Table 2

Identified proteolytic enzymes from hypoxia-acclimated (Hyp) and normoxia-acclimated (Norm) Daphnia pulex

Spot no.

Specificity

Hyp: Norm

Matched peptide

sequencesa)

Sequence

coverageb)

Mascot

scorec)

Mr predicted/

Mr geld)

pI predicted/

pI gele)

SP

Length

Functionf)

Model name [Protein ID, Reference ID]


28

1.2

DDLTETLK

EPNNPDDAIPVNTAR

ITTPAEDR

ITTPAEDRR

VIVTETDYLK

VIVTETDYLKK

KLVALLDATPTR

LVALLDATPTR

TIANYIHWR

TETTLMIANLK

TLVDDATWMDDGTK

KDFLTLR

LEEQILTDPHSPSR

VIGPLSNNEDFAR

18.0%

876

75.4/72

4.36/4.4

Peptidase M13

estExt_Genewise1Plus.C_750105

[200882, 200882]

IYGSYQACR

YVELSNK

ELHAYIR

VLGVAPPVGR

VWLEAENAK

6.6%

210

73.4/72

4.81/4.4

19

Peptidase M2

PASA_GEN_6000071 [307230, 307230]

SGQAVEYLPGR

TYTVAADDAR

3.6%

116

64.1/67

4. 66/4.4

19 (?)

Carboxylesterase, type B

PASA_GEN_25200006 [304160, 304160]

NADEAVAEGCNNR

IVTTDIADQSK

4.6%

135

58.4/67

4.34/4.4

Sphingomyelin phosphodiesterase

PASA_GEN_2900053 [304453, 304453]

TYTVDGPR

IVTTDIADQSK

3.6%

88

59.4/67

4.57/4.4

Sphingomyelin phosphodiesterase

PASA_GEN_13800028 [301526, 301526]


31

0.8*

TFENRDMPLVK

KAIVVDGGIHAR

AIVVDGGIHAR

NRKPNAGIGGIPCIGTDMNR

KPNAGIGGIPCIGTDMNR

GGAGIPFSYTVEMR

DEGTFGFQLPAR

QILPNNEEVWEGVK

VMAESLF

22.4%

475

44.8/30

4.82/4.75

16

Carboxypeptidase A

estExt_Genewise1Plus.C_150058

[195011, 195011]

KAIVVDGGIHAR

AIVVDGGIHAR

LTAVYGTR

GGAGIPFSYTVEMR

VMAESLF

10.3%

246

44.8/30

4.87/4.75

16

Carboxypeptidase A

NCBI_GNO_1500041 [315693, 315693]

GVTDLTIFR

VVAGEHSLR

6.5%

135

29.1/30

4.88/4.75

15

Trypsin

SNAP_00016212 [231152, 248154]


32

0.9

IVGGTQASPNEFPYQISLR

LGSHICGASIYK

HEHVSYSSR

GSYGTNAITDSMICAGFR

22.7%

177

26.7/23

5.43/4.98

17

Trypsin

estExt_fgenesh1_kg.C_230008

[230885, 230885]


36

0.85

VVAGEHSLR

SVDVPVVDDDTCNR

8.9%

149

27.2/30

4.32/4.39

Trypsin

e_gw1.85.43.1 [59836, 59836]

LTAAEEPTRVEIR

IRNDVALIK

7.5%

80

31.5/30

5.48/4.39

15

Trypsin

PASA_GEN_2900126 [304512, 304512]


37

0.85

GVTDLTIFR

VVAGEHSLR

VVAGEHSLRTDSGLEQNR

9.8%

159

29.1/29

4.88/4.39

15

Trypsin

SNAP_00016212 [231152, 248154]

VVAGEHSLR

SVDVPVVDDDTCNR

8.9%

149

27.2/29

4.32/4.39

Trypsin

e_gw1.85.43.1 [59836, 59836]


38

1.18

GLADADIAVFK

LIWMGQYNR

YYRDELAGK

10.7%

123

29.8/29

4.5/4.46

19

Placental protein 11

PASA_GEN_12200001 [301221, 301221]

GLADADIAVFK

LIWMGQYNR

YYRDELAGK

8.0%

123

38.7/29

4.57/4.46

20

Placental protein 11

PASA_GEN_6000032 [307196, 307196]

VVAGEHSLR

SVDVPVVDDDTCNR

8.9%

149

27.2/29

4.32/4.46

Trypsin

e_gw1.85.43.1 [59836, 59836]

GVTDLTIFR

VVAGEHSLR

6.5%

80

29.1/29

4.88/4.46

15

Trypsin

SNAP_00016212 [231152, 248154]


39

0.92

VVAGEHSLR

SVDVPVVDDDTCNR

8.9%

149

27.2/29

4.32/4.59

Trypsin

e_gw1.85.43.1 [59836, 59836]

GVTDLTIFR

VVAGEHSLR

6.5%

120

29.1/29

4.88/4.59

15

Trypsin

SNAP_00016212 [231152, 248154]


40

0.57

TTEEYYVSVQK

TGGGCYSYIGR

6.5%

112

26.9/25

5.32/4.47

Astacin-like metalloprotease (ACN)

FRA_fgenesh1_kg.C_scaffold_182000002

[347623, 93694]

GVTDLTIFR

VVAGEHSLR

6.5%

109

30.7/25

4.82/4.47

15

Trypsin

SNAP_00016212 [231152, 248154]


41

1.16

LTAAEEPTR

LTAAEEPTRVEVR

IINDVALIK

9.1%

141

25.3/25

4.52/4.65

Trypsin

e_gw1.29.198.1 [52244, 52244]


Identification was based on 2D gel electrophoresis and nano-HPLC-ESI-MS/MS analysis of trypsin-digested proteins matched against the "Frozen Gene Catalog" of the D. pulex protein database [26], which contains all manual curations as of July 3, 2007 as well as automatically annotated models chosen from the "Filtered Models" v1.1 reference set. The compiled information includes the spot number (Figure 1A, B), the hypoxia-to-normoxia expression ratio, the number and sequences of matched peptides, the sequence coverage, the Mascot score as a statistical measure of identification probability, the theoretical and experimental molecular weight (Mr) and isolectric point (pI) of the mature protein (without signal peptide), the predicted length of the N-terminal signal peptide (SP) in extracellular proteins, the putative function of the protein, as well as the gene model name and protein identification number for the locus. The protein IDs may differ from those contained in the "Filtered Models v1.1" reference set. The Reference ID can be used to retrieve the corresponding models from this reference set. Underlined and bold-printed sequences indicate peptides that are specific for a globin gene.

a) Matched peptide sequences: tryptic peptide sequences identified via nano-HPLC-ESI-MS/MS.

b) Sequence coverage %: percentage of predicted protein sequence covered by matched peptides.

c) Probability based Mascot score: -10*Log(P), where P is the probability that the observed match is a random event. Scores > 38 indicate identity or extensive homology (p < 0.05). Protein scores are derived from ions scores as a non-probabilistic basis for ranking protein hits. The Mascot-score calculation was performed using whole-protein sequence (including the N-terminal signal peptide in case of extracellular proteins).

d) Mr predicted/Mr gel: molecular mass of predicted protein/of protein on gel.

e) pI predicted/pI gel: isoelectric point of predicted proteins/of proteins on gel.

f) Function of identified proteins was obtained either via automated blastp search provided by JGI or after manual curation of a gene model.

* p < 0.05 (t-Test)

Zeis et al. BMC Physiology 2009 9:7   doi:10.1186/1472-6793-9-7

Open Data