Table 3 The peptides with in vivo PTMs identified by both MODa and PEAKS 6 34 unique peptides of 18 proteins had new PTMs (labeled by underline) compared to the Uniprot annotation information

R.SYSCQVTHEGSTVEK[Methylation]. T

sp|B9A064

192 ~ 206

Immunoglobulin lambda-like polypeptide 5 OS = Homo sapiens GN = IGLL5 PE = 2 SV = 2

M.T[Acetylation]DGDYDYLIK.L

sp|O00194

2 ~ 11

Ras-related protein Rab-27B OS = Homo sapiens GN = RAB27B PE = 1 SV = 4

K.GDAGPP[Hydroxylation]GPAGPAGPPGPI.G

sp|P02452

836 ~ 862

Collagen alpha-1(I) chain OS = Homo sapiens GN = COL1A1 PE = 1 SV = 5

K.GDAGPP[Hydroxylation]GPAGPAGPPGPIGNVGAPGAK.G

R.EGAPGAEGSP[Hydroxylation]GR.D

1015 ~ 1026

K.DGEAGAQGPP[Hydroxylation]GPAGPAGER.G

613 ~ 631

R.DGNP[Hydroxylation]GSDGLPGR.D

sp|P02461

1013 ~ 1024

Collagen alpha-1(III) chain OS = Homo sapiens GN = COL3A1 PE = 1 SV = 4

R.DGNPGSDGLP[Hydroxylation]GR.D

R.TVAACNLPIVR[Methylation].G

sp|P02760

283 ~ 293

Protein AMBP OS = Homo sapiens GN = AMBP PE = 1 SV = 1

K.N[Oxidation or Hydroxylation] WGLSVYADKPETTK.E

sp|P02763

139 ~ 153

Alpha-1-acid glycoprotein 1 OS = Homo sapiens GN = ORM1 PE = 1 SV = 1

K.AGVET[Dehydration] TTPSK.Q

sp|P0CG05

51 ~ 60

Ig lambda-2 chain C regions OS = Homo sapiens GN = IGLC2 PE = 1 SV = 1

N.AMQVINNYQR[Methylation]. R

sp|P10153

53 ~ 62

Non-secretory ribonuclease OS = Homo sapiens GN = RNASE2 PE = 1 SV = 2

R.WGYSSTAITR[Methylation]. Q

sp|P10253

376 ~ 385

Lysosomal alpha-glucosidase OS = Homo sapiens GN = GAA PE = 1 SV = 4

K.TGPIGPQGAP[Hydroxylation]GK.P

sp|P20908

1422 ~ 1433

Collagen alpha-1(V) chain OS = Homo sapiens GN = COL5A1 PE = 1 SV = 3

R.HS[Dehydration] PQEAPHVQYER.L

sp|P26992

25 ~ 37

Ciliary neurotrophic factor receptor subunit alpha OS = Homo sapiens GN = CNTFR PE = 1 SV = 2

R.LGPGMADICK[Methylation]. N

tr|B1AVU8

233 ~ 242

Proactivator polypeptide OS = Homo sapiens GN = PSAP PE = 4 SV = 1

K.AIPVAQDLNAPSDWDS[Phosphorylation] R.G

tr|B2RDA1

190 ~ 206

`Osteopontin OS = Homo sapiens GN = SPP1 PE = 2 SV = 1

K.ANDES[Phosphorylation] NEHSDVIDSQELSK.V

236 ~ 254

K.YPDAVATWLNPDPSQK[Methylation]. Q

36 ~ 51

R.GKDS[Phosphorylation] YETSQLDDQSAETHSHK.Q

207 ~ 227

K.AAT[Dehydration] GECTATVGK.R

tr|B4DPP8

90 ~ 101

Kininogen-1 OS = Homo sapiens GN = KNG1 PE = 2 SV = 1

K.LGQSLDCN[Oxidation or Hydroxylation] AEVYVVPWEK.K

333 ~ 350

K.YNSQNQSNNQFVLYR[Methylation]. I

32 ~ 46

R.GPWCY[Oxidation or Hydroxylation] VSGEAGVPEK.R

tr|B4DRR9

79 ~ 93

HGFL OS = Homo sapiens GN = PIK3IP1 PE = 2 SV = 1

R.GPWCYVSGEAGVPEK[Methylation]. R

K.CVN[Oxidation or Hydroxylation] HYGGYLCLPK.T

tr|B4DW75

3 ~ 15

EGF containing fibulin-like extracellular matrix protein 1 OS = Homo sapiens GN = EFEMP1 PE = 2 SV = 1

R.TSSYLCQYQCVN[Oxidation or Hydroxylation] EPGK.F

162 ~ 177

K.QNLLAPQNAVS[Phosphorylation] SEETNDFKQETLPSK.S

tr|C9JXD2

52 ~ 77

Osteopontin OS = Homo sapiens GN = SPP1 PE = 4 SV = 1 Epidermal growth factor OS = Homo sapiens GN = EGF PE = 4 SV = 1

K.QNLLAPQNAVSS[Phosphorylation] EETNDFK.Q

52 ~ 70

K.CIN[Oxidation or Hydroxylation] TEGGYVCR.C

tr|E7EVD2

888 ~ 898

N.SSCVN[Oxidation or Hydroxylation] TPGSFSCVCPEGFR.L

tr|E9PEA4

114 ~ 132

Uromodulin_ secreted form OS = Homo sapiens GN = UMOD PE = 4 SV = 1

R.D[Oxidation or Hydroxylation] WVSVVTPAR.D

409 ~ 418

R.DGPCGT[Dehydration] VLTR.N

419 ~ 428

R.MAETCVPVLR[Methylation]. C

246 ~ 255

R.STEYGEGYACDT[Dehydration] DLR.G

219 ~ 233

T.CVN[Oxidation or Hydroxylation] VVGSYLCVCPAGYR.G

159 ~ 175

V.N[Oxidation or Hydroxylation] VVGSYLCVCPAGYR.G

161 ~ 175

K.FEHCNFNDVTTR[Methylation]. L

tr|E9PNW4

67 ~ 78

CD59 glycoprotein OS = Homo sapiens GN = CD59 PE = 4 SV = 1

R.LRENELT[Dehydration] YYCCK.K

79 ~ 90

R.LRENELTYYCCK[Methylation]. K

R.YPNQVYYR[Methylation]. P

tr|F5GY30

96 ~ 103

Major prion protein OS = Homo sapiens GN = PRNP PE = 3 SV = 1

K.EGNPGPLGPIGP[dihydroxy] PGVR.G

tr|H7C157

827 ~ 842

Collagen alpha-2(V) chain OS = Homo sapiens GN = COL5A2 PE = 4 SV = 1