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Table 1 Test matrix phosphopeptides

From: Phosphoproteomes of Strongylocentrotus purpuratus shell and tooth matrix: identification of a major acidic sea urchin tooth phosphoprotein, phosphodontin

Glean3_entry

Protein

Peptide

No. of P

Best Motif

Cleavage

Tot. no.5

041361b,2

P19 (Q8MUL3; Sp-P19)

K. 33IEEGQAS GEGAGEEGK48 .D (Fig. 2)

1 3

-

KR

KD

1

2

048671a,b

Similar to SM30

(Sp-SM30-E)

R. 76QPGFGNPGT PGGR88 .Q (Fig. 1)

1 3

ERK/MAPK

KR

2

054192,4

Src family tyrosine kinase (B6DS93; Sp-SFK3)

R. 357IIEDEY IAR365 .E (S1.1)

1

EGFR

KR

2

086782

Similar to protein kinase C-delta 1

(Sp-Pkcd)

K. 725VALS PTDTSMLS S INQR741 .Q (S1.2)

2

CK1

KR

1

11637

Hypothetical protein (Leu-rich repeats)

(Sp-Lrr/Igr_14)

R. 290LGNLPIS R297 .E (S1.3)

1

NEK6

KR

KRD

2

3

13143

Hypothetical protein; Glu-rich motif (~aa108-154)

(Sp-Hypp_2072)

R. 332LIT PTNSS DEEEEK345 .D (S1.4)

3

CAMK2 CK2

KR

KRD

3

4

14937

Hypothetical protein; domains: partial Glyco_hydro_30, Ion_trans

(Sp-Trpm3)

K. 1217NFDDGS LELK1226 .A (S1.5)

1

PLK1

KD

KRD

3

1

15408

Hypothetical protein; Glu-rich motif (~aa85-339), Ser-rich motif (~aa1075-1113) (Sp-Hypp_3054)

K. 984QAESSGVS PT NSVGDVPDVIMVDG NK1009 .T (S1.6)

2

CK1

KR

1

15870

271232

Similar to ribosomal protein P1/SP-RPLP1 (Sp-Rpip1)

K. 94DES EES DDDMGFGLFD109 -- (S1.7)

2

CK1

KR

KD

8

1

16285

Hypothetical protein/similar to FLJ00139 protein, partial; domain:LIM2 (~aa50-110); partial overlap with Glean3:16293

R. 204FNASGS PVGSPQLER218 .H (S1.8)

R. 204FNASGS PVGS PQLER218 .H (S1.9)

1

2

GSK3

ERK/MAPK

KR

KR

1

3

 

(Sp-Hypp_126/Sp-Hypp_820)

K. 1057PLLS DGEEVEK1069 .E (S1.10)

1

CK2

KR

KD

KRD

8

11

19

  

R. 1086 S AALS DDDDQSPVPPAPR1102 .K (S1.11)

2

PKA, CK1

KR

3

18255

Hypothetical protein; domain:

LIM (~aa673-724); Glu-rich motif (~aa358-564), Ser-rich motif (~aa595-661) (Sp-Hypp_912)

K. 332DAVPVVIIESPS SDDLK348 .S (S1.12)

1

CK1

KR

KD

KRD

5

5

3

18389

Hypothetical protein; K-rich motif (~aa211-264) (Sp-Hypp_2383)

R. 140VTPLPVITEELS DPEESPR157 .N (S1.13)

1

CK2

KRD

2

186492

Similar to pleckstrin homology domain containing, family F (with FYVE domain) 2

(Sp-Plekhf2)

R. 204NAAPLDQDS DDDDDDDEDIDAITR227 .N

(S1.14)

1

-

KR

6

18666

Hypothetical protein/similar to Arg/Ser-rich splicing factor 4 (~aa1768-2208) (Sp-Zcchc11)

R. 1947DDPDAAEALVPGDDLS EEK1965 .R (S1.15)

1

-

KR

KD

KRD

7

5

1

20139

Hypothetical protein

(Sp-Cola2L_2)

R. 295FVQDDS ES NEADEDAPR311 .Y (S1.16)

2

-

KR

40

  

R. 295FVQDDS ES NEADEDAPRYPLAPQR318.N

(S1.17)

2

-

KR

3

  

R. 339NVAEAAGLSS NEVTQVK355 .Q (Fig. 3)

1

CK2

KR

KRD

22 79

  

R. 370QQQPLPFS EQQQEYR384 .Q (S1.18)

1

NEK6

KR

1

20613

Hypothetical protein (Sp-Hypp_2525)

K. 79AQDS ISS ITK88 .E (S1.19)

2

CK1

KD

2

217392

Similar to ribosomal protein P0/P1/P2; also contained in entry 11703 (Sp-Arp)

K. 233KEES EEES DDDMGFGLFD250 -- (S1.20)

2

CK1, CK2

KR

3

249914

Hypothetical protein

R. 142GPS LFGR148 .I (S1.21)

1

PKA/

AKT

KR

KRD

9

3

255152

Similar to sodium bicarbonate cotransporter (Sp-Slc4a_10)

K. 1094LSGS PLPTVR1103 .N (S1.22)

1

NEK6

KD

KRD

6

16

268632

Similar to eukaryotic translation initiation factor 3, subunit 8

(Sp-Eif3c)

R. 35FFLS DDDEEETK46 .R (S1.23)

1

CK2

KR

KRD

3

8

27937

116842

Similar to dynein light chain-1

(Sp-Dynlc2_6a/Sp-Dynlc2_4d)

K. 47DIASY IKK54 .E (S1.24)

1

EGFR

KD

1

  1. 1a,b, protein identified previously in test or spine matrix (1a) [10] or tooth matrix (1b) [11]. 2, known phosphoprotein in sea urchin or other eukaryotic species or similar to a known phosphoprotein. 3, non-phosphorylated peptide(s) also identified in the present or previous [10, 11] studies. 4, also in tooth matrix phosphoproteome (Table 2). 5, total number of this phosphopeptide with PEP < 0.01. KR, cleavage with lysyl endopeptidase and trypsin; KD, cleavage with lysyl endopeptidase and endoproteinase Asp-N; KRD, successive cleavage with lysyl endopeptidase, trypsin and endoprotease Asp-N. Phosphorylation sites with a localization probability ≥ 0.75 [39] are printed in bold and underlined. Phosphorylation sites with localization probability 0.5-0.75 are underlined. The entries are ordered according to increasing entry number. For scores and other relevant information see Additional file 1 (Additional file 1: Test matrix protein phosphorylation sites). Annotated best identification spectra are shown in Additional file 2 (Additional file 2: Selected spectra of test matrix phosphopeptides); numbering in brackets is the same as in Additional File 2. SpBase http://sugp.caltech.edu/SpBase/ annotations are given in brackets.
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