Msconvert Capabilities

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Conversion: Appears to be successful Conversion: Appears to be successful
<br>X!Tandem search: Search completed, slight differences with the ReAdW converted mzXML file <br>X!Tandem search: Search completed, slight differences with the ReAdW converted mzXML file
-<br>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+<br>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:<br/>
 + 
 +CALCSTAT FOR READW 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)
 + 
 +CALCSTAT FOR MSCONVERT 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)
<h3>mzML</h3> <h3>mzML</h3>

Revision as of 22:47, 28 April 2010

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: OK
TPP: PeptideProphet results were all probability=0. Why? WEIRD.

msconvert

mzXML

Conversion: produces truncated file. Zhi says that msconvert is not able to convert MRM data to mzXML format. So we don't expect this to work.
X!Tandem search:
TPP:

mzML

Conversion: OK
X!Tandem search: Terry had to edit runtandemsearch to make it work on mzML. Then, search ran for 7 days without completing. Zhi thinks she has seen the same problem.
TPP:


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

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:

CALCSTAT FOR READW 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)

CALCSTAT FOR MSCONVERT 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.
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--once completed, zztandempostproccessing.log file was will of warnings
TPP:

mzML

Conversion:
X!Tandem search:
TPP:

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