mspredictr

An R package for calculating peptide sequence and fragment masses relevant to mass spectrometry, along with some peptide string manipulation tools. Some of the functions with mass calculations and string manipulations have been written in Rust for a speed advantage.

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 <- path_to_example() |> read_spectra()

Plot spectrum with peak matching

ms2data |> subset(spectrum_num == 1) |> plot_spectrum(peptides = 'HAVSEGTK')