KLPELNWR[pS]DEEDED[pS]DFGEEQR / 3 / 4.59 / 3.257 / B / M(3)
00352475.3 / 28 kDa heat- and acid-stable phosphoprotein / [pS]LDSDE[pS]EDEDDDYQQKR / 2 / 5.342 / 3.594 / A / M(3)
00356888.4 / fibronectin type III domain containing 3a / M[pS]SPPP[pS]PQKCP[pS]PISEHNGLIK / 3 / 4.677 / 2.57 / B / M(3)
00396671.1 / ATP-binding cassette sub-family F member 1 / SKPAAAD[pS]EGEEEEEDTAK / 2 / 5.31 / 3.64 / B / M(3)
00407425.1 / Isoform 2 of Myosin-18A / FSHSYL[pS]D[pS]DTEAK / 2 / 5.842 / 4.843 / B / M(3)
00407425.1 / Isoform 2 of Myosin-18A / SSSPTSHWKPLAPDP[pS]DDEHDPVD[pS]ISRPR / 3 / 3.964 / 2.886 / B / M(1,6)
00420295.4 / Acetyl-Coenzyme A carboxylase alpha / FIIGSV[pS]EDN[pS]EDEISNLVK / 2 / 5.109 / 4.755 / B / M(3,10)
00420329.1 / Activating signal cointegrator / EEA[pS]DDDMEGDEAVVR / 2 / 5.921 / 3.269 / A / M(3,10)
00420807.3 / Splicing factor, arginine/Serine-rich 1 (ASF/SF2) / VKVDGPR[pS][pS]pYGR / 3 / 1.871 / 2.468 / B
00420807.3 / Splicing factor, arginine/Serine-rich 1 (ASF/SF2) / VKVDGPR[pS]P[pS]YGR / 3 / 3.046 / 2.374 / B
00453826.2
/ Matrin-3 / SYSPDGKE[pS]P[pS]DKK / 2 / 3.514 / 2.542 / B / M(2,6)
00453865.4 / Nolc1 protein / KAAAQTQPADSSDDSSDDSDS[pS][pS]EEEKKPPAK / 3 / 4.982 / 3.275 / B
00459443.4 / PREDICTED: similar to tankyrase 1-binding protein of 182 kDa / ASRVP[pS][pS]DEEVVEEPQSR / 2 / 4.938 / 4.205 / B / M(2,12)
00459443.4 / PREDICTED: similar to tankyrase 1-binding protein of 182 kDa / VP[pS][pS]DEEVVEEPQSR / 2 / 4.874 / 3.059 / A / M(2,12)
00462746.4 / Isoform 2 of C-jun-amino-terminal kinase-interacting protein 4 / [pS]ASQS[pS]LDKLDQELK / 2 / 3.965 / 3.719 / B / M(3)
00462746.4 / Isoform 2 of C-jun-amino-terminal kinase-interacting protein 4 / SASQ[pS][pS]LDKLDQELK / 2 / 3.573 / 3.68 / B / M(3,6)
00464316.2
/ Actin-binding LIM protein 3 / RF[pS][pS]GGEEEDFDR / 2 / 4.056 / 2.539 / B / M(3,10)
00466069.2 / Elongation factor 2 / F[pT]DTRKDEQER / 3 / 1.927 / 1.986 / B / M(3)
00468999.4 / Phosphatidate cytidylyltransferase 2 / LDGETA[pS]DSESR / 2 / 3.563 / 3.006 / B / M(1)
00480490.2 / mitochondrial tumor suppressor 1 isoform / VTVTEDPHID[pS]HDND[pS]DIQSSTEELTLR / 3 / 4.319 / 2.369 / B / M(3)
00556768.1 / Thyroid hormone receptor-associated protein 3 / [pS]R[pS]RSFSK / 2 / 2.071 / 2.122 / A
00556768.1 / Thyroid hormone receptor-associated protein 3 / WAHDKF[pS]GEEGEIEDDE[pS]GTENREEK / 3 / 4.525 / 4.916 / A / M(3)
00556768.1 / Thyroid hormone receptor-associated protein 3 / WAHDKF[pS]GEEGEIEDDE[pS]GTENR / 3 / 6.818 / 5.165 / B / M(3)
00556768.1 / Thyroid hormone receptor-associated protein 3 / WAHDKF[pS]GEEGEIEDDESG[pT]ENREEK / 3 / 5.966 / 3.312 / B / M(2,3)
00556861.3 / PREDICTED: similar to serine/arginine repetitive matrix 2 / [pS]R[pS]I[pS]PCPK / 2 / 1.574 / 2.396 / B
00605037.1 / Isoform 1 of Serine/arginine repetitive matrix protein 1 / KETE[pS]EAEDDNLDDLER / 2 / 3.785 / 4.292 / B / M(3)
00605037.1 / Isoform 1 of Serine/arginine repetitive matrix protein 1 / KE[pT]E[pS]EAEDDNLDDLER / 2 / 6.125 / 5.457 / B / M(3)
00605686.2 / Similar to protein phosphatase 1 / TREQE[pS][pS]GEEDNDLSPEER / 2 / 6.047 / 3.924 / B / M(3,12)
00620904.2 / 99 kDa protein / ARDVE[pS][pS]DDEGYDWGPATDL / 2 / 4.054 / 2.821 / B / M(3)
00678532.3 / Bone marrow macrophage cDNA / SH[pS]LPN[pS]LDYAQASER / 2 / 3.479 / 3.677 / B / M(3,10)

*, the double-underlined [pS] ([pS]) marked in peptide sequence represents the phosphorylation site that has not been reported before.

**, A: the phosphopeptides eluted in 1ststep by an80% acetonitrile solution containing 6% TFA;

B: the phosphopeptides eluted in 2ndstep by a solutionof NH4OH.

***, M: mouse.

Reference:

(1)Munton, R. P.; Cullen, R. T.; Zatchej, M. L.; Weinandy, F.; Waidelich, M.; Longo, M.; Gehrig, P.; Potthast, F.; Rutishauser, D.; Gerrits, B.; Panse, C.; Schlapbach, R.; Mansuy, I. M.Qualitative and quantitative analyses of protein phosphorylation in naive and stimulated mouse synaptosomal preparations. Mol. Cell. Proteomics, 2007, 6, 283-293.

(2)Trinidad, J. C.;Specht, C. G.; Thalhammer, A.; Schoepfer, R.; Burlingame, A. L., Comprehensive identification of phosphorylation sites in postsynaptic density preparations. Mol. Cell. Proteomics, 2006, 5, 914-922.

(3)Villén，J.；Beausoleil, S. A.; Gerber, S. A.; Gygi, S. P. Large-scale phosphorylation analysis of mouse liver. Proc. Natl. Acad. Sci. USA, 2007, 104, 1488-93.

(4)Jin, W. H.; Dai, J.; Zhou, H.; Xia, Q.C.; Zou, H. F.; Zeng, R. Phosphoproteome analysis of mouse liver using immobilized metal affinity purification and linear ion trap mass spectrometry. Rapid. Commun. Mass. Spectrom., 2004, 18, 2169-76

(5)Kopito, R. R.; Lodish, H. F. Primary structure and transmembrane orientation of the murine anion exchange protein. Nature, 1985, 316, 234-238.

(6)Carninci, P.; Kasukawa, T.; Katayama, S. The transcriptional landscape of the mammalian genome. Science, 2005, 309, 1559-1563.

(7)Okuda, T.; Kondoh, H. Identification of new genes ndr2 and ndr3 which are related to Ndr1/RTP/Drg1 but show distinct tissue specificity and response to N-myc. Biochem. Biophys. Res. Commun. 1999, 266, 208-215.

(8)Puente, L. G.; Voisin, S.; Lee, R. E. C.; Megeney,L.A. Reconstructing the regulatory kinase pathways of myogenesis from phosphopeptide data. Mol. Cell. Proteomics, 2006, 5, 2244-2251.

(9)Shu, H. J.; Chen, S.; Bi, Q.; Mumby, M.; Brekken, D. L. Identification of phosphoproteins and their phosphorylation sites in the WEHI-231 B lymphoma cell line. Mol.Cell.Proteomics, 2004, 3, 279-86.

(10) Trinidad, J. C; Thalhammer, A.; Specht, C. G.; Lynn, A. J.; Baker, P. R.; Schoepfer, R.; Burlingame, A. L. Quantitative analysis of synaptic phosphorylation and protein expression. Mol. Cell. Proteomics, submitted.

(11) Collins, M. O.; Yu, L.; Coba, M. P.; Husi, H.; Campuzan, I.; Blackstock, W. P.; Choudhary, J. S.; Grant, S.G.N. Proteomic analysis of in vivo phosphorylated synaptic proteins. J.Biol. Chem, 2005, 280, 5972-5982.

(12) Ballif, B. A.; Villén, J.; Beausoleil, S. A.; Schwartz, D.; Gygi, S. P. Phosphoproteomic analysis of the developing mouse brain. Mol. Cell Proteomics, 2004, 3, 1093-1101.