User talk:Farnad Zaghi: Difference between revisions

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== Proteomic E-coli Project ==  
== Proteomic E-coli Project ==  


[[Image:[https://www.flickr.com/photos/24433864@N07/14320953067/]]]
[[Image:https://www.flickr.com/photos/24433864@N07/14320953067/]]


[[File:Köppen-vereinfacht.svg|thumb|center|upright=2.0|alt=Map of the world. A tan band stretches from northern Africa through central China; most of Australia and parts of south Africa and the western Americas are also tan. Dark greens dominate the northern hemisphere. Lighter greens cover much land near the equator. Polar areas are white, the north fringed with light blue.|Macroclimates of the earth. Tans represent desert, dark greens humid continental, and light green tropical rainforest. Light blue and white represent tundra and ice cap.]]


'''Mascot Wizard Results'''
'''Mascot Wizard Results'''

Revision as of 13:25, 25 June 2014

Proteomic E-coli Project

File:Https://www.flickr.com/photos/24433864@N07/14320953067/


Mascot Wizard Results


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 no hit http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111207/F015434.dat&sessionID=FZaghi_81508037746369 Invirtogel_E1_0001

no hit http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111207/F015433.dat&sessionID=FZaghi_81508037746369 Invirtogel_E3_0001

no hit http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111207/F015432.dat&sessionID=FZaghi_81508037746369 Invirtogel_E5_0001

gi|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 gi|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 gi|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 gi|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 gi|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 gi|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 gi|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 gi|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

gi|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 gi|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 gi|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 gi|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 gi|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 gi|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 gi|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

gi|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 gi|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 gi|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 gi|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 gi|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 gi|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

gi|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 gi|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

gi|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 other Entries with the same sequence have found in different strains of E coli. Such as gi|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. gi|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. gi|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 gi|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

gi|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 gi|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

gi|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 gi|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 gi|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 gi|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 gi|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

gi|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 gi|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 gi|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 gi|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 gi|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 gi|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

no hit http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111211/F015492.dat&sessionID=FZaghi_206677355780492 Invirtogel_F9_0001


MS/MS Results

Filename NCBI gi number Uniprot KB ID Protein Name Mascot Score # acceptable peptides Precursor RMS ppm error Product RMS Error (avg. of accepted peptides) Comment Mascot Search Results URL (Select Summary) (Protein URL) B1_DDA_S_042811_4ul_1_CID.PKL GI:29788785|ref NP_821133 tubulin beta chain [Homo sapiens] 361 6 5 6.5 Proteins matching the same set of peptides as gi|7106439|ref the tubulin beta-5 chain [Mus musculus] http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111117/F015215.dat http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111117/F015215.dat&hit=gi%7c7106439%7cref&px=1&ave_thresh=26&_sigthreshold=0.05&_server_mudpit_switch=0.001 GI:17986283|ref NP_006000 tubulin alpha-1A chain [Homo sapiens] 359 5 6 12.6 Proteins matching the same set of peptides as gi|6755901|ref in Mus musculus http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111117/F015215.dat&hit=gi%7c5174735%7cref&px=1&ave_thresh=26&_sigthreshold=0.05&_server_mudpit_switch=0.001 gi|5174735|ref NP_006079 tubulin beta-2C chain 219 5 5 8.8 the protein has a unique peptide eventhought it share another 4 pepide with nonhemologus protien http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111117/F015215.dat&hit=gi%7c5174735%7cref&px=1&ave_thresh=26&_sigthreshold=0.05&_server_mudpit_switch=0.001 gi|4501885|ref  NP_001092 actin, cytoplasmic 1 [Homo sapiens] 209 2 3 30 eventhough the protien has to peptide score above the identety and hemology thershold I am not reporting it since the peptides have poor spectrum http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111117/F015215.dat&hit=gi%7c4501885%7cref&px=1&ave_thresh=26&_sigthreshold=0.05&_server_mudpit_switch=0.001 gi|4507729|ref NP_001060 tubulin beta-2A chain [Homo sapiens 170 4 5 9.25 http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111117/F015215.dat&hit=gi%7c4507729%7cref&px=1&ave_thresh=26&_sigthreshold=0.05&_server_mudpit_switch=0.001

B1_DDA_S_042811_4ul_2_CID.PKL gi|4501885|ref NP_001092 actin, cytoplasmic 1 [Homo sapiens] 154 3 5 14.3 http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111117/F015250.dat http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111117/F015250.dat&hit=gi%7c4501885%7cref&px=1&ave_thresh=25&_sigthreshold=0.05&_server_mudpit_switch=0.001 gi|4501887|ref  NP_001605 actin, cytoplasmic 2 [Homo sapiens] 154 3 5 14.3 http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111117/F015250.dat&hit=gi%7c4501887%7cref&px=1&ave_thresh=25&_sigthreshold=0.05&_server_mudpit_switch=0.001 gi|63055057|ref NP_001017992 beta-actin-like protein 2 [Homo sapiens] 2 1 16.5 one of the peptide has been used already for another protien however it may use as a second peptide with above identity thereshold to avoid "one hit wonder" but I don’t report this protien. http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111117/F015250.dat&hit=gi%7c63055057%7cref&px=1&ave_thresh=25&_sigthreshold=0.05&_server_mudpit_switch=0.001

B2_DDA_S_042811_4ul_1_CID.PKL NO HIT DECOY ON http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111117/F015253.dat gi|14389309|ref NP_116093 tubulin alpha-1C chain [Homo sapiens] 301 5 7 13 http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111117/F015257.dat http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111117/F015258.dat&hit=gi%7c14389309%7cref&px=1&ave_thresh=26&_sigthreshold=0.05&_server_mudpit_switch=0.001 GI:57013276|ref NP_006073 tubulin alpha-1B chain [Homo sapiens] 301 5 7 13 gi|34740335|ref tubulin alpha-1B chain containing the same sequence in [Mus musculus] from NCBI http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111117/F015258.dat&hit=gi%7c34740335%7cref&px=1&ave_thresh=26&_sigthreshold=0.05&_server_mudpit_switch=0.001 http://www.ncbi.nlm.nih.gov/protein/57013276 gi|5174735|ref NP_006079 tubulin beta-2C chain [Homo sapiens] 207 5 6 8.8 http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111117/F015258.dat&hit=gi%7c5174735%7cref&px=1&ave_thresh=26&_sigthreshold=0.05&_server_mudpit_switch=0.001

gi|4503471|ref NP_001393 elongation factor 1-alpha 1 [Homo sapiens] 154 2 3 8 since the spectra belong to a 1D gel , there are non hemolugous protien available in the sample http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111117/F015258.dat&hit=gi%7c4503471%7cref&px=1&ave_thresh=26&_sigthreshold=0.05&_server_mudpit_switch=0.001

B2_DDA_S_042811_4ul_2_CID.PKL gi|4501885|ref  NP_001092 actin, cytoplasmic 1 [Homo sapiens] 154 3 4 16 ERRO-Tolerant OFF http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111117/F015261.dat http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111117/F015261.dat&hit=gi%7c4501885%7cref&px=1&ave_thresh=25&_sigthreshold=0.05&_server_mudpit_switch=0.001 gi|4501887|ref NP_001605 actin, cytoplasmic 2 [Homo sapiens] 154 3 4 16 http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111117/F015261.dat&hit=gi%7c4501887%7cref&px=1&ave_thresh=25&_sigthreshold=0.05&_server_mudpit_switch=0.001 gi|63055057|ref NP_001017992 beta-actin-like protein 2 95 2 1 16.5 http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111120/F015269.dat&hit=gi%7c63055057%7cref&px=1&ave_thresh=25&_sigthreshold=0.05&_server_mudpit_switch=0.001 the protein has a unique peptide eventhought it share another pepide with nonhemologus protien gi|4501885|ref  NP_001092 actin, cytoplasmic 1 [Homo sapiens] 154 4 4 12.5 ERRO-Tolerant ON http://128.59.63.100/mascot/cgi/master_results.pl?file=../data/20111117/F015265.dat http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111117/F015261.dat&hit=gi%7c4501885%7cref&px=1&ave_thresh=25&_sigthreshold=0.05&_server_mudpit_switch=0.001 gi|4501887|ref NP_001605 actin, cytoplasmic 2 [Homo sapiens] 154 4 4 12.5 http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111117/F015261.dat&hit=gi%7c4501887%7cref&px=1&ave_thresh=25&_sigthreshold=0.05&_server_mudpit_switch=0.001 gi|5453597|ref NP_006126 F-actin-capping protein subunit alpha-1 122 3 4 10.3 http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111117/F015265.dat&hit=gi%7c5453597%7cref&px=1&ave_thresh=25&_sigthreshold=0.05&_server_mudpit_switch=0.001 gi|63055057|ref NP_001017992 beta-actin-like protein 2 95 2 1 7.5 http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111120/F015270.dat&hit=gi%7c63055057%7cref&px=1&ave_thresh=25&_sigthreshold=0.05&_server_mudpit_switch=0.001 gi|4501883|ref  NP_001604 actin, aortic smooth muscle 84 2 3 7.5 http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111120/F015270.dat&hit=gi%7c4501883%7cref&px=1&ave_thresh=25&_sigthreshold=0.05&_server_mudpit_switch=0.001 gi|4501889|ref   NP_001606 actin, gamma-enteric smooth muscle propeptide 84 2 3 7.5 http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111120/F015270.dat&hit=gi%7c4501889%7cref&px=1&ave_thresh=25&_sigthreshold=0.05&_server_mudpit_switch=0.001 gi|4885049|ref  NP_005150 actin, alpha cardiac muscle 1 proprotein 84 2 3 7.5 http://128.59.63.100/mascot/cgi/protein_view.pl?file=../data/20111120/F015270.dat&hit=gi%7c4885049%7cref&px=1&ave_thresh=25&_sigthreshold=0.05&_server_mudpit_switch=0.001

Personal/Lab Info

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