peakBin

[Marina Zavolskova]

Hello, everyone

I have a question about peakBin()

Here is a spectra of initial data:

After such steps as 

peakPick()

peakAlign()

peakFilter()

I applied 

file_P_A_F_B <- file_P_A_F%>%
     peakBin(ref = mz(file_P_A_F), tolerance=10, units="ppm")%>%
     process()

and a lot of peaks disappeared:

however, if I take bigger tolerance, it duplicates peaks:

this pictures are all for one pixel

please could you explain how use peakBin correctly?

thank in advance

Marina