Fragment ion mass tolerance

[Viktor Granholm]

Hi group,

I know this is possible to set the precursor mass tolerance with the 'precursor-window' parameter, but is there any way to set the fragment ion mass tolerance?

Thank you,

Viktor

[William Noble]

Hi Viktor,

Crux does not have an option analogous to Mascot's fragment ion mass
tolerance. In practice, Crux's fragment ion mass tolerance is a
function of the --mz-bin-width option, so you can make this value
smaller to get finer discretization on the MS2 m/z axis.

Bill

[Viktor Granholm]

Thank you Bill,

can I roughly approximate the bin width as the mass tolerance window size, in Da? Or does it use another unit/mechanism?

Viktor

2011/9/27 William Noble <thab...@gmail.com>

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[Bill Noble]

The --mz-bin-width option uses units of mass-to-charge (Th), not mass.

Bill

[Viktor Granholm]

Thanks,

I've added the following line to my parameter file:

mz-bin-width=0.05

When trying different values of the parameter, however, ranging from 0.01 to 1.5, I obtain the exact same results, the output files are identical. (Except from the search.params.txt which correctly indicates that I've used different values for mz-bin-width).

Have I missed something, or is it likely that the mz-bin-width has such small effect on the outcome? The spectra are high resolution HCD Orbitrap spectra.

/Viktor

2011/9/28 Bill Noble <thab...@gmail.com>

The --mz-bin-width option uses units of mass-to-charge (Th), not mass.

Bill

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[William Noble]

Hi Viktor,
I would expect the results to not differ dramatically, but to differ at least a little bit.  Can you send a sample input file and command line, and I'll see what we can figure out?
Thanks.
Bill

[Sean]

Viktor,

Did you set --xcorr-var-bin to T? This option will turn on the
variable binning code in crux. It is off (F) by default.

Thanks,
Sean

On Oct 7, 8:50 am, William Noble <thaba...@gmail.com> wrote:
> Hi Viktor,
> I would expect the results to not differ dramatically, but to differ at
> least a little bit.  Can you send a sample input file and command line,
> and I'll see what we can figure out?
> Thanks.
> Bill
>
> On 10/07/2011 04:30 AM, Viktor Granholm wrote:
>
>
>
>
>
>
>
> > Thanks,
> > I've added the following line to my parameter file:
> > mz-bin-width=0.05
> > When trying different values of the parameter, however, ranging from
> > 0.01 to 1.5, I obtain the exact same results, the output files are
> > identical. (Except from the search.params.txt which correctly
> > indicates that I've used different values for mz-bin-width).
>
> > Have I missed something, or is it likely that the mz-bin-width has
> > such small effect on the outcome? The spectra are high resolution HCD
> > Orbitrap spectra.
>
> > /Viktor
>

> > 2011/9/28 Bill Noble <thaba...@gmail.com <mailto:thaba...@gmail.com>>

>
> >     The --mz-bin-width option uses units of mass-to-charge (Th), not mass.
>
> >     Bill
>
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[Viktor]

Hi Sean and Bill,

I had missed the --xcorr-var-bin parameter. With that on, it works and
gives the expected results.

Thanks,
Viktor