Msconvert Capabilities

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Conversion: using remoteconvert.pl --convertWith readw, file successfully converted. Conversion: using remoteconvert.pl --convertWith readw, file successfully converted.
<br>X!Tandem search:search ran successfully, slight differences with the msconvert mzXML file <br>X!Tandem search:search ran successfully, slight differences with the msconvert mzXML file
-<br>TPP:TPP Search successful--calctppstat for mzXML+<br>TPP:TPP Search successful--calctppstat for mzXML by ReAdW similar to that of calctppstat for mzXML file by msconvert, slight differences, comparison is below:
 +CALCSTAT FOR READW DIRECTORY FILES
 + 
 +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 DIRECTORY FILES
 + 
 +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)
<h2>msconvert</h2> <h2>msconvert</h2>

Revision as of 22:26, 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, comparison is below: CALCSTAT FOR READW DIRECTORY FILES

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 DIRECTORY FILES

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)

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

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:

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