I am trying to squeak additional mass accuracy out of an LTQ by collecting
MS1 data with Enhanced Scan and in Profile mode so the data will have
isotopic resolution. This had the expected result of shifting the
frequency of peptides observed at a particular error down from ~0.75 (when
collected using normal scan rate and centroid mode) to center the curve
over an error of 0 (when collected using enhanced scan rate and profile
mode). Nice.
I processed the raw files with msconvert and used the --filter "peakPicking
true 1-1" argument and run it through TPP v 4.6.2 with Tandem as the search
engine. This has worked fine on samples until today when this latest data
set (which is a pull down experiment), xinteract fails to produce a pep.xml
file and results in a warning that says:
WARNING: Mixture model quality test failed for charge (1+).
WARNING: Mixture model quality test failed for charge (2+).
WARNING: Mixture model quality test failed for charge (3+).
The tandem.pep.xml file contains many high scoring peptides. And there are
good +1,+2 & +3 spectral matches.
I am wondering if there is an argument to msconvert that I am missing. Or
maybe my approach to collecting the data is incompatible with TPP? Or
could this be a problem with K-score vs native tandem scoring? I haven't
tried another search using native Tandem scoring yet.
Below is the output from TPP.
Thanks in advance for any help.
Cheers,
Brian
EXECUTING: cd /usr/local/tpp/data/projects/lindsey/xiap-ide12;
/usr/local/tpp/bin/xinteract -Ninteract-XIAP-IDE12.pep.xml -p0.05 -l5 -Op
-dDECOY 140226-XIAP-IDE12-5pct.tandem.pep.xml
/usr/local/tpp/bin/xinteract (TPP v4.6 OCCUPY rev 2, Build 201302151642
(linux))
running: "/usr/local/tpp/bin/InteractParser 'interact-XIAP-IDE12.pep.xml'
'140226-XIAP-IDE12-5pct.tandem.pep.xml' -L'5'"
file 1: 140226-XIAP-IDE12-5pct.tandem.pep.xml
SUCCESS: CORRECTED data file
/usr/local/tpp/data/projects/lindsey/xiap-ide12/140226-XIAP-IDE12-5pct.mzML
in msms_run_summary tag ...
processed altogether 22365 results
INFO: Results written to file:
/usr/local/tpp/data/projects/lindsey/xiap-ide12/interact-XIAP-IDE12.pep.xml
command completed in 6 sec
running: "/usr/local/tpp/bin/DatabaseParser 'interact-XIAP-IDE12.pep.xml'"
command completed in 1 sec
running: "/usr/local/tpp/bin/RefreshParser 'interact-XIAP-IDE12.pep.xml'
'/usr/local/tpp/data/dbase/ixodes-plus-crap_DECOY.fasta'"
- Building Commentz-Walter keyword tree... - Searching the tree...
- Linking duplicate entries... - Printing results...
command completed in 6 sec
running: "/usr/local/tpp/bin/PeptideProphetParser
'interact-XIAP-IDE12.pep.xml' MINPROB=0.05 DECOY=DECOY"
Using Decoy Label "DECOY".
(X! Tandem (k-score))
init with X! Tandem (k-score) trypsin
MS Instrument info: Manufacturer: Thermo Scientific, Model: UNKNOWN,
Ionization: nanoelectrospray, Analyzer: radial ejection linear ion trap,
Detector: electron multiplier
PeptideProphet (TPP v4.6 OCCUPY rev 2, Build 201302151642 (linux))
AKeller@ISB
read in 2445 1+, 9959 2+, 9950 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
Initialising statistical models ...
Found 10751 Decoys, and 11603 Non-Decoys
Iterations: .........10.........20........
WARNING: Mixture model quality test failed for charge (1+).
WARNING: Mixture model quality test failed for charge (2+).
WARNING: Mixture model quality test failed for charge (3+).
model complete after 29 iterations
command completed in 4 sec
running: "/usr/local/tpp/bin/ProphetModels.pl -i
interact-XIAP-IDE12.pep.xml -d DECOY"
Analyzing interact-XIAP-IDE12.pep.xml ...
Parsing search results
"/usr/local/tpp/data/projects/lindsey/xiap-ide12/140226-XIAP-IDE12-5pct (X!
Tandem (k-score))"...
=> Total of 0 hits.
=> Total of 0 decoy hits.
=> Total of 0 excluded hits.
Warning: empty y range [0:0], adjusting to [0:1]
Warning: empty y range [0:0], adjusting to [0:1]
plot "interact-XIAP-IDE12.pep_FVAL.tsv" using 1:17 title "Observed" with
line lc -1 , "interact-XIAP-IDE12.pep_FVAL.tsv" using 1:18 title "Model
Pos" with line lc 3 , "interact-XIAP-IDE12.pep_FVAL.tsv" using 1:19 title
"Model Neg" with line lc 1
^
"interact-XIAP-IDE12.pep_FVAL.gp", line 23: warning: Skipping data file
with no valid points
Warning: empty y range [0:0], adjusting to [0:1]
plot "interact-XIAP-IDE12.pep_FVAL.tsv" using 1:20 title "Observed" with
line lc -1 , "interact-XIAP-IDE12.pep_FVAL.tsv" using 1:21 title "Model
Pos" with line lc 3 , "interact-XIAP-IDE12.pep_FVAL.tsv" using 1:22 title
"Model Neg" with line lc 1
^
"interact-XIAP-IDE12.pep_FVAL.gp", line 25: warning: Skipping data file
with no valid points
Warning: empty y range [0:0], adjusting to [0:1]
plot "interact-XIAP-IDE12.pep_PPPROB.tsv" using 2:1 title "PeptideProphet"
with line lt 1 lc 3 , x notitle with line lt 0 lc -1
^
"interact-XIAP-IDE12.pep_PPPROB.gp", line 17: warning: Skipping data file
with no valid points
plot "interact-XIAP-IDE12.pep_IPPROB.tsv" using 2:1 title "iProphet" with
line lt 1 lc 3 , "interact-XIAP-IDE12.pep_PPPROB.tsv" using 2:1 title
"PeptideProphet" with line lt 1 lc 1 , x notitle with line lt 0 lc -1
^
"interact-XIAP-IDE12.pep_IPPROB.gp", line 17: warning: Skipping data file
with no valid points
plot "interact-XIAP-IDE12.pep_IPPROB.tsv" using 2:1 title "iProphet" with
line lt 1 lc 3 , "interact-XIAP-IDE12.pep_PPPROB.tsv" using 2:1 title
"PeptideProphet" with line lt 1 lc 1 , x notitle with line lt 0 lc -1
^
"interact-XIAP-IDE12.pep_IPPROB.gp", line 17: warning: Skipping data file
with no valid points
command completed in 0 sec
running: "/usr/local/tpp/cgi-bin/PepXMLViewer.cgi -I
/usr/local/tpp/data/projects/lindsey/xiap-ide12/interact-XIAP-IDE12.pep.xml"
Segmentation fault (core dumped)
command "/usr/local/tpp/cgi-bin/PepXMLViewer.cgi -I
/usr/local/tpp/data/projects/lindsey/xiap-ide12/interact-XIAP-IDE12.pep.xml"
exited with non-zero exit code: 35584
QUIT - the job is incomplete
Command FAILED
RETURN CODE:35584
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