Hi Chris, It turns out that the mzXML files included for this tutorial have a corrupt index, which makes the new versions of our tools throw an error. Since this tutorial was provided and the data is hosted by external collaborators, I will contact them to ask them to update the data files.
In the meantime, you can fix the mzXML files in the following way: - In Petunia (the GUI), go to the "Index mxXML Files" page, found under the "mzXML Utils" tab. - Select all 6 mzXML files in the Tutorial folder, then hit the "Re-Index..." button. - This will create files named "raft4041.new.mzXML" etc. You will need to RENAME these .new files to the original file names (i.e. get rid of the ".new" part) -- do this under Windows Explorer (you may need to either delete or move the original files, as the names will collide). You should at this point be able to continue working on the conversion step of the tutorial; please let us know if this does not work. I would also recommend following the Tandem tutorial that we have linked from the top of that page. Cheers, --Luis On Fri, Oct 7, 2011 at 8:36 AM, Chris L <[email protected]> wrote: > Hi again, > I am trying to follow the SEQUEST data analysis tutorial in the > following link > http://tools.proteomecenter.org/wiki/index.php?title=TPP_Tutorial > I am having problem with opening my converted pepXML files in pepXML > viewer. > Below are the screenshots of what is happening (click on the picture > to zoom in): > This screenshot shows my conversion settings > http://flic.kr/p/atDywi > This is the log file I got after the commands are completed (same with > all six output files) > http://flic.kr/p/atGeEs > Here's what happens when I tried to opening one of them via the "View" > option in the output files pane > http://flic.kr/p/atDyh8 > Any suggestion is appreciated. Thanks! > > Regards, > Chris > > > On Oct 7, 8:13 am, Chris L <[email protected]> wrote: > > Hi Luis, > > > > Yes, I overlooked it. Setting it to SEQUEST solved the problem. Thanks > > a lot! > > ps. It is my first time using TPP, so I get to have some leeway > > right? :) > > > > Regards, > > Chris > > > > On Oct 6, 5:52 pm, Luis Mendoza <[email protected]> > > wrote: > > > > > > > > > > > > > > > > > Hi Chris, > > > Which tutorial are you referring to? Please also note that you must > set the > > > "pipeline type" to "Sequest" on the home page if you wish to convert > .out > > > files to pepXML; leaving it set to "Tandem" will tell the software to > only > > > look for files of that type. > > > Cheers, > > > --Luis > > > > > On Thu, Oct 6, 2011 at 5:48 PM, Chris L <[email protected]> wrote: > > > > Dear all, > > > > > > I am attempting the tutorial steps for TPP. The tutorial instructed > me > > > > to choose .out files to convert to pepXML; however, the TPP shows it > > > > cannot detect compatible file (.tandem) I am wondering whether I am > > > > suppose to convert .out files into .tandem files, or should I try > > > > downloading .tandem files somewhere? Any input is appreciated. Thank > > > > you. > > > > > > Sincerely, > > > > Chris L > > > > > > -- > > > > 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. > > -- > 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. > > -- 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.
