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

Zeis, Bettina; Lamkemeyer, Tobias; Paul, Rüdiger J; Nunes, Frank; Schwerin, Susanne; Koch, Marita; Schütz, Wolfgang; Madlung, Johannes; Fladerer, Claudia; Pirow, Ralph

doi:10.1186/1472-6793-9-7

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 sequences^a)	Sequence coverage^b)	Mascot score^c)	M_r predicted/ M_r gel^d)	pI predicted/ pI gel^e)	SP Length	Function^f) 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 (M_r) 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) M_r predicted/M_r 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)

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