Jagan, Hopefully searches run as in steps 1 through 4 have no issues with visualizing the spectra.
Regarding points 6 and 7, I can't tell you definitely why there's a difference in scan counts without knowing specifics of how the MGF was created. If I had to guess, one thing that accounts for the scan count differences is that the mzXML contains both MS1 and MS/MS scans whereas the MGF file only has MS/MS scans in it. Likely that MGF contains just a subset of all MS/MS scans from the raw file due to not meeting some criteria. Both of these reasons and many others could easily explain the scan count differences. For a definitive explanation of why maybe the MS/MS counts don't match up, you need to go back to the tool that generated the MGF to figure out what it did. I didn't bother downloading your raw file but you'll hopefully find that it has the same number of total scans as the mzXML does (unless you have empty scans in the raw file). Regarding what you did in step 5, the mzXML created from the mgf starts with scan number 0 which is a tad unorthodox as 1 is the required first scan for a valid mzXML. But that's not necessarily the reason why you can't visualize spectra from this step 5 workflow. As I stated in the previous post, this mgf *must* contain the right information encoded in the TITLE line that the TPP expects. The first spectrum that got translated to scan 0 in the mzXML must have a TITLE like that conforms to something like TITLE=<basename>.0.0.<charge> and the second spectrum that got translated to scan 1 in the mzXML must have a TITLE line that appears as TITLE=<basename>.1.1.<charge>. You can pad the scan numbers if you wish like MzXML2Search does: <basename>.00001.00001.<charge>. And this TITLE information should exist in the mgf before you do the search. On Sun, Nov 7, 2010 at 4:30 PM, Jagan Kommineni <[email protected]>wrote: > Dear Jimmy, > > Here are the steps that we followed in converting files. > > 1. Original RAW file has been converted into mzXML file using msconvert in > Windows Environment. > > \bin\msconvert\msconvert.exe --mzXML --64 --mz64 --inten64 --filter > "peakPicking true 1-" > jagan-J2205.RAW<https://search.apcf.edu.au/dbdownloads/jagan-J2205.RAW.zip> > > > 2. mzXML file is converted into mgf format using mzXML2Search.exe in > Windows Environment. > > bin\ISB\mzXML2Search.exe" -mgf jagan2205.mzXML > > 3. The generated mgf file has been used to run OMSSA search and then pepXML > file has been created to view from the results with pepXMLViewer. > Step 3 is performed in Linux environment. > > 4. Whenever user specifes to run prophets (peptide and protein prophets) on > the server we transfer the mzXML file otherwise we transfer only mgf files > to perform stanard OMSSA search. > > 5. In the latter case where user wants perform standard OMSSA search we > don't have mzXML file but on the fly I am trying to generate mzXML file from > the mgf file using msconvert. > > I have used same parameters that used to generate RAW to mzXML file in > generating mzXML file from mgf. > > /var/www/APCF_WEB/tpp/bin/msconvert --mzXML --64 --mz64 --inten64 --filter > "peakPicking true 1-" jagan-J2205.mgf > > 6. The scan count in mzXML generated from RAW file is 9800 whereas scan > count in mzXML file generated from MGF file is 3444. > Here are respective entries in mzXML files ... > > <msRun scanCount="9800" startTime="PT0.1826S" endTime="PT5340.21S"> > <msRun scanCount="3444" startTime="PT1.88S" endTime="PT5339.11S"> > > 7. The number of entries in mgf file is 3444. > > [r...@apcf-hn3 downloads]# grep "BEGIN IONS" jagan-J2205.mgf|wc -l > 3444 > > 8. I put all the files on APCF Community Wiki Page and can be downloaded > from the following web pointer > > " > https://search.apcf.edu.au/wiki/index.php/Apcfwiki:Community_Portal#APCF_Files_for_Jimmy_Eng_and_TPP_team > ". > > 9. I don't have any issues in viewing the petide and protein information > from the pepXML file. > > we have also tried by using -L15000 in running mzXML2Search.exe but there > no difference in the scan count of mgf file. > > > > with regards, > > Jagan Kommineni > > > > On Fri, Nov 5, 2010 at 1:56 PM, Jimmy Eng <[email protected]> wrote: > >> Jagan, >> >> Start with your mzXML file. Generate mgf using "MzXML2Search -mgf >> yourfile.mzXML". Use this to do your omssa search and hopefully this fixes >> your problem. >> >> Compare the TITLE lines of the mgf generated by MzXML2Search with your >> "standard" mgf you used for the search. That difference is the reason why >> you can't see spectra as the required encoded information (mzXML base name >> and scan #) are likely not in the mgf file you used to search. Without this >> information encoded in a specific way, there's no way that the TPP will know >> which spectrum belongs to which peptide ID. >> >> Good luck! >> >> (Also, you should be able to export pep.xml directly from omssa using the >> "-op" option but presumably this isn't a part of the problem.) >> >> On Thu, Nov 4, 2010 at 7:14 PM, Jagan Kommineni < >> [email protected]> wrote: >> >>> Dear All, >>> >>> I havn't received my presvious message myself as the memeber of this >>> group and hence i am here with sending once again. >>> >>> Soory for the inconvinience if you already received my previous message. >>> >>> >>> Here is my previous message: >>> ======================= >>> >>> On Thu, Nov 4, 2010 at 5:06 PM, Jagan Kommineni < >>> [email protected]> wrote: >>> >>>> Dear All, >>>> >>>> I would like to view the OMSSA results with pepXMLViewer as there some >>>> compatibility issues with the latest version of OMSSA and OMSSA Browser. >>>> >>>> I have taken standard mgf file and run OMSSA search against it and >>>> produced xml formatted output. >>>> >>>> Then I have used omssa2pepXML (part of the OMSSA distribution) to >>>> generate pepXML file. I have also generated mzXML file using latest version >>>> of the msconvert from the build of ProteoWizard release: 2.1.2351 >>>> (2010-11-3) on Linux box. >>>> >>>> I am able to view pepXML file using pepXML Viewer, but few things are >>>> missing. When I click first few rows of the "IONS" column I am able to view >>>> the display (not sure how much extent this display is correct) but after >>>> that when I click any item in the same column I am getting an error message >>>> "Error-cannot parse scan number ...". >>>> >>>> I suspect this is due to the fact that the mzXML was generated from mgf >>>> file which itself doesn't contain retention time information. >>>> >>>> I wonder is there anyway I can able to produce reasonable views with >>>> mzXML file generated from the mgf file. >>>> >>>> Please note that I didn't have these problems when I produce mzXML file >>>> from the RAW files. >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> with regards, >>>> >>>> -- >>>> Dr. Jagan Kommineni >>>> Systems Administrator and Duty Programmer >>>> Australian Proteomics Computational Facility >>>> Ludwig Institute for Cancer Research, >>>> 6th Floor, Royal Melbourne Hospital, >>>> Royal Parade, Parkville, Victoria >>>> Ph:03 9341-3177. >>>> >>>> >>> >>> >>> -- >>> Dr. Jagan Kommineni >>> Systems Administrator and Duty Programmer >>> Australian Proteomics Computational Facility >>> Ludwig Institute for Cancer Research, >>> 6th Floor, Royal Melbourne Hospital, >>> Royal Parade, Parkville, Victoria >>> Ph:03 9341-3177. >>> >>> -- >>> You received this message because you are subscribed to the Google Groups >>> "spctools-discuss" group. >>> To post to this group, send email to [email protected]. >>> To unsubscribe from this group, send email to >>> [email protected]<spctools-discuss%[email protected]> >>> . >>> For more options, visit this group at >>> http://groups.google.com/group/spctools-discuss?hl=en. >>> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]<spctools-discuss%[email protected]> >> . >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> > > > > -- > Dr. Jagan Kommineni > Systems Administrator and Duty Programmer > Australian Proteomics Computational Facility > Ludwig Institute for Cancer Research, > 6th Floor, Royal Melbourne Hospital, > Royal Parade, Parkville, Victoria > Ph:03 9341-3177. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]<spctools-discuss%[email protected]> > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
