Hi all,
1. I have successfully imported mzXML, pepXML and protXML created by TPP to CPAS, finished the quantitative analysis by xpress software. The one problem we faced is the failure to see MS1 spectrum (or EIC) in CPAS website. Can anyone tell us the possibility for checking the quantified MS spectrum (or EIC)in this kind of workflow? Thanks.

2. We have also try to directly import mzXML into CPAS to run the xpress analysis. One error message appear as follow:
28 一月 2008 12:01:25,578 INFO : Mascot search for 1-1.mzXML
28 一月 2008 12:01:25,593 INFO : =======================================
28 一月 2008 12:01:25,640 INFO : MzXML2Search output
28 一月 2008 12:01:25,640 INFO : =======================================
28 一月 2008 12:02:02,203 INFO : running: MzXML2Search -mgf 1-1.mzXML
28 一月 2008 12:02:02,421 INFO :
28 一月 2008 12:02:02,421 INFO : MzXML2Search - Mascot Generic Format
28 一月 2008 12:02:02,421 INFO :
28 一月 2008 12:02:02,421 INFO : Reading 1-1.mzXML
28 一月 2008 12:02:02,421 INFO : Getting the index offset
28 一月 2008 12:02:02,421 INFO : Reading the index
28 一月 2008 12:02:05,593 INFO : scan: 1 000% 2 000% 3 000%
28 一月 2008 12:02:05,609 INFO : Done.
28 一月 2008 12:22:50,281 INFO : PeptideProphet v3.0 April 1, 2004 (TPP v3.4 SQUALL rev.0, Build 200711281212(Win32)) AKeller@ISB
28 一月 2008 12:22:50,281 INFO : read in 2274 1+, 2544 2+, 5615 3+, 0 4+, and 0 5+ spectra
28 一月 2008 12:22:50,281 INFO : Initialising statistical models ...
28 一月 2008 12:22:50,421 INFO : iteration 1 2 3 4
28 一月 2008 12:22:50,812 INFO : command completed in 1 sec
28 一月 2008 12:22:50,812 INFO :
28 一月 2008 12:22:50,812 INFO : running: "XPressPeptideParser "1-1.pep.xml" -nK,6.02 -nR,6.02 -dF:\Chi\SILAC_mzxml"
28 一月 2008 12:22:51,234 INFO : Error - peptide CDSAIMYADK at start scan 12154 with previous MS scan at 12143
28 一月 2008 12:22:51,234 INFO : ... the gap is too large.
28 一月 2008 12:22:51,234 INFO :
28 一月 2008 12:22:51,250 INFO :
28 一月 2008 12:22:51,250 INFO : command "XPressPeptideParser "1-1.pep.xml" -nK,6.02 -nR,6.02 -dF:\Chi\SILAC_mzxml" exited with non-zero exit code: 1
28 一月 2008 12:22:51,250 INFO : QUIT - the job is incomplete
28 一月 2008 12:22:51,250 INFO :
28 一月 2008 12:22:51,250 INFO : command "XPressPeptideParser "1-1.pep.xml" -nK,6.02 -nR,6.02 -dF:\Chi\SILAC_mzxml" failed: Operation not permitted
28 一月 2008 12:22:51,265 ERROR: Failed running xinteract.

We guess it may due to we perform one MS spectrum followed by 12 MS2 analysis. If it is a right guess or it means anything else? Thanks.
Amy