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, 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:
