Hi,
I've been running some searches on bruker MALDI data.
The overall processing is as follows;
1. Convert original raw data to mzML using CompassExport
2. Convert mzML file to mgf using msconvert
3. Submit mgf file for searching with Mascot
4. Attempt to convert mascot dat file to pep.xml
This step fails with the following output (using latest development version of
tpp, or with latest release ). (see bottom of email for output)
The search seemed to succeed in mascot so it seems to be an error with
Mascot2XML.
Any help would be much appreciated. I'd be happy to upload an example file ....
and in the interim here is one of the entries from the file.
Many thanks
Ira
--gc0p4Jq0M2Yt08jU534c0p
Content-Type: application/x-Mascot; name="query49"
title=scan%3d465
rtinseconds=2569.998
index=356
charge=1+
mass_min=42.978138
mass_max=942.880249
int_min=22.03
int_max=136.2
num_vals=59
num_used1=-1
Ions1=85.891281:91.3,174.844437:57.05,311.813507:81.99,375.793213:101,450.780975:69.69,632.835754:89.87,926.932861:136.2,128.844223:76.01,240.782654:50.81,243.792587:48.49,356.814117:69.49,454.723877:69.17,591.914917:62.51,929.205750:134.9,119.835655:50.81,146.810730:44.12,313.753174:46.04,432.699707:66.65,490.830780:59.32,931.451904:119.3,69.872475:50.47,178.782593:43.7,272.742065:43.81,408.824493:45.39,942.880249:115,117.840309:49.52,198.775986:42.92,324.805359:42.99,344.773254:39.04,109.852356:47.57,187.770813:39.76,133.594757:43.39,160.772324:39.08,56.943443:39.36,226.134232:38.81,67.875641:38.61,171.799027:38.8,111.822693:35.59,176.832809:38.53,42.978138:23.79,50.916721:27.19,52.566887:26.87,54.913723:22.46,72.841072:34.07,76.249527:23.81,82.256073:22.03,93.497459:24.16,94.913765:31.94,96.887436:34.87,115.820259:35.2,157.781494:33.38,162.763641:32.95,180.753448:29.66,189.855454:30.07,194.830963:27.97,196.772705:34.92,201.053894:36.89,216.776947:38.16,220.865006:34.84
Output from Mascot2XML
Mascot2XML F019018.dat
-D/sharedData/TPP/Databases/OnMascot/SPHuman/sphuman_20101013_DECOY.fasta
filepath: /sharedData/TPP/Data/MALDI/1011/MT237/, extn: F019018
A stored as 71.0779
B stored as 114.595
C stored as 160.194
D stored as 115.087
E stored as 129.114
F stored as 147.174
G stored as 57.0513
H stored as 137.139
I stored as 113.158
J stored as 0
K stored as 128.172
L stored as 113.158
M stored as 131.196
N stored as 114.103
O stored as 0
P stored as 97.1152
Q stored as 128.129
R stored as 156.186
S stored as 87.0773
T stored as 101.104
U stored as 150.038
V stored as 99.1311
W stored as 186.21
X stored as 111
Y stored as 163.173
Z stored as 128.622
c stored as 17.0073
n stored as 1.00794
variable modification 1, delta mass 0.9848 for Deamidated-N (N):
residues: N
nterm: 0
cterm: 0
protterm: 0
warning: cannot open "F019018.mzXML" for reading scan numbers.
Warning: could not find scan numbers of spectrum scan=637
Set to 0000
Warning: could not find scan numbers of spectrum scan=72
...... lots of warnings like the one above
Warning: could not find scan numbers of spectrum scan=284
Set to 0000
Warning: could not find scan numbers of spectrum scan=673
Set to 0000
Sample enzyme has not been specified, "Trypsin" from .dat file assumed
trypsin : cut(KR) nocuts(P) sense(C)
prev_aa and next_aa have already been read from .dat file.
Replacing 1913 protein id with full ids by parsing through the database...
searching
/sharedData/TPP/Databases/OnMascot/SPHuman/sphuman_20101013_DECOY.fasta.....5%.....10%.....15%.....20%.....30%.....35%.....40%.....45%.....50%.....60%.....65%.....70%.....75%.....80%.....90%.....95%...done
481. opening scan=671.out
warning: cannot open "F019018.mzXML" for reading MS instrument info.
error: only found 0 periods in scan=11
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