Thank you, Joe.
So this time, we were able to convert raw to mzML, then mgf, did the
mascot search . But still couldn't convert .dat to pepXML. please
see error message below. Thanks.
Attempting to run the following commands
run_in c:/Inetpub/wwwroot/ISB/data; c:\Inetpub\tpp-bin\Mascot2XML c:/
Inetpub/wwwroot/ISB/data/12032011_60min_PaG_XC_HP101_01.dat -Dc:/
Inetpub/wwwroot/ISB/data/NCBInr_20120128.fasta -Etrypsin
Output so far:
# Commands for session 5EJFN64ZU on Tue Jan 31 14:32:33 2012
# BEGIN COMMAND BLOCK
###### BEGIN Command Execution ######
[Tue Jan 31 14:32:33 2012] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/
data; c:\Inetpub\tpp-bin\Mascot2XML c:/Inetpub/wwwroot/ISB/data/
12032011_60min_PaG_XC_HP101_01.dat -Dc:/Inetpub/wwwroot/ISB/data/
NCBInr_20120128.fasta -Etrypsin
OUTPUT:
filepath: c:/Inetpub/wwwroot/ISB/data/, extn:
12032011_60min_PaG_XC_HP101_01
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
protterm: 0
variable modification 2, delta mass 15.9949 for Oxidation (M):
residues: M
nterm: 0
cterm: 0
protterm: 0
trypsin : cut(KR) nocuts(P) sense(C)
prev_aa and next_aa have already been read from .dat file.
Replacing 86418 protein id with full ids by parsing through the
database...
searching c:/Inetpub/wwwroot/ISB/data/NCBInr_20120128.fastaFail to get
line from sequence database
command "c:\Inetpub\tpp-bin\Mascot2XML c:/Inetpub/wwwroot/ISB/data/
12032011_60min_PaG_XC_HP101_01.dat -Dc:/Inetpub/wwwroot/ISB/data/
NCBInr_20120128.fasta -Etrypsin" failed: Operation not permitted
END OUTPUT
RETURN CODE:256
###### End Command Execution ######
# All finished at Tue Jan 31 14:33:53 2012
# END COMMAND BLOCK
On Jan 31, 1:41 pm, Joseph Slagel <[email protected]>
wrote:
> Hi,
>
> Please try using Protowizard's msconvert (which comes bundled with TPP) to
> do the conversion instead of ReAdW. The older ReAdW isn't being supported
> and doesn't automatically come bundled with TPP and has to be installed
> seperately, hence the error.
>
> -Joe
>
>
>
>
>
>
>
> On Tue, Jan 31, 2012 at 10:02 AM, XC <[email protected]> wrote:
> > one thing I can think of is that last week, we didn't do the database
> > search through TPP. we did the search through Proteome discoverer as
> > interface. then copy the resulting .dat files and the .fasta file
> > into C:\Inetpub\wwwroot\ISB\data. but we didn't change the file
> > name.
> > So today, we tried to start from the raw data. but when we tried to
> > convert raw to mzXML, we got teh error message as shown below.
> > Thanks..
>
> > Attempting to run the following commands
>
> > c:\Inetpub\tpp-bin\ReAdW -v --mzXML c:/Inetpub/wwwroot/ISB/data/
> > 12032011_60min_PaG_XC_HP101_01.raw
>
> > Output so far:
>
> > # Commands for session 5EJFN64ZU on Tue Jan 31 12:33:25 2012
> > # BEGIN COMMAND BLOCK
> > ###### BEGIN Command Execution ######
> > [Tue Jan 31 12:33:25 2012] EXECUTING: c:\Inetpub\tpp-bin\ReAdW -v --
> > mzXML c:/Inetpub/wwwroot/ISB/data/12032011_60min_PaG_XC_HP101_01.raw
> > OUTPUT:
> > The system cannot find message text for message number 0x2331 in the
> > message file for Application.
> > END OUTPUT
> > RETURN CODE:256
> > ###### End Command Execution ######
> > # All finished at Tue Jan 31 12:33:25 2012
> > # END COMMAND BLOCK
>
> > On Jan 27, 3:48 pm, Luis Mendoza <[email protected]>
> > wrote:
> > > Hello,
> > > There appears to be a couple of issues going on.
>
> > > The first is that Mascot2XML cannot find scan numbers in the .dat
> > > file. How did you do the Mascot search? For the TPP to support
> > > Mascot results, you must start with an mzML (or mzXML) file, convert
> > > that to an .mgf (using MzXML2Search), and search that file with
> > > Mascot. Once you retrieve the .dat file, you should rename it to the
> > > original base name of the mzML file (instead of Fxxxxxx.dat). Convert
> > > this to pepXML, and the scan numbers should be there!
>
> > > Second, you also need to specify the sequence database (in fasta
> > > format) that you used in the search. It seems that you selected the
> > > .dat file as that input, which is incorrect.
>
> > > Hope this helps,
> > > --Luis
>
> > > On Thu, Jan 26, 2012 at 2:29 PM, XC <[email protected]> wrote:
> > > > 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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