Msconvert Capabilities

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Testing of MSconvert is in progress and results will be posted here as they come.

1 Agilent
- 1.1 trapper
  - 1.1.1 mzXML
- 1.2 msconvert
  - 1.2.1 mzXML
  - 1.2.2 mzML
2 Thermo
- 2.1 ReAdW
  - 2.1.1 mzXML
- 2.2 msconvert
  - 2.2.1 mzXML
  - 2.2.2 mzML
3 Analyst
- 3.1 mzWiff
  - 3.1.1 mzXML
- 3.2 msconvert
  - 3.2.1 mzXML
  - 3.2.2 mzML

[edit]

Agilent

Raw file type: .d directory
raw-to-mzXML converter: trapper

[edit]

trapper

[edit]

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.

[edit]

msconvert

[edit]

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

[edit]

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

[edit]

Thermo

Raw file type: .RAW file
raw-to-mzXML converter: ReAdW

[edit]

ReAdW

[edit]

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)

[edit]

msconvert

[edit]

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)

[edit]

mzML

Conversion: Conversion seemed to work. TPP tests did not work with mzML file format
X!Tandem search:
TPP:TPP Search failed

[edit]

Analyst

Raw file type: .wiff file
raw-to-mzXML converter: mzWiff

[edit]

mzWiff

[edit]

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:

[edit]

msconvert

[edit]

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+).

[edit]

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+).

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=Msconvert_Capabilities"

Msconvert Capabilities

From SPCTools

Current revision

Contents

Agilent

trapper

mzXML

msconvert

mzXML

mzML

Thermo

ReAdW

mzXML

msconvert

mzXML

mzML

Analyst

mzWiff

mzXML

msconvert

mzXML

mzML

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