Msconvert Capabilities
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| Revision as of 23:36, 19 May 2010 Gsun (Talk | contribs) ← Previous diff |
Current revision Gsun (Talk | contribs) |
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| Mayu decoy-based protein FDR analysis on interact-ipro.pep.xml | Mayu decoy-based protein FDR analysis on interact-ipro.pep.xml | ||
| Running the following command: | Running the following command: | ||
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| xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909211605 (linux)) | xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909211605 (linux)) | ||
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| running: "/tools/bin/TPP/tpp-4.3.1/bin/InteractParser 'interact-highprob.pep.xml' 'BSA_Myo_GAPDH_A_2.pep.xml' 'NEP_Plate1_5pmol1.pep.xml' -X'BSA_Myo_GAPDH_A_2' -L'7'" | running: "/tools/bin/TPP/tpp-4.3.1/bin/InteractParser 'interact-highprob.pep.xml' 'BSA_Myo_GAPDH_A_2.pep.xml' 'NEP_Plate1_5pmol1.pep.xml' -X'BSA_Myo_GAPDH_A_2' -L'7'" | ||
| file 1: BSA_Myo_GAPDH_A_2.pep.xml | file 1: BSA_Myo_GAPDH_A_2.pep.xml | ||
Current revision
Testing of MSconvert is in progress and results will be posted here as they come.
Contents |
Agilent
Raw file type: .d directory
raw-to-mzXML converter: trapper
trapper
mzXML
Conversion: OK
X!Tandem search: Tandem Search completed, but with errors
TPP:Script is printed below:
Running Peptide Prophet with -p0 xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909211605 (linux)) running: "/tools/bin/TPP/tpp-4.3.1/bin/InteractParser 'interact-prob.pep.xml' 'BSA_Myo_GAPDH_A_2.pep.xml' 'NEP_Plate1_5pmol1.pep.xml' -X'BSA_Myo_GAPDH_A_2' -L'7'" file 1: BSA_Myo_GAPDH_A_2.pep.xml file 2: NEP_Plate1_5pmol1.pep.xml processed altogether 9339 results results written to file /proteomics/gsun/trapper-test/trapper/interact-prob.pep.shtml command completed in 2 sec running: "/tools/bin/TPP/tpp-4.3.1/bin/PeptideProphetParser 'interact-prob.pep.xml' DECOYPROBS ACCMASS DECOY=DECOY_ MINPROB=0 EXTRAITRS=3" using Accurate Mass Bins Using Decoy Label "DECOY_". Decoy Probabilities will be reported. (X! Tandem (k-score)) (minprob 0) WARNING: Found semi-cleavage in refinement mode and semi-cleavage not used in the first pass. Turning off NTT model. adding Accurate Mass mixture distr init with X! Tandem (k-score) trypsin ERROR: two instrument ionisations: NSI and MS_CHIP command "/tools/bin/TPP/tpp-4.3.1/bin/PeptideProphetParser 'interact-prob.pep.xml' DECOYPROBS ACCMASS DECOY=DECOY_ MINPROB=0 EXTRAITRS=3" exited with non-zero exit code: 256 QUIT - the job is incomplete Running NSS NRS NSE NSI NSM Model EM: Computing NSS values ... Computing NRS values ... Computing NSE values ... Computing NSI values ... Computing NSM values ... Iterations: .done results written to file /proteomics/gsun/trapper-test/trapper/interact-ipro.pep.shtml Mayu decoy-based protein FDR analysis on interact-ipro.pep.xml Running the following command: perl Mayu.pl -A ./interact-ipro.pep.xml -C /regis/dbase/IPI/ipi.HUMAN.v3.26.fasta -E DECOY_ -G 0.003 -H 16 -verbose -PmFDR -M . >& ./Mayu.log ./Mayu.log: File exists. /bin/mv: No match. /bin/mv: No match. sed: can't read Mayu_out.csv: No such file or directory PSM FDR Protein IDs Decoys Protein FDR (lower bound) grep: Mayu_out.csv: No such file or directory True protein ID count may be lower if redundancy in database. Complete results in Mayu_out.csv, Mayu_out.txt, and Mayu.log. ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v4.3 JETSTREAM rev 1, Build 200909211605 (linux)) (xml input) (normalize NSP for Protein Length) (report Protein Length) (using degen pep info) . . . reading in /proteomics/gsun/trapper-test/trapper/interact-ipro.pep.xml. . . . . . read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 no data - quitting================================================================ Rerunning Peptide Prophet with -p0.5 xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909211605 (linux)) running: "/tools/bin/TPP/tpp-4.3.1/bin/InteractParser 'interact-highprob.pep.xml' 'BSA_Myo_GAPDH_A_2.pep.xml' 'NEP_Plate1_5pmol1.pep.xml' -X'BSA_Myo_GAPDH_A_2' -L'7'" file 1: BSA_Myo_GAPDH_A_2.pep.xml file 2: NEP_Plate1_5pmol1.pep.xml processed altogether 9339 results results written to file /proteomics/gsun/trapper-test/trapper/interact-highprob.pep.shtml command completed in 2 sec running: "/tools/bin/TPP/tpp-4.3.1/bin/PeptideProphetParser 'interact-highprob.pep.xml' DECOYPROBS ACCMASS DECOY=DECOY_ MINPROB=0.5 EXTRAITRS=3" using Accurate Mass Bins Using Decoy Label "DECOY_". Decoy Probabilities will be reported. (X! Tandem (k-score)) WARNING: Found semi-cleavage in refinement mode and semi-cleavage not used in the first pass. Turning off NTT model. adding Accurate Mass mixture distr init with X! Tandem (k-score) trypsin ERROR: two instrument ionisations: NSI and MS_CHIP command "/tools/bin/TPP/tpp-4.3.1/bin/PeptideProphetParser 'interact-highprob.pep.xml' DECOYPROBS ACCMASS DECOY=DECOY_ MINPROB=0.5 EXTRAITRS=3" exited with non-zero exit code: 256 QUIT - the job is incomplete ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v4.3 JETSTREAM rev 1, Build 200909211605 (linux)) (xml input) (normalize NSP for Protein Length) (report Protein Length) (using degen pep info) . . . reading in /proteomics/gsun/trapper-test/trapper/interact-ipro.pep.xml. . . . . . read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5 no data - quitting================================================================ Illegal division by zero at /sbeams/bin/calctppstat.pl line 539, <INFILE> line 252.
msconvert
mzXML
Conversion: Conversion completed
X!Tandem search:Tandem Search completed
TPP:Results Follow Below:
INFO: Reading ProteinProphet file 'interact-prob.prot.xml' PepP 8/ 58 0.138 | ProP 1 ( 7, 7) /proteomics/gsun/trapper-test/msconvert P threshold for FDR 0.01=0.88 Decoy results: PP Incor FDR 0.01=1 Decoy IDs at FDR 0.01=0 Decoy IDs at P<0.001=-1 Total IDs at P<0.001=27 Decoy fraction P<0.001=-0.0370 At PepPro FDR 0.010 FDR based on decoys=-0.0000 FDR after discard=-0.0000 For FDR 0.01, sensitivity=0.889 at P=0.88 Peptide Count at FDR 0.01: Distinct peptides = 7 Singletons = 6 (0.86) Doubletons = 1 (0.14) Number of PSMs per MSrun: NEP_Plate1_5pmol1 : 8 Charge 3: 8 (FDR 0.01) Queries=58 Enzymatic Termini 1: 6 Enzymatic Termini 2: 2 Fraction semi-tryptics: 0.7500 N missed cleavages 0: 8 (FDR 0.01) Total Modifications at FDR 0.01: Modification: None: 8 Mass diffs for P > 0.88: Mean: 0.344625 StDev: 0.96667204329375 Mass diffs for P > 0.88: Min: -0.003 Max: 2.737 -0.750 -> -0.250 0 | -0.250 -> 0.250 7 |************************************************** 0.250 -> 0.750 0 | 0.750 -> 1.250 0 | 1.250 -> 1.750 0 | 1.750 -> 2.250 0 | 2.250 -> 2.750 1 |******* 2.750 -> 3.250 0 | ProteinProphet info: Proteins identified at P>0.9=1 Distinct modified peptides at P>0.88=7 P threshold for protein group FDR 0.01=0.0000 Protein groups identified at FDR 0.01=0
mzML
Conversion: Conversion Completed
X!Tandem search: Tandem Search completed
TPP:Results follow below:
INFO: Reading ProteinProphet file 'interact-prob.prot.xml' PepP 7/ 58 0.121 | ProP 1 ( 6, 6) /proteomics/gsun/trapper-test/msconvert/mzML P threshold for FDR 0.01=0.25 Decoy results: PP Incor FDR 0.01=2 Decoy IDs at FDR 0.01=0 Decoy IDs at P<0.001=-1 Total IDs at P<0.001=47 Decoy fraction P<0.001=-0.0213 At PepPro FDR 0.010 FDR based on decoys=-0.0000 FDR after discard=-0.0000 For FDR 0.01, sensitivity=1.000 at P=0.25 Peptide Count at FDR 0.01: Distinct peptides = 6 Peptide Count at FDR 0.01: Distinct peptides = 6 Singletons = 5 (0.83) Doubletons = 1 (0.17) Number of PSMs per MSrun: NEP_Plate1_5pmol1.mzML : 7 Charge 3: 7 (FDR 0.01) Queries=58 Enzymatic Termini 1: 5 Enzymatic Termini 2: 2 Fraction semi-tryptics: 0.7143 N missed cleavages 0: 7 (FDR 0.01) Total Modifications at FDR 0.01: Modification: None: 7 Mass diffs for P > 0.25: Mean: 0.393142857142857 StDev: 1.03355058392118 Mass diffs for P > 0.25: Min: -0.003 Max: 2.737 -0.750 -> -0.250 0 | -0.250 -> 0.250 6 |************************************************** 0.250 -> 0.750 0 | 0.750 -> 1.250 0 | 1.250 -> 1.750 0 | 1.750 -> 2.250 0 | 2.250 -> 2.750 1 |******** 2.750 -> 3.250 0 | ProteinProphet info: Proteins identified at P>0.9=1 Distinct modified peptides at P>0.25=6 P threshold for protein group FDR 0.01=0.0000 Protein groups identified at FDR 0.01=0
Thermo
Raw file type: .RAW file
raw-to-mzXML converter: ReAdW
ReAdW
mzXML
Conversion: using remoteconvert.pl --convertWith readw, file successfully converted.
X!Tandem search:search ran successfully, slight differences with the msconvert mzXML file
TPP:TPP Search successful--calctppstat for mzXML by ReAdW similar to that of calctppstat for mzXML file by msconvert, slight differences, histograms are relatively different, numbers are relatively close to one another, through most numbers are different--a few number are the same, results are very close--see below(section msconvert: mzXML)
msconvert
mzXML
Conversion: Appears to be successful
X!Tandem search: Search completed, slight differences with the ReAdW converted mzXML file
TPP:Peptide prophet completed with warnings,protein prophet failed. Search completed----calctppstat for mzXML by ReAdW similar to that of calctppstat for mzXML file by msconvert, slight differences, histograms are relatively different, numbers are relatively close to one another, through most numbers are different--a few number are the same, results are very close, comparisons are below:
Calctppstat results for ReAdW file conversion
138 regis /proteomics/gsun/raw-test/ReAdW> /regis/sbeams/bin/calctppstat.pl --write --full --FDRthresh interact-prob.pep.xml INFO: Reading ProteinProphet file 'interact-prob.prot.xml' PepP 25/ 2621 0.010 | ProP 9 ( 16, 25) /proteomics/gsun/raw-test/ReAdW P threshold for FDR 0.01=0.98 Decoy results: PP Incor FDR 0.01=0 Decoy IDs at FDR 0.01=0 Decoy IDs at P<0.001=-1 Total IDs at P<0.001=1493 Decoy fraction P<0.001=-0.0007 At PepPro FDR 0.010 FDR based on decoys=-0.0000 FDR after discard=-0.0000 For FDR 0.01, sensitivity=0.160 at P=0.98 Peptide Count at FDR 0.01: Distinct peptides = 16 Singletons = 12 (0.75) Doubletons = 2 (0.12) Number of PSMs per MSrun: hui052703_15_1 : 25 Charge 1: 8 (FDR 0.01) Queries=146 Charge 2: 11 (FDR 0.01) Queries=2475 Charge 3: 6 (FDR 0.01) Queries=2475 Enzymatic Termini 1: 17 Enzymatic Termini 2: 8 Fraction semi-tryptics: 0.6800 N missed cleavages 0: 22 (FDR 0.01) N missed cleavages 1: 1 (FDR 0.01) N missed cleavages 2: 2 (FDR 0.01) Fraction of missed cleavages: 0.1200 Total Modifications at FDR 0.01: Modification: C[160]: 5 Modification: M[147]: 8 Modification: None: 14 Mass diffs for P > 0.98: Mean: 1.349 StDev: 0.981512735526137 Mass diffs for P > 0.98: Min: -0.154 Max: 3.230 -0.750 -> -0.250 0 | -0.250 -> 0.250 5 |***************************************** 0.250 -> 0.750 1 |******** 0.750 -> 1.250 6 |************************************************** 1.250 -> 1.750 3 |************************* 1.750 -> 2.250 5 |***************************************** 2.250 -> 2.750 3 |************************* 2.750 -> 3.250 2 |**************** 3.250 -> 3.750 0 | ProteinProphet info: Proteins identified at P>0.9=9 Distinct modified peptides at P>0.98=16 P threshold for protein group FDR 0.01=0.9541 Protein groups identified at FDR 0.01=8 Decoy IDs P>0 at protein group FDR 0.01=0 (0.0000) Decoy IDs P>0 at protein group FDR 0.03=0 (0.0000) Decoy IDs P>0 at protein group FDR 0.04=0 (0.0000)
Calctppstat results for msconvert file conversion
143 regis /proteomics/gsun/raw-test/msconvert> /regis/sbeams/bin/calctppstat.pl --write --full --FDRthresh interact-prob.pep.xml INFO: Reading ProteinProphet file 'interact-prob.prot.xml' PepP 18/ 2621 0.007 | ProP 10 ( 13, 23) /proteomics/gsun/raw-test/msconvert P threshold for FDR 0.01=0.98 Decoy results: PP Incor FDR 0.01=0 Decoy IDs at FDR 0.01=0 Decoy IDs at P<0.001=-1 Total IDs at P<0.001=1481 Decoy fraction P<0.001=-0.0007 At PepPro FDR 0.010 FDR based on decoys=-0.0000 FDR after discard=-0.0000 For FDR 0.01, sensitivity=0.110 at P=0.98 Peptide Count at FDR 0.01: Distinct peptides = 10 Singletons = 6 (0.60) Doubletons = 2 (0.20) Number of PSMs per MSrun: hui052703_15_1 : 18 Charge 1: 8 (FDR 0.01) Queries=146 Charge 2: 4 (FDR 0.01) Queries=2475 Charge 3: 6 (FDR 0.01) Queries=2475 Enzymatic Termini 1: 12 Enzymatic Termini 2: 6 Fraction semi-tryptics: 0.6667 N missed cleavages 0: 15 (FDR 0.01) N missed cleavages 1: 1 (FDR 0.01) N missed cleavages 2: 2 (FDR 0.01) Fraction of missed cleavages: 0.1667 Total Modifications at FDR 0.01: Modification: C[160]: 4 Modification: M[147]: 6 Modification: None: 10 Mass diffs for P > 0.98: Mean: 1.373 StDev: 1.09399618237854 Mass diffs for P > 0.98: Min: -0.154 Max: 3.230 -0.750 -> -0.250 0 | -0.250 -> 0.250 5 |************************************************** 0.250 -> 0.750 0 | 0.750 -> 1.250 2 |******************** 1.250 -> 1.750 3 |****************************** 1.750 -> 2.250 4 |**************************************** 2.250 -> 2.750 2 |******************** 2.750 -> 3.250 2 |******************** 3.250 -> 3.750 0 | ProteinProphet info: Proteins identified at P>0.9=10 Distinct modified peptides at P>0.98=13 P threshold for protein group FDR 0.01=0.9484 Protein groups identified at FDR 0.01=9 Decoy IDs P>0 at protein group FDR 0.01=0 (0.0000) Decoy IDs P>0 at protein group FDR 0.02=0 (0.0000) Decoy IDs P>0 at protein group FDR 0.03=0 (0.0000)
mzML
Conversion: Conversion seemed to work. TPP tests did not work with mzML file format
X!Tandem search:
TPP:TPP Search failed
Analyst
Raw file type: .wiff file
raw-to-mzXML converter: mzWiff
mzWiff
mzXML
Conversion: used /regis/sbeams/bin/remoteconvert.pl --default --convertWith mzWiff QS20061230_P0094_C1_08_AQv1.1.wiff, file converted, but not output files created or received. Zip file empty. Tried using ep server, new problem arose. Zhi says that mzWiff has many problems and some files it just cannot convert. This is probably what is happening.
X!Tandem search:
TPP:
msconvert
mzXML
Conversion:Tried /regis/sbeams/bin/remoteconvert.pl --default --convertWith msconvert QS20061230_P0094_C1_08_AQv1.1.wiff, could not connect with server. Also tried /regis/sbeams/bin/remoteconvert.pl --default --server th --convertWith msconvert QS20061230_P0094_C1_08_AQv1.1.wiff, also could not connect to server.
Tried using both actual file and symbolic link for .wiff file; same problem as above.
X!Tandem search:started runtandemsearch but it didn't complete
TPP: Once runtandemsearch completed, zztandempostproccessing.log file was full of warnings--WARNING: Mixture model quality test failed for charge (2+).
WARNING: Mixture model quality test failed for charge (3+).
mzML
Conversion: File appears to have been converted
X!Tandem search: Tandem search completed
TPP: TPP analysis had warnings--WARNING: Mixture model quality test failed for charge (2+).
