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Table 4 The peptides identified by both software packages, and the corresponding proteins identified by either of the two software packages

From: Unrestrictive identification of post-translational modifications in the urine proteome without enrichment

Protein group (PEAKS PTM)cc

Peptide (Both)

Protein (MODa)c

5

K.AAT[Dehydration]GECTATVGK.R

 

8

  

49

K.AGAAAGGP[Oxidation or Hydroxylation]GVSGVCVCK.S

tr|B4E1N2

75

K.AGVET[Dehydration]TTPSK.Q

 

15

K.AIPVAQDLNAPSDWDS[Phosphorylation]R.

 

22

G

 

36

 

15

K.ANDES[Phosphorylation]NEHSDVIDSQELS

 

22

K.V

 

3

K.CCAAADPHECYAK[Methylation].V

tr|A6NBZ8

2

 

1

 

500

K.CIN[Oxidation or Hydroxylation]HYGGYLCLPR.S

tr|E9PKA3

90

K.CVN[Oxidation or Hydroxylation]HYGGYLCLPK.T

 

369

 

249

K.DGETGAAGPP[Oxidation or Hydroxylation]GPAGPAGER.G

tr|G8JLI4

15

 

22

 

36

 

21

 

304

K.EGNPGPLGPIGP[dihydroxy]PGVR.G

 

100

K.EGPVGLP[Oxidation or Hydroxylation]GIDGR.P

tr|F5H299

285

K.FELTGIPPAPR[Methylation].G

tr|A8K7Q2

1

K.FQNALLVR[Methylation].Y

tr|A6NBZ8

3

 

2

 

21

 

15

 

22

 

36

 

100

K.EGPVGLP[Oxidation or Hydroxylation]GIDGR.P

tr|F5H299

249

K.GEVGPP[Oxidation or Hydroxylation]GPAGSAGAR.G

tr|G8JLI4

 

K.GPP[Oxidation or Hydroxylation]GPQGPAGEQGPR.G

 

5

K.LGQSLDCN[Oxidation or Hydroxylation]AEVYVVPWEK.K

 

8

 

28

K.LHNLNSN[Oxidation or Hydroxylation]WFPAGSK.P

tr|B3KTI1

37

 

31

 

103

K.NGETGPQGPP[Oxidation or Hydroxylation]GPTGPGGDK.G

tr|E7ENY8

8

K.QNLLAPQNAVSS[Phosphorylation]EETNDFK.Q

tr|A6NBZ8

3

K.VHTECCHGDLLECADD[Methylation]R.A

 

2

 

1

 

3

K.VHTECCHGDLLECADDR[Methylation].A

 

2

 

1

 

5

K.YNSQNQSNNQFVLYR[Methylation].I

 

8

 

15

K.YPDAVATWLNPDPSQK[Methylation].Q

 

22

 

957

M.S[Acetylation]SSGTPDLPVLLTDLK.I

tr|E7ER57

100

P.GIAGHHGDQGAP[Oxidation or Hydroxylation]GSVGPAGPR.G

tr|F5H299

34

R.ALVFVDNHDNQR[Methylation].G

tr|B3KTI1

28

 

37

 

31

 

13

R.AVLPQEEEGS[Dehydration]GGGQLVTEVTK.K

tr|B7Z8R6

10

R.CKPVNTFVHEPLVDVQNVCFQE[Methylation]K.V

tr|G3V357

48

R.CVN[Oxidation or Hydroxylation]TYGSYECK.C

tr|F5H2N7

1

R.ETYGEMADCCAK[Methylation].Q

tr|A6NBZ8

15

R.GKDS[Phosphorylation]YETSQLDDQSAETHSHK.Q

 

36

 

100

R.GLHGEFGLP[Oxidation or Hydroxylation]GPAGPR.G

 
 

R.GPP[Oxidation or Hydroxylation]GESGAAGPTGPIGSR.G

 
 

R.GPSGPP[Oxidation or Hydroxylation]GPDGNK.G

 

103

R.GPTGPIGPP[Oxidation or Hydroxylation]GPAGQPGDK.G

tr|E7ENY8

13

R.HHGPT[Dehydration]ITAK.L

tr|B7Z8R6

10

R.HIIVACEGS[Dehydration]PYVPVHF.D

tr|G3V357

8

R.HS[Dehydration]PQEAPHVQYER.L

 

11

R.LGPGMADICK[Methylation].N

 

19

R.NPDSSTTGP[dihydroxy]WCYTTDPTVR.R

tr|C9JQ37

20

 

19

R.SGIECQLWR[Methylation].S

 

20

 

84

R.SYSCQVTHEGSTVEK[Methylation].T

 

73

 

100

R.TGEVGAVGP[Oxidation or Hydroxylation]PGFAGEK.G

tr|F5H299

 

R.TGEVGAVGPP[Oxidation or Hydroxylation]GFAGEK.G

 

90

R.TSSYLCQYQCVN[Oxidation or Hydroxylation]EPGK.F

 

13

R.VVAQGVGIPEDSIFT[Dehydration]MADR.G

tr|B7Z8R6

16

S.LQCYNCPNPTADCK[Methylation].T

tr|E9PI80

  1. cIn PEAKS 6, one peptide can belong to several protein groups. In contrast, in MODa, one peptide can only belong to one protein.