Msconvert Capabilities
From SPCTools
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:
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.
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:
