[PeptideProphet]How to define "accurate mass"

[jun]

Hi, everyone. i'm a rookie user of TPP tools through network browser
interface. the instrument i am using is an LTQ orbitrap. when I came
to the "analyze peptide" step, I got confused with the PeptideProphet
option "Use accurate mass binning". I think it can be enabled when
using very small precursor tolerance, such as 5 ppm. But the protrocol
i follow is set precuesor tolerance to 50 ppm and set the filter to 5
ppm through Bioworks interface. Can I enable the "use accurate mass
binning" using the tolerance of 50 ppm??

i appraciate your answers!

[David Shteynberg]

Hi Jun,

You should use the accurate mass model when you are processing data
from high-mass-accuracy instruments (e.g. Orbitrap and FT) and you are
using monoisotopic precursor masses in your search params.

-David

[jun]

Hi, David

well, I am using an LTQ Orbitrap instrument and set the precursor mass
type to monoisotopic. And I was suggested by a technical support
engineer from ThermoFisher that seeting the precursor tolerance to 50
ppm would be better than just restrcting it to 10 ppm. I was wondering
if this range can fit the conditions for "accurate mass binning"?

thanks for your attention!

-Jun

[David Shteynberg]

Yes.

[Gautam Saxena]

If the MS is a linear ion trap and that therefore the precursor tolerance is set to +- 2 Da for OMSSA and +1 and -3 Da for X!Tandem, would "accurate mass binning" still apply? My initial thoughts are no, since those don't seem like high accuracy settings, but I'm not sure I fully understand the use of "accurate mass binning".