Thanks. I have used TPP before but didn't do any sequest search since I don't have TPP on the same computer where Bioworks is installed due to some issues.
At the end though I can't bring the pep.XML files to 'Scaffold' which is my objective. Tamanna On Wed, Mar 10, 2010 at 7:08 PM, Darryl Davis <[email protected]> wrote: > 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]<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]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
