Hi Matt My limited experience with xtandem and mgf files is that they are not 100% compatible, however if you stick to local charge=Z+ (where Z is any number > 0) within BEGIN and END ions for each spectrum you should be fine (at least for xtandem downloadable from the GPM site).
The MGF file format is explained very clearly at http://www.matrixscience.com/help/data_file_help.html#GEN regards Eugene -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Brian Pratt Sent: Tuesday, 14 December 2010 8:22 AM To: [email protected] Subject: Re: [spctools-discuss] How to make X! Tandem respect input charge state? A naive readthrough of the code in trans_proteomic_pipeline\extern\xtandem\src\loadmspectrum.cpp ... else if(strstr(pLine,"CHARGE=") != NULL) { pValue = strchr(pLine,'='); pValue++; specCurrent.m_fZ = (float)atof(pValue); } ... makes me think it should work, but of course there are lots of other lines of code that could mess up... On Mon, Dec 13, 2010 at 12:41 PM, Eric Deutsch <[email protected]> wrote: > Might need to be: > > CHARGE=4+ > > > >> -----Original Message----- >> From: [email protected] [mailto:spctools- >> [email protected]] On Behalf Of Matt Chambers >> Sent: Monday, December 13, 2010 12:18 PM >> To: [email protected] >> Subject: Re: [spctools-discuss] How to make X! Tandem respect input >> charge state? >> >> The input is like: >> BEGIN IONS >> TITLE=Foo.5986.5986.4 >> RTINSECONDS=123.4 >> PEPMASS=748.617 946661.3125 >> CHARGE=4 >> 259.9697876 24.20503426 >> 261.1176758 4.82276392 >> ... >> END IONS >> >> -Matt >> >> >> On 12/13/2010 1:08 PM, Brian Pratt wrote: >> > The code does appear to be looking for and recording the value of >> > "CHARGE=" - but that gets lost along the way? Or does your MGF >> > possibly describe charge in another fashion? I have the impression >> > there are variants. >> > >> > Brian >> > >> > On Mon, Dec 13, 2010 at 9:09 AM, Matt Chambers >> > <[email protected]> wrote: >> >> Is there a way to make X! Tandem respect charge state(s) specified >> in an MGF >> >> file? I haven't tried mzXML/mzML (this is the TPP version) yet, >> would it >> >> work for those formats? >> >> >> >> -Matt >> >> -- >> 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 spctools- >> [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. This communication is intended only for the named recipient and may contain information that is confidential, legally privileged or subject to copyright; the Ludwig Institute for Cancer Research Ltd does not waive any rights if you have received this communication in error. The views expressed in this communication are those of the sender and do not necessarily reflect the views of the Ludwig Institute for Cancer Research Ltd. -- 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.
