Hello,
I'm a grad student trying to put a SWATH library together. To learn how to
do this I looked up this paper by the Aebersold lab in 2015 which walks the
reader through the
process: https://www.nature.com/nprot/journal/v10/n3/full/nprot.2015.015.html
I'm following the protocol which pointed me to download the X!Tandem
parameters below. Using these parameters, I get the error messages (farther
below) when trying to search the converted mzXML files using X!Tandem on
TPP. Any tips? I saw from a discussion in this group in 2013 that this may
be a parameter issue (Comet search has been running for hours but seems to
be working/hasn't given any errors) so I'll keep troubleshooting there.
Thanks!
Parameters:
<?xml version="1.0"?>
<?xml-stylesheet type="text/xsl" href="tandem-input-style.xsl"?>
<bioml>
<note>spectrum parameters</note>
<note type="input" label="spectrum, parent monoisotopic mass error
minus">50</note>
<note type="input" label="spectrum, parent monoisotopic mass error
plus">50</note>
<note>PRECURSOR MASS TOLERANCE. This is monoisotopic mass, so for
non-accurate-mass instruments, for which the precursor is often taken
nearer to the isotopically averaged mass, an asymmetric tolerance (-2.0 Da
to 4.0 Da) is preferable. This somewhat imitates a (-3.0 Da to 3.0 Da)
window for averaged mass (but not exactly).</note>
<note type="input" label="spectrum, parent monoisotopic mass isotope
error">no</note>
<note type="input" label="spectrum, fragment monoisotopic mass error
units">ppm</note>
<note>The value for this parameter may be 'Daltons' or 'ppm': all other
values are ignored</note>
<note type="input" label="spectrum, parent monoisotopic mass error
units">ppm</note>
<note>The value for this parameter may be 'Daltons' or 'ppm': all other
values are ignored</note>
<note type="input" label="spectrum, fragment monoisotopic mass
error">100</note>
<note>This parameter has no effect in k-score scoring.</note>
<note type="input" label="spectrum, fragment mass type">monoisotopic</note>
<note>values are monoisotopic|average </note>
<note>spectrum conditioning parameters</note>
<note type="input" label="spectrum, use conditioning">no</note>
<note>For k-score scoring, it is recommended spectrum conditioning be
turned OFF for best performance. All of the spectrum filtering and
preprocessing options below in this section will be inactive.</note>
<note type="input" label="spectrum, dynamic range">10000.0</note>
<note type="input" label="spectrum, total peaks">400</note>
<note type="input" label="spectrum, maximum parent charge">5</note>
<note type="input" label="spectrum, use noise suppression">yes</note>
<note type="input" label="spectrum, minimum parent m+h">600.0</note>
<note type="input" label="spectrum, minimum fragment mz">125.0</note>
<note type="input" label="spectrum, minimum peaks">10</note>
<note type="input" label="spectrum, threads">1</note>
<note type="input" label="spectrum, sequence batch size">1000</note>
<note>residue modification parameters</note>
<note type="input" label="residue, modification mass">57.021464@C</note>
<note>STATIC MODIFICATION. The format of this parameter is m@X, where m is
the modfication mass in Daltons and X is the appropriate residue to modify.
Lists of modifications are separated by commas. For example, to modify M
and C with the addition of 16.0 Daltons, the parameter line would be
+16.0@M,+16.0@C. Positive and negative values are allowed.</note>
<note type="input" label="residue, potential modification
mass">15.994915@M</note>
<note>VARIABLE MODIFICATION. The format of this parameter is the same as
the format for residue, modification mass (see above).</note>
<note type="input" label="residue, potential modification motif"></note>
<note>VARIABLE MODIFICATION IN A MOTIF. The format of this parameter is
similar to residue, modification mass, with the addition of a modified
PROSITE notation sequence motif specification. For example, a value of
80@[ST!]PX[KR] indicates a modification of either S or T when followed by
P, and residue and the a K or an R. A value of 204@N!{P}[ST]{P} indicates a
modification of N by 204, if it is NOT followed by a P, then either an S or
a T, NOT followed by a P. Positive and negative values are allowed. </note>
<note>protein parameters</note>
<note type="input" label="protein, taxon">no default</note>
<note>SEQUENCE DATABASE TO SEARCH. This refers to identifiers in
taxonomy.xml.</note>
<note type="input" label="protein, cleavage site">[RK]|{P}</note>
<note type="input" label="protein, cleavage semi">no</note>
<note>ENZYME SPECIFICITY. This setting corresponds to the enzyme trypsin.
The first characters in brackets represent residues N-terminal to the bond
- the '|' pipe - and the second set of characters represent residues
C-terminal to the bond. The characters must be in square brackets (denoting
that only these residues are allowed for a cleavage) or french brackets
(denoting that these residues cannot be in that position). Use UPPERCASE
characters. To denote cleavage at any residue, use [X]|[X] and reset the
scoring, maximum missed cleavage site parameter (see below) to something
like 50. </note>
<note type="input" label="protein, modified residue mass file"></note>
<note type="input" label="protein, N-terminal residue modification
mass"></note>
<note type="input" label="protein, C-terminal residue modification
mass"></note>
<note type="input" label="protein, homolog management">no</note>
<note>if yes, an upper limit is set on the number of homologues kept for a
particular spectrum</note>
<note type="input" label="protein, quick acetyl">no</note>
<note type="input" label="protein, quick pyrolidone">no</note>
<note>model refinement parameters</note>
<note type="input" label="refine">no</note>
<note type="input" label="refine, modification mass"></note>
<note type="input" label="refine, sequence path"></note>
<note type="input" label="refine, tic percent">10</note>
<note type="input" label="refine, spectrum synthesis">yes</note>
<note type="input" label="refine, maximum valid expectation
value">0.1</note>
<note type="input" label="refine, potential N-terminus
modifications"></note>
<note type="input" label="refine, potential C-terminus
modifications"></note>
<note type="input" label="refine, unanticipated cleavage">no</note>
<note type="input" label="refine, potential modification mass"></note>
<note type="input" label="refine, point mutations">no</note>
<note type="input" label="refine, use potential modifications for full
refinement">no</note>
<note type="input" label="refine, point mutations">no</note>
<note type="input" label="refine, potential modification motif"></note>
<note>scoring parameters</note>
<note type="input" label="scoring, algorithm">k-score</note>
<note type="input" label="scoring, minimum ion count">4</note>
<note type="input" label="scoring, maximum missed cleavage sites">2</note>
<note type="input" label="scoring, x ions">no</note>
<note type="input" label="scoring, y ions">yes</note>
<note type="input" label="scoring, z ions">no</note>
<note type="input" label="scoring, a ions">no</note>
<note type="input" label="scoring, b ions">yes</note>
<note type="input" label="scoring, c ions">no</note>
<note type="input" label="scoring, cyclic permutation">no</note>
<note>if yes, cyclic peptide sequence permutation is used to pad the
scoring histograms</note>
<note type="input" label="scoring, include reverse">no</note>
<note>if yes, then reversed sequences are searched at the same time as
forward sequences</note>
<note type="input" label="scoring, cyclic permutation">no</note>
<note type="input" label="scoring, include reverse">no</note>
<note>output parameters</note>
<note type="input" label="output, log path"></note>
<note type="input" label="output, message">1234567890</note>
<note type="input" label="output, sequence path"></note>
<note type="input" label="output, path">output.xml</note>
<note type="input" label="output, sort results by">spectrum</note>
<note>values = protein|spectrum (spectrum is the default)</note>
<note type="input" label="output, path hashing">no</note>
<note>values = yes|no</note>
<note type="input" label="output, xsl path">tandem-style.xsl</note>
<note type="input" label="output, parameters">yes</note>
<note>values = yes|no</note>
<note type="input" label="output, performance">yes</note>
<note>values = yes|no</note>
<note type="input" label="output, spectra">no</note>
<note>values = yes|no</note>
<note type="input" label="output, histograms">no</note>
<note>values = yes|no</note>
<note type="input" label="output, proteins">yes</note>
<note>values = yes|no</note>
<note type="input" label="output, sequences">no</note>
<note>values = yes|no</note>
<note type="input" label="output, one sequence copy">no</note>
<note>values = yes|no, set to yes to produce only one copy of each protein
sequence in the output xml</note>
<note type="input" label="output, results">all</note>
<note>values = all|valid|stochastic</note>
<note type="input" label="output, maximum valid expectation
value">0.1</note>
<note>value is used in the valid|stochastic setting of output,
results</note>
<note type="input" label="output, histogram column width">30</note>
<note>values any integer greater than 0. Setting this to '1' makes cutting
and pasting histograms into spread sheet programs easier.</note>
<note type="description">ADDITIONAL EXPLANATIONS</note>
<note type="description">Each one of the parameters for X! tandem is
entered as a labeled note node. In the current version of X!, keep those
note nodes on a single line.</note>
<note type="description">The presence of the type 'input' is necessary if a
note is to be considered an input parameter. </note>
<note type="description">Any of the parameters that are paths to files may
require alteration for a particular installation. Full path names usually
cause the least trouble, but there is no reason not to use relative path
names, if that is the most convenient.</note>
<note type="description">Any parameter values set in the 'list path,
default parameters' file are reset by entries in the normal input file, if
they are present. Otherwise, the default set is used. </note>
<note type="description">The 'list path, taxonomy information' file must
exist.</note>
<note type="description">The directory containing the 'output, path' file
must exist: it will not be created.</note>
<note type="description">The 'output, xsl path' is optional: it is only of
use if a good XSLT style sheet exists.</note>
</bioml>
Errors:
Command 1 [Mon Oct 16 17:31:01 2017] [ Show / Hide ]
*EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data; c:\Inetpub\tpp-bin\tandem
c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_001.tandem.params *
X! TANDEM Jackhammer TPP (2013.06.15.1 - LabKey, Insilicos, ISB)
Loading spectra
(mzParser)................................................................................
loaded.
Spectra matching criteria = 158033
Pluggable scoring enabled.
Starting threads .
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
command "c:\Inetpub\tpp-bin\tandem
c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_001.tandem.params" failed: No such
process
*Command FAILED*
RETURN CODE:768
Command 2 [Mon Oct 16 17:31:24 2017] [ Show / Hide ]
*EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data;
c:\Inetpub\tpp-bin\Tandem2XML
c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_001.tandem
c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_001.tandem.pep.xml *
Failed to open input file
'c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_001.tandem'.
command "c:\Inetpub\tpp-bin\Tandem2XML
c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_001.tandem
c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_001.tandem.pep.xml" failed:
Operation not permitted
*Command FAILED*
RETURN CODE:256
Command 3 [Mon Oct 16 17:31:24 2017] [ Show / Hide ]
*EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data; c:\Inetpub\tpp-bin\tandem
c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_010.tandem.params *
X! TANDEM Jackhammer TPP (2013.06.15.1 - LabKey, Insilicos, ISB)
Loading spectra
(mzParser)................................................................................
loaded.
Spectra matching criteria = 158770
Pluggable scoring enabled.
Starting threads .
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
command "c:\Inetpub\tpp-bin\tandem
c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_010.tandem.params" failed: Unknown
error
*Command FAILED*
RETURN CODE:65280
Command 4 [Mon Oct 16 17:31:48 2017] [ Show / Hide ]
*EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data;
c:\Inetpub\tpp-bin\Tandem2XML
c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_010.tandem
c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_010.tandem.pep.xml *
Failed to open input file
'c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_010.tandem'.
command "c:\Inetpub\tpp-bin\Tandem2XML
c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_010.tandem
c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_010.tandem.pep.xml" failed:
Operation not permitted
*Command FAILED*
RETURN CODE:256
Command 5 [Mon Oct 16 17:31:48 2017] [ Show / Hide ]
*EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data; c:\Inetpub\tpp-bin\tandem
c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_016.tandem.params *
X! TANDEM Jackhammer TPP (2013.06.15.1 - LabKey, Insilicos, ISB)
Loading spectra
(mzParser)................................................................................
loaded.
Spectra matching criteria = 158289
Pluggable scoring enabled.
Starting threads .
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
command "c:\Inetpub\tpp-bin\tandem
c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_016.tandem.params" failed: Unknown
error
*Command FAILED*
RETURN CODE:65280
Command 6 [Mon Oct 16 17:32:30 2017] [ Show / Hide ]
*EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data;
c:\Inetpub\tpp-bin\Tandem2XML
c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_016.tandem
c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_016.tandem.pep.xml *
Failed to open input file
'c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_016.tandem'.
command "c:\Inetpub\tpp-bin\Tandem2XML
c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_016.tandem
c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_016.tandem.pep.xml" failed:
Operation not permitted
*Command FAILED*
RETURN CODE:256
All commands finished at *Mon Oct 16 17:32:30 2017*
-Steven
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