User talk:Farnad Zaghi

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Proteomic E-coli Project

Two-dimensional gel electrophoresis of E. Coli, followed by MALDI-TOF spectra were acquired for protein identification. 2D Gel Explenation.jpg

Mascot Wizard Results

result

Spot Number NCBI accession (gI) number Uniprot accession # Theor-etical Mass Theor-etical pI RMS error (ppm) # peptides matched % Coverage Mascot Protein Score Mascot Score Highest Non-Homologous Protein Name Summary URL Protein View URL Revised Protein Summary Additional Protein View Additional Protein View Comment input_data_file '
1 (E1) no hit http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111207/F015434.dat&sessionID=FZaghi_81508037746369 Invirtogel_E1_0001
2 (E3) no hit http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111207/F015433.dat&sessionID=FZaghi_81508037746369 Invirtogel_E3_0001
3 (E5) no hit http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111207/F015432.dat&sessionID=FZaghi_81508037746369 Invirtogel_E5_0001
4 (E7) 297521112|ref NP_06939498 19514 5.17 30 10 69% 120 87 malate dehydrogenase [Escherichia coli OP50] http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111207/F015435.dat&sessionID=FZaghi_81508037746369 http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015435.dat&hit=1 malate dehydrogenase and malate dehydrogenase NAD-dependent for deifferent strant of E coli Invirtogel_E7_0001
15803770|ref NP_289804 32488 5.61 31 11 44% 112 87 malate dehydrogenase [Escherichia coli O157:H7 EDL933] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015435.dat&hit=2
91212656|ref YP_542642 35207 6.03 31 11 41% 109 87 malate dehydrogenase [Escherichia coli UTI89] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015435.dat&hit=9
170018520|ref YP_001723474 32478 5.61 31 11 44% 112 87 malate dehydrogenase [Escherichia coli ATCC 8739] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015435.dat&hit=6
209920706|ref YP_002294790 32504 5.61 31 11 44% 112 87 malate dehydrogenase [Escherichia coli SE11 http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015435.dat&hit=8
218555800|ref YP_002388713 32461 5.61 30 10 37% 95 87 malate dehydrogenase [Escherichia coli IAI1] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015435.dat&hit=19
218706850|ref YP_002414369 32487 6.21 30 10 37% 95 87 "malate dehydrogenase [Escherichia coli UMN026]
" http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015435.dat&hit=20
110643470|ref YP_671200 32502 5.61 30 10 37% 95 87 malate dehydrogenase [Escherichia coli 536] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015435.dat&hit=21
194429110|ref ZP_03061640 32488 5.61 31 11 44% 112 87 malate dehydrogenase, NAD-dependent [Escherichia coli B171] http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111207/F015435.dat&sessionID=FZaghi_81508037746369
191168165|ref ZP_03029961 32477 5.61 30 10 37% 95 87 malate dehydrogenase, NAD-dependent [Escherichia coli B7A] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015435.dat&hit=17
300898002|ref ZP_07116376 35206 6.85 30 10 35% 92 87 malate dehydrogenase, NAD-dependent [Escherichia coli MS 198-1] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015435.dat&hit=22
301022169|ref ZP_07186088 35207 6.36 30 10 35% 92 87 malate dehydrogenase, NAD-dependent [Escherichia coli MS 69-1] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015435.dat&hit=23
300937348|ref ZP_07152185 35223 6.36 30 10 35% 92 87 malate dehydrogenase, NAD-dependent [Escherichia coli MS 21-1] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015435.dat&hit=24
300817513|ref ZP_07097729 35196 6.36 30 10 35% 92 87 malate dehydrogenase, NAD-dependent [Escherichia coli MS 107-1] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015435.dat&hit=25
300979785|ref ZP_07174711 35221 6.36 30 10 35% 92 87 malate dehydrogenase, NAD-dependent [Escherichia coli MS 200-1] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015435.dat&hit=26
5 (E9) 16130476|ref NP_417046 45459 6.03 24 16 27% 169 NONE serine hydroxymethyltransferase [Escherichia coli str. K-12 substr. MG1655] http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111207/F015415.dat&sessionID=FZaghi_450724603025029 http://128.59.63.100/mascot/cgi/protein_view.pl?file=..%2Fdata%2F20111207%2FF015415.dat;hit=2 serine/ glycine hydroxymethyltransferase for different strains of E coli Invirtogel_E9_0001
15803076|ref NP_289107 45487 6.03 24 16 27% 169 NONE serine hydroxymethyltransferase [Escherichia coli O157:H7 EDL933] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015415.dat&hit=3
218706054|ref YP_002413573 45445 6.03 24 16 27% 169 NONE serine hydroxymethyltransferase [Escherichia coli O157:H7 EDL933] http://128.59.63.100/mascot/cgi/protein_view.pl?file=..%2Fdata%2F20111208%2FF015472.dat;hit=7
26248915|ref NP_754955 45746 6.13 24 16 27% 167 NONE serine hydroxymethyltransferase [Escherichia coli CFT073 http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111208/F015472.dat&hit=8
291283776|ref YP_003500594 45501 6.13 24 16 27% 167 NONE Serine hydroxymethyltransferase [Escherichia coli O55:H7 str. CB9615] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111208/F015472.dat&hit=10
297521279|ref ZP_06939665 16829 7.74 44 11 51% 128 serine hydroxymethyltransferase [Escherichia coli OP50] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111208/F015472.dat&hit=16
300898338|ref ZP_07116686 45732 6.13 24 16 27% 167 NONE glycine hydroxymethyltransferase [Escherichia coli MS 198-1]. http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111208/F015472.dat&hit=9
301024834|ref ZP_07188471 45776 6.13 24 15 26% 155 NONE glycine hydroxymethyltransferase [Escherichia coli MS 69-1] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111208/F015472.dat&hit=11
7 (E11) 16131841|ref NP_418439 47777 5.16 23 29 61% 293 210 isocitrate lyase [Escherichia coli str. K-12 substr. MG1655] http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111207/F015436.dat&sessionID=FZaghi_81508037746369 http://128.59.63.100/mascot/cgi/protein_view.pl?file=..%2Fdata%2F20111207%2FF015436.dat;hit=1 227886989|ref for E coli 83972, gi|218561077|ref for E coli S88, gi|91213527|ref for E coli UTI89, gi|15804601|ref for E coli O157:H7 EDL933 , gi|291285425|ref for E coli O55:H7 str. CB9615, gi|26250784|ref for E coli CFT073, and gi|300820055|ref for E coli MS 107-1.
193062786|ref ZP_03043879 51533 5.06 18 13 33% 85 293 6-phosphogluconate dehydrogenase, decarboxylating [Escherichia coli E22] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015436.dat&hit=63 It has been reported as a Mixture with aboave Protien ID.
16129099|ref NP_415654 46070 5.15 18 22 60% 210 293 "e14 prophage; isocitrate dehydrogenase, specific for NADP+ [Escherichia coli str. K-12 substr. MG1655]
[Escherichia coli str. K-12 substr. MG1655].
" http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015436.dat&hit=24 Invirtogel_E11_0001
300922666|ref ZP_07138763 46011 5.35 17 20 55% 179 293 isocitrate dehydrogenase, NADP-dependent [Escherichia coli MS 182-1] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015436.dat&hit=63
6 (F1) 15803822|ref NP_289856 36717 4.98 31 14 46% 199 NONE DNA-directed RNA polymerase subunit alpha [Escherichia coli O157:H7 EDL933] http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111207/F015431.dat&sessionID=FZaghi_81508037746369 http://128.59.63.100/mascot/cgi/protein_view.pl?file=..%2Fdata%2F20111207%2FF015431.dat;hit=1 Invirtogel_F1_0001
227883427|ref ZP_04001232 36691 4.98 31 14 46% 199 NONE DNA-directed RNA polymerase subunit alpha [Escherichia coli 83972] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015431.dat&hit=6
8 (F5) 15804735|ref NP_290776 57447 4.81 15 22 44% 243 NONE chaperonin GroEL [Escherichia coli O157:H7 EDL933] http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111207/F015437.dat&sessionID=FZaghi_81508037746369 http://128.59.63.100/mascot/cgi/protein_view.pl?file=..%2Fdata%2F20111211%2FF015491.dat;hit=4 homologous protein find in different strains of E coli Invirtogel_F5_0001
15834378|ref NP_313151 57464 4.81 15 22 44% 243 NONE chaperonin GroEL [Escherichia coli O157:H7 str. Sakai] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111211/F015491.dat&hit=6
110644502|ref YP_672232 57464 4.85 15 22 44% 243 NONE chaperonin GroEL [Escherichia coli 536] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111211/F015491.dat&hit=7
260870948|ref YP_003237350 57709 4.85 15 22 44% 243 NONE chaperonin Cpn60 [Escherichia coli O111:H- str. 11128] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111211/F015491.dat&hit=11
297520397|ref ZP_06938783 35245 4.85 21 11 36% 112 NONE chaperonin GroEL [Escherichia coli OP50] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111211/F015491.dat&hit=51
9 (F7) 300926981|ref ZP_07142741 77677 5.24 29 37 62% 313 100 translation elongation factor G [Escherichia coli MS 182-1] http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111207/F015430.dat&sessionID=FZaghi_304826335457584 http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111211/F015490.dat&hit=23 homologous protein find in different strains of E coli Invirtogel_F7_0001
218706934|ref YP_002414453 77762 5.21 28 37 61% 311 100 elongation factor G [Escherichia coli UMN026] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111211/F015490.dat&hit=23
15803853|ref NP_289887 77704 5.24 28 38 63% 324 100 elongation factor G [Escherichia coli O157:H7 EDL933] http://128.59.63.100/mascot/cgi/protein_view.pl?file=..%2Fdata%2F20111207%2FF015430.dat;hit=1
297517420|ref ZP_06935806 58232 5.16 28 27 55% 211 100 elongation factor G [Escherichia coli OP50] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111211/F015490.dat&hit=23
297518827|ref ZP_06937213 20222 5.33 29 11 78% 101 100 elongation factor G [Escherichia coli OP50] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111211/F015490.dat&hit=57
15803116|ref NP_289147 96041 5.37 34 22 29% 100 324 protein disaggregation chaperone [Escherichia coli O157:H7 EDL933] http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111211/F015490.dat&hit=60 reported as a mixture with above protein ID
10 (F9) no hit http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111211/F015492.dat&sessionID=FZaghi_206677355780492 Invirtogel_F9_0001

Mascot Daemon Results

Spot Number accession seq_database result number task_UID hit_mass hit_score title_text result_comment input_data_file result_url
1 (E1) 289448397|ref NCBInr_081610.fasta 5 2 35020 83 PE-PGRS family protein [Mycobacterium tuberculosis CPHL_A] NOT Accepted. The protien ID does not belong to any of E coli strains. C:\Documents and Settings\XPMUser\Desktop\Protiomic\farnadZaghi_c\Invirtogel_E1_0001.dat http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111212/F015500.dat
157154780|ref YP_001461306 5 4 21143 64 putative fimbrial protein [Escherichia coli E24377A] NOT Accepted. There are only 4 weak peaks matching with spectrum and no matching for the strong peaks. C:\Documents and Settings\XPMUser\Desktop\Protiomic\farnadZaghi_c\Invirtogel_E1_0001.dat http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111212/F015500.dat
2 (E3) 213029173|ref NCBInr_081610.fasta 6 2 10695 47 membrane component of 2-aminoethylphosphonate transporter [Salmonella enterica subsp. enterica serovar Typhi str. 404ty] NOT Accepted. The protien ID does not belong to any of E coli strains. C:\Documents and Settings\XPMUser\Desktop\Protiomic\farnadZaghi_c\Invirtogel_E3_0001.dat http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111212/F015501.dat
3 (E5) 46143512|ref NCBInr_081610.fasta 7 2 109967 44 COG2931: RTX toxins and related Ca2+-binding proteins [Actinobacillus pleuropneumoniae serovar 1 str. 4074] NOT Accepted. The protien ID does not belong to any of E coli strains. C:\Documents and Settings\XPMUser\Desktop\Protiomic\farnadZaghi_c\Invirtogel_E5_0001.dat http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111212/F015502.dat
4 (E7) 194334347|ref NCBInr_081610.fasta 8 2 27113 58 Uroporphyrinogen-III synthase [Prosthecochloris aestuarii DSM 271] NOT Accepted. The protien ID does not belong to any of E coli strains. C:\Documents and Settings\XPMUser\Desktop\Protiomic\farnadZaghi_c\Invirtogel_E7_0001.dat http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111212/F015503.dat

Keywords: E.coli protein expression, protein fragments, 2D gel electrophoresis, MALDI, limited proteolysis

  (abv) matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS)

Personal/Lab Info

User:Farnad_Zaghi,User:Julius_B._Lucks, User:Jason_R._Kelly and User:Reshma_P._Shetty.