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Table 2 Identified proteolytic enzymes from hypoxia-acclimated (Hyp) and normoxia-acclimated (Norm) Daphnia pulex

From: Acclimatory responses of the Daphnia pulex proteome to environmental changes. I. Chronic exposure to hypoxia affects the oxygen transport system and carbohydrate metabolism

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]
  1. 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.
  2. a) Matched peptide sequences: tryptic peptide sequences identified via nano-HPLC-ESI-MS/MS.
  3. b) Sequence coverage %: percentage of predicted protein sequence covered by matched peptides.
  4. 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).
  5. d) Mr predicted/Mr gel: molecular mass of predicted protein/of protein on gel.
  6. e) pI predicted/pI gel: isoelectric point of predicted proteins/of proteins on gel.
  7. f) Function of identified proteins was obtained either via automated blastp search provided by JGI or after manual curation of a gene model.
  8. * p < 0.05 (t-Test)
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