You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Hi,
I am using generate.formula to annotate masses with charge +1 from high resolution masss spectrometers within a small uncertainty specified by the windows parameter.
I am uncertain about how this window parameter is included in the calculations as it seems that the charge is added after the calculation of the molecular formula.
For instance, I have a mass of 69.03353 and a charge of +1
library(rcdk)
mass<-69.03353window<-0.000345# correspond to a 5 ppm mass error# manual calculation of lower bound window range: mass - window = 69.03353 - 0.000345 = 69.033185# manual calculation of upper bound window range: mass + window = 69.03353 + 0.000345 = 69.033875element_range<-list(c('C', 0,4), c('H', 0,11), c('O', 0,2), c('P', 0,1))
match<-rcdk::generate.formula(
mass,
window=window,
elements=element_range,
validation=FALSE,
charge=1
)
This does not give match for any formula with the specified element range.
However, the theoretical m/z of C4H5O+ is: 69.0335 which is within the window range. The neutral monoisotopic mass of C4H5O is 69.0340 and above the window range and I was wondering if the charge is added after the calculcations and therefore charged species cannot be correctly found?
The text was updated successfully, but these errors were encountered:
Hi,
I am using generate.formula to annotate masses with charge +1 from high resolution masss spectrometers within a small uncertainty specified by the windows parameter.
I am uncertain about how this window parameter is included in the calculations as it seems that the charge is added after the calculation of the molecular formula.
For instance, I have a mass of 69.03353 and a charge of +1
This does not give match for any formula with the specified element range.
However, the theoretical m/z of C4H5O+ is: 69.0335 which is within the window range. The neutral monoisotopic mass of C4H5O is 69.0340 and above the window range and I was wondering if the charge is added after the calculcations and therefore charged species cannot be correctly found?
The text was updated successfully, but these errors were encountered: