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
>>
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