Hi Ruby, A couple of more things on top of what Jimmy just posted: 1) While probably not the reason your conversion is failing, there is a way to specify a semi-enzyme search when converting to pepXML: you want to use -Esemitrypsin as a parameter to Out2XML. Unfortunately, that option is not in Petunia (the GUI), but it will be on the next release of the TPP. (Alternatively, I can send you a special version that has it.)
2) You are correct; we are recommending the use of msconvert and the mzML format. We still keep mzXML converters supported on the GUI, since many people still use them. You can find msconvert under the "mzML" tab in Petunia. If you wish to use msconvert to generate an mzXML file, however, you will need to use it via the command-line. Hope this helps, --Luis On Tue, Mar 1, 2011 at 2:08 PM, Jimmy Eng <[email protected]> wrote: > Ruby, > > The problem likely has nothing to do with the -Etrypsin option in the > Out2XML command. Do you have a bunch of *.out files in the directory > c:\Inetpub\wwwroot\ISB\data\RG_81_2\ > > Are those files named something like RG_81_2.00001.00001.1.out? > > - Jimmy > > On Tue, Mar 1, 2011 at 1:58 PM, Ruby <[email protected]> wrote: > > Hi- > > I just downloaded the latest version of TPP this week, so version: > > TPP v4.4 VUVUZELA rev 1, Build 201010121551 (MinGW) > > > > I'm still really hoping for an answer for the -Etrypsin error.....I'm > > stuck until I get that figured out. > > > > Thanks!! > > Ruby > > > > On Feb 28, 12:04 pm, Joe Slagel <[email protected]> wrote: > >> Hi Rudy, > >> > >> For both questions you have, what version of TPP are you using? and I'm > >> assuming you are trying to convert the .RAW to mzXML using the petunia > >> interface? (And I'll defer to others on your first question...unless > you > >> don't get an answer). > >> > >> -Joe > >> > >> > >> > >> On Sat, Feb 26, 2011 at 6:02 PM, Ruby <[email protected]> wrote: > >> > Hi- > >> > 1) I'm trying to use the TPP to process my Sequest search results. > >> > (since I have access to sequest only on a cluster, I'm not able to use > >> > the TPP to setup the search, which is what I'd like to do). Rather, > >> > I'm trying to use the .out files for peptide & proteinprophet > >> > processing. > >> > >> > However, I get this error when I try to process my directory that has > >> > the .out files from the Sequest search. > >> > >> > command "c:\Inetpub\tpp-bin\Out2XML c:/Inetpub/wwwroot/ISB/data/ > >> > RG_81_2 1 -Etrypsin" failed: Unknown error > >> > >> > Is this due to the fact that I did a semi-enzyme search? How can I > >> > work around this? I didn't see a semi-enzyme choice in the 'options' > >> > section of the convert to pepXML page. > >> > >> > 2) I'd like to do an XTandem search via the TPP. When I try to > >> > convert .RAW to mzXML, I get this error: > >> > 'c:\Inetpub\tpp-bin\ReAdW' is not recognized as an internal or > >> > external command, operable program or batch file. > >> > >> > I thought that TPP wasn't using ReAdW anymore, but rather the > >> > MSConverter. I have downloaded the MSFileReader, but what parts of > >> > that go in the tpp-bin directory?? Basically, how do I get it > >> > configured so that it uses MSConvert for processing the .RAW files? > >> > >> > Thanks! > >> > Ruby > >> > >> > -- > >> > 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. > >> > >> -- > >> Joe Slagel > >> Institute for Systems Biology > >> [email protected] > >> (206) 732-1362 > > > > -- > > 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.
