I am attaching a file that has cmd line options for dta to mzXML to .out to pepXML (like Bioworks view of results). This workflow works and I am sure someone has a better way of doing it. DD
On Wed, Mar 10, 2010 at 6:21 PM, Darryl Davis <[email protected]> wrote: > OK find the same sort of response on my side. I think it really wants the > .raw file around since I can produce .out from .dta as long as .raw file is > loaded. I can then convert this to .srf that has results. If the .raw file > is not there gives error that analysis file does not match results. > > Good news is the .out files are gd. so maybe now you can use TPP pipeline > .out to pepXML converter (Out2XML). > > Which leads to "other" tools. You could take .dta and convert to mzXML > using TPP then do your sequest search from there. > > There are many other tools that have been developed to work w/ dtas > themselves but hopefully the above works. > > I am guessing that you have an .mgf because it isnt a Thermo data run? If > this is the case then ofcourse you could have taken that proprietary format > and converted it then ran it through TPP to get Sequest results as well. > > Good luck, > DD > > On Wed, Mar 10, 2010 at 4:44 PM, Tamanna S Rahman < > [email protected]> wrote: > >> Hi Darryl, >> >> Thanks for your lead. >> >> I could run the the search but could not view the search results in >> bioworks. After converting the DTA and OUT files to SRF I could open the >> search results but found no hits listed eventhough some of the OUT files has >> peptides identified >> >> Then I brought the DTA and OUT (as well as SRF separately) files to >> scaffold and Theres turned out to be no results either. >> Any idea why it could happen?? >> >> Also what are the other tools for sequest search using MGF, DTA etc.?? >> >> Thanks >> Tamanna >> >> >> On Wed, Mar 10, 2010 at 12:14 PM, Darryl Davis <[email protected]> wrote: >> >>> For dta work try Actions- Sequest search. Choose folders w/ DTAs >>> deselect use SRF file. Deselect dta generation. Choose sequest.params file >>> and then start search. >>> >>> If you have mgf or dta format already there are other tools than Bioworks >>> to use (ofcourse I state the obvious). >>> DD >>> >>> >>> On Wed, Mar 10, 2010 at 11:54 AM, Tamanna Sultana < >>> [email protected]> wrote: >>> >>>> Does anyone knows a way of importing MGF or DTA files to Bioworks for >>>> a Sequest search? >>>> >>>> I have a dataset in *.mgf format and I would like to do a Sequest >>>> search. >>>> >>>> 1. I could not import mgf to bioworks. I know that sequest uses *.dta >>>> file for search, so I converted the mgf to dta but failed to import >>>> the dta to bioworks. Bioworks seem to accept *.RAW only. >>>> >>>> 2. I saw under tools in 'Bioworks' I could import spectral data in >>>> mzdata format, that did not work either. >>>> >>>> Anyone have any suggestion?? >>>> Thanks >>>> Tamanna >>>> >>>> -- >>>> 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. >>> >> >> >> >> -- >> Tamanna S Rahman >> -- >> 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.
dta to mzXML to Sequest .out to pepXML
Description: Binary data
