Thank for your help Jimmy; the binary worked fine and we are now able to search mascot with the N-terminus acetylation modification.
On Jul 2, 10:13 pm, Jimmy Eng <[email protected]> wrote: > Ron, > > Here's a compiled Mascot2XML.exe binary for you: > > http://tinyurl.com/24a8jna > > Regarding the errors you're seeing yourself, I'd just type 'make' in > the 'src' directory in your msys/mingw window. I don't know how to > target building just a specific binary but hopefully another developer > can chime in with instructions if possible. > > - Jimmy > > On Fri, Jul 2, 2010 at 10:13 AM, Ronald W. Finnegan <[email protected]> wrote: > > > > > I downloaded the MascotConverter.cxx rev 4945 checked in by Jimmy on > > 4-15-10 and copied it to this location within the TPP source > > distribution: C:\TPP431src\tpp\src\Parsers\Algorithm2XML\Mascot2XML\ > > > I am getting these errors when I run the makefile command: > > > lnt...@nimh-lntvm1 /c/tpp431src/tpp/src > > $ makefile mascot2xml > > ./makefile: line 52: /c/tpp431src/tpp/src/: is a directory > > ./makefile: line 53: include: command not found > > ./makefile: line 56: FASTAR_DIR: command not found > > ./makefile: line 57: syntax error near unexpected token `${LGPL},1' > > ./makefile: line 57: `ifeq (${LGPL},1) ' > > > can someone please provide a suggestion as to how i might get this to > > work? > > > thanks > > > Ron > > > On Jul 1, 8:36 pm, Brian Pratt <[email protected]> wrote: > >> Have a look at > >> this:http://tools.proteomecenter.org/wiki/index.php?title=TPP:Building_Win... > > >> On Thu, Jul 1, 2010 at 3:00 PM, Ronald W. Finnegan <[email protected]> > >> wrote: > > >> > can you recommend a compiler that i can use to run makefile on a 64 > >> > bit windows server? > > >> > On Jul 1, 1:42 pm, Brian Pratt <[email protected]> wrote: > >> >> You'll need to get the entire source tree from > >> >> /sashimi/trunk/trans_proteomic_pipeline/ down, them cd to > >> >> /sashimi/trunk/trans_proteomic_pipeline/src and "make _Mascot2XML". > > >> >> On Thu, Jul 1, 2010 at 9:58 AM, Ronald W. Finnegan <[email protected]> > >> >> wrote: > > >> >> > I have downloaded the MascotConverter.cxx source file. > > >> >> > How do I compile the MascotConverter file so that the TPP source file > >> >> > dependencies are met? > > >> >> > On Jul 1, 12:35 pm, Jimmy Eng <[email protected]> wrote: > >> >> > >http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteom... > > >> >> > > This just points you to the Mascot2XML source files (which are > >> >> > > dependent on other source files in the TPP project). > > >> >> > > On Thu, Jul 1, 2010 at 6:22 AM, Ronald W. Finnegan > >> >> > > <[email protected]> wrote: > > >> >> > > > Jimmy, > > >> >> > > > I am using the Mascot2XML from the last TPP version released > >> >> > > > 9-9-2009. Can you please point me to the trunk where I can > >> >> > > > download > >> >> > > > rev 4945 from your April 15, 2010 check-in? > > >> >> > > > thanks > > >> >> > > > Ron > > >> >> > > > On Jun 30, 7:02 pm, Jimmy Eng <[email protected]> wrote: > >> >> > > >> I have faint memories of dealing with this but I'm away from > >> >> > > >> work so > >> >> > > >> can't confirm. This might've been fixed in rev 4945 check-in on > >> >> > > >> April > >> >> > > >> 15th; my check-in log message for Mascot2XML was "parsing update > >> >> > > >> for > >> >> > > >> entry with protein n-term modification which doesn't seem to be > >> >> > > >> handled by current code". > > >> >> > > >> Are you able to compile Mascot2XML from trunk and see if the > >> >> > > >> problem > >> >> > > >> goes away? Otherwise, I'll follow-up with this next week when > >> >> > > >> I'm > >> >> > > >> back at work. > > >> >> > > >> On Tue, Jun 29, 2010 at 5:59 AM, Ronald W. Finnegan > >> >> > > >> <[email protected]> wrote: > > >> >> > > >> > Can anyone tell me if this bug reported back in April 2009 has > >> >> > > >> > been > >> >> > > >> > fixed: > > >> >> > > >> > Thermo Orbitrap RAW file is inputted into tpp -> convert to > >> >> > > >> > mzxml -> > >> >> > > >> > convert to mgf -> run mascot -> convert to pepXML > > >> >> > > >> > The problem is as follows: > > >> >> > > >> > When I use the mascot default modification Acetyl (protein > >> >> > > >> > N-term), > >> >> > > >> > the TPP converter that converts the mascot output .DAT file to > >> >> > > >> > pepXML > >> >> > > >> > format creates the following header in the pepXML file: > > >> >> > > >> > <aminoacid_modification aminoacid=" " mass="42.010559" > >> >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> > >> >> > > >> > <aminoacid_modification aminoacid="N" mass="156.053486" > >> >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> > >> >> > > >> > <aminoacid_modification aminoacid="-" mass="42.010559" > >> >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> > >> >> > > >> > <aminoacid_modification aminoacid="t" mass="42.010559" > >> >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> > >> >> > > >> > <aminoacid_modification aminoacid="e" mass="42.010559" > >> >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> > >> >> > > >> > <aminoacid_modification aminoacid="r" mass="42.010559" > >> >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> > >> >> > > >> > <aminoacid_modification aminoacid="m" mass="42.010559" > >> >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> > > >> >> > > >> > If you look at this header closely, the entries are not only > >> >> > > >> > meaningless, but there is something funny to be seen if you > >> >> > > >> > look at > >> >> > > >> > the aminoacid="" entries: > > >> >> > > >> > aminoacid=" " > >> >> > > >> > aminoacid="N" > >> >> > > >> > aminoacid="-" > >> >> > > >> > aminoacid="t" = N - term > >> >> > > >> > aminoacid="e" > >> >> > > >> > aminoacid="r" > >> >> > > >> > aminoacid="m" > > >> >> > > >> > as far as I know the aminoacid property should indicate > >> >> > > >> > aminoacid > >> >> > > >> > letters and not be spelling out N-term. This is obviously a > >> >> > > >> > parsing > >> >> > > >> > error occurring somewhere during the conversion. > > >> >> > > >> > Here is the link the original thread: > > >> >> > > >> >http://groups.google.com/group/spctools-discuss/browse_thread/thread/... > > >> >> > > >> > thanks > > >> >> > > >> > Ron > > >> >> > > >> > -- > >> >> > > >> > 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 > >> >> > > >> > athttp://groups.google.com/group/spctools-discuss?hl=en.-Hidequotedtext- > > >> >> > > >> - Show quoted text - > > >> >> > > > -- > >> >> > > > 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 > >> >> > > > athttp://groups.google.com/group/spctools-discuss?hl=en.-Hidequotedtext > >> >> > > > - > > >> >> > > - Show quoted text - > > >> >> > -- > >> >> > 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 > >> >> > athttp://groups.google.com/group/spctools-discuss?hl=en.-Hidequoted > >> >> > text - > > >> >> - Show quoted text - > > >> > -- > >> > 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 > >> > athttp://groups.google.com/group/spctools-discuss?hl=en.-Hide quoted > >> > text - > > >> - Show quoted text - > > > -- > > 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 > > athttp://groups.google.com/group/spctools-discuss?hl=en.- Hide quoted text - > > - Show quoted text - -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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