Hi there,
we are trying to run some Mascot search results through TPP. We copied
the .dat files and the .fasta file for database into C:\Inetpub\wwwroot
\ISB\data. in the TPP interface, we went to the "pepXML" tab under
"analysis pipeline(Mascot)", added the files, then hit the "convert to
pepXML" button. then we got something as shown at the end. Anyone know
why? Thanks a lot.
we use TPP v4.5 (rapture) rev 1, PERL 5.12.4.1205, winXP.
# Commands for session MUT6YN88F on Thu Jan 26 17:22:12 2012
# BEGIN COMMAND BLOCK
###### BEGIN Command Execution ######
[Thu Jan 26 17:22:12 2012] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/
data/4953; c:\Inetpub\tpp-bin\Mascot2XML c:/Inetpub/wwwroot/ISB/data/
4953/F004954.dat -Dc:/Inetpub/wwwroot/ISB/data/4953/F004954.dat -
Etrypsin
OUTPUT:
filepath: c:/Inetpub/wwwroot/ISB/data/4953/, extn: F004954
A stored as 71.0371
B stored as 114.535
C stored as 103.009
D stored as 115.027
E stored as 129.043
F stored as 147.068
G stored as 57.0215
H stored as 137.059
I stored as 113.084
J stored as 0
K stored as 128.095
L stored as 113.084
M stored as 131.04
N stored as 114.043
O stored as 0
P stored as 97.0528
Q stored as 128.059
R stored as 156.101
S stored as 87.032
T stored as 101.048
U stored as 150.954
V stored as 99.0684
W stored as 186.079
X stored as 111
Y stored as 163.063
Z stored as 128.551
c stored as 17.0027
n stored as 1.00782
variable modification 1, delta mass 57.0215 for Carbamidomethyl (C):
residues: C
nterm: 0
cterm: 0
--------------------------------------------------------------------------------
...skipping 8796 lines of output... [ view all ]
--------------------------------------------------------------------------------
Warning: could not find scan numbers of spectrum Spectrum3799scans:
7221,
Set to 0000
Warning: could not find scan numbers of spectrum Spectrum4340scans:
8033,
Set to 0000
Warning: could not find scan numbers of spectrum Spectrum4762scans:
8683,
Set to 0000
Warning: could not find scan numbers of spectrum Spectrum4765scans:
8688,
Set to 0000
Warning: could not find scan numbers of spectrum Spectrum5492scans:
9762,
Set to 0000
Warning: could not find scan numbers of spectrum Spectrum5478scans:
9744,
Set to 0000
Warning: could not find scan numbers of spectrum Spectrum2940scans:
5953,
Set to 0000
Warning: could not find scan numbers of spectrum Spectrum2937scans:
5949,
Set to 0000
Warning: could not find scan numbers of spectrum Spectrum2931scans:
5940,
Set to 0000
Warning: could not find scan numbers of spectrum Spectrum4262scans:
7902,
Set to 0000
Warning: could not find scan numbers of spectrum Spectrum5067scans:
9157,
Set to 0000
Warning: could not find scan numbers of spectrum Spectrum5856scans:
10228,
Set to 0000
Warning: could not find scan numbers of spectrum Spectrum5846scans:
10216,
Set to 0000
Warning: could not find scan numbers of spectrum Spectrum4395scans:
8121,
Set to 0000
trypsin : cut(KR) nocuts(P) sense(C)
prev_aa and next_aa have already been read from .dat file.
Replacing 35007 protein id with full ids by parsing through the
database...
searching c:/Inetpub/wwwroot/ISB/data/4953/F004954.datwarning, size of
protein exceeds 50000
Sequence line exceeds 40000characters
command "c:\Inetpub\tpp-bin\Mascot2XML c:/Inetpub/wwwroot/ISB/data/
4953/F004954.dat -Dc:/Inetpub/wwwroot/ISB/data/4953/F004954.dat -
Etrypsin" failed: Operation not permitted
END OUTPUT
RETURN CODE:256
###### End Command Execution ######
# All finished at Thu Jan 26 17:23:02 2012
# END COMMAND BLOCK
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