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. Image: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 hithttp://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111207/F015434.dat&sessionID=FZaghi_81508037746369Invirtogel_E1_0001
2 (E3)no hithttp://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111207/F015433.dat&sessionID=FZaghi_81508037746369Invirtogel_E3_0001
3 (E5)no hithttp://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111207/F015432.dat&sessionID=FZaghi_81508037746369Invirtogel_E5_0001
4 (E7)297521112|ref NP_06939498195145.17301069%12087malate dehydrogenase [Escherichia coli OP50]http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111207/F015435.dat&sessionID=FZaghi_81508037746369http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015435.dat&hit=1malate dehydrogenase and malate dehydrogenase NAD-dependent for deifferent strant of E coliInvirtogel_E7_0001
15803770|ref NP_289804 324885.61311144%11287malate 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_542642352076.03311141%10987malate dehydrogenase [Escherichia coli UTI89]http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015435.dat&hit=9
170018520|refYP_001723474324785.61311144%11287malate 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 325045.61311144%11287malate dehydrogenase [Escherichia coli SE11http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015435.dat&hit=8
218555800|refYP_002388713 324615.61301037%9587malate 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 324876.21301037%9587"malate dehydrogenase [Escherichia coli UMN026]
"http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015435.dat&hit=20
110643470|refYP_671200325025.61301037%9587malate 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 324885.61311144%11287malate 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 324775.61301037%9587malate 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 352066.85301035%9287malate 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_07186088352076.36301035%9287malate 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|refZP_07152185352236.36301035%9287malate 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_07097729351966.36301035%9287malate 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|refZP_07174711 352216.36301035%9287malate 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 454596.03241627%169NONEserine 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_450724603025029http://128.59.63.100/mascot/cgi/protein_view.pl?file=..%2Fdata%2F20111207%2FF015415.dat;hit=2serine/ glycine hydroxymethyltransferase for different strains of E coliInvirtogel_E9_0001
15803076|ref NP_289107 454876.03241627%169NONEserine 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_002413573454456.03241627%169NONEserine 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 457466.13241627%167NONEserine hydroxymethyltransferase [Escherichia coli CFT073http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111208/F015472.dat&hit=8
291283776|ref YP_003500594455016.13241627%167NONESerine 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_06939665168297.74441151%128serine hydroxymethyltransferase [Escherichia coli OP50]http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111208/F015472.dat&hit=16
300898338|refZP_07116686457326.13241627%167NONEglycine 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_07188471457766.13241526%155NONEglycine 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 477775.16232961%293210isocitrate 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_81508037746369http://128.59.63.100/mascot/cgi/protein_view.pl?file=..%2Fdata%2F20111207%2FF015436.dat;hit=1227886989|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|refZP_03043879515335.06181333%852936-phosphogluconate dehydrogenase, decarboxylating [Escherichia coli E22]http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111207/F015436.dat&hit=63It has been reported as a Mixture with aboave Protien ID.
16129099|refNP_415654 460705.15182260%210293"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=24Invirtogel_E11_0001
300922666|ref ZP_07138763 460115.35172055%179293isocitrate 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|refNP_289856367174.98311446%199NONEDNA-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_81508037746369http://128.59.63.100/mascot/cgi/protein_view.pl?file=..%2Fdata%2F20111207%2FF015431.dat;hit=1Invirtogel_F1_0001
227883427|ref ZP_04001232 366914.98311446%199NONEDNA-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|refNP_290776574474.81152244%243NONEchaperonin GroEL [Escherichia coli O157:H7 EDL933]http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111207/F015437.dat&sessionID=FZaghi_81508037746369http://128.59.63.100/mascot/cgi/protein_view.pl?file=..%2Fdata%2F20111211%2FF015491.dat;hit=4homologous protein find in different strains of E coliInvirtogel_F5_0001
15834378|ref NP_313151574644.81152244%243NONEchaperonin 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 574644.85152244%243NONEchaperonin 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 577094.85152244%243NONEchaperonin 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_06938783352454.85211136%112NONEchaperonin GroEL [Escherichia coli OP50]http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111211/F015491.dat&hit=51
9 (F7)300926981|refZP_07142741776775.24293762%313100translation 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_304826335457584http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111211/F015490.dat&hit=23homologous protein find in different strains of E coliInvirtogel_F7_0001
218706934|ref YP_002414453 777625.21283761%311100elongation factor G [Escherichia coli UMN026]http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111211/F015490.dat&hit=23
15803853|refNP_289887777045.24283863%324100elongation 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_06935806582325.16282755%211100elongation factor G [Escherichia coli OP50]http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111211/F015490.dat&hit=23
297518827|refZP_06937213202225.33291178%101100elongation 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 960415.37342229%100324protein disaggregation chaperone [Escherichia coli O157:H7 EDL933]http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111211/F015490.dat&hit=60reported as a mixture with above protein ID
10 (F9)no hithttp://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111211/F015492.dat&sessionID=FZaghi_206677355780492Invirtogel_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|refNCBInr_081610.fasta523502083PE-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.dathttp://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111212/F015500.dat
157154780|ref YP_001461306542114364putative 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.dathttp://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111212/F015500.dat
2 (E3)213029173|refNCBInr_081610.fasta621069547membrane 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.dathttp://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111212/F015501.dat
3 (E5)46143512|refNCBInr_081610.fasta7210996744COG2931: 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.dathttp://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111212/F015502.dat
4 (E7)194334347|refNCBInr_081610.fasta822711358Uroporphyrinogen-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.dathttp://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.
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