A simple tool for calculating peptide sequence and fragment masses.
Installation
To install, open R and type:
install.packages("devtools")
devtools::install_github("jeffsocal/mspredictr")
Get Started
Calculate the mass of a peptide sequence
library(mspredictr)
peptide_mass("SAMPLER")
#> [1] 802.4007
Calculate the mass of a peptide sequence with a mass modification
peptide_mass("SA[M15.998]PLER")
#> [1] 818.3987
Generate a table of expected fragment masses
fragments("SA[M15.998]PLER", charge = 1)
#> ion mz z seq pair pos type
#> 1 b1+ 88.03931 1 S p01 1 b
#> 2 b2+ 159.07643 1 SA p02 2 b
#> 3 y1+ 175.11894 1 R p06 1 y
#> 4 y2+ 304.16153 1 ER p05 2 y
#> 5 b3+ 306.11491 1 SA[M15.998] p03 3 b
#> 6 b4+ 403.16767 1 SA[M15.998]P p04 4 b
#> 7 MH++ 410.20663 2 SA[M15.998]PLER p00 NA precursor
#> 8 y3+ 417.24559 1 LER p04 3 y
#> 9 y4+ 514.29836 1 PLER p03 4 y
#> 10 b5+ 516.25173 1 SA[M15.998]PL p05 5 b
#> 11 b6+ 645.29432 1 SA[M15.998]PLE p06 6 b
#> 12 y5+ 661.33684 1 [M15.998]PLER p02 5 y
#> 13 y6+ 732.37396 1 A[M15.998]PLER p01 6 y
#> 14 MH+ 819.40599 1 SA[M15.998]PLER p00 NA precursor
Read in spectra using the msreadr
package
library(msreadr)
ms2data <- msreadr::path_to_example() |> read_spectra()
Plot spectrum with peak matching
ms2data |> subset(spectrum_num == 1) |> plot_spectrum(peptides = 'HAVSEGTK')