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Aerith

Aerith

Aerith is an R package that provides interfaces to read and write mass spectrum scans, calculate the theoretical isotopic peak envelope of peptide precursors and their B Y ions, score and visualize the PSM (peptide and spectra match), and visualize the TIC (total ion current) using Rcpp. In Final Fantasy VII, Aerith is the last surviving Cetra or “Ancient” who can communicate with the planet. In stable isotope analysis such as SIP (stable isotope probe), we study Earth or even the universe by analyzing isotopes of elements.

Install

You can download the source package in release to install or install from github directly by following code in R.

library(devtools)
install_github("xyz1396/Aerith")
library(Aerith)

Read and write Mass spectrum scan

Now we only support read .FT1 or .FT2 files well generated by Raxport.net

Read .FT1 file

ft1 <- readAllScanMS1("demo.FT1")

Read .FT2 file

ft2 <- readAllScanMS2("demo.FT2")

Read .mzML file. You need to install mzR first

ft1 <- readMzmlMS1("demo.mzML")
ft2 <- readMzmlMS2("demo.mzML")

Write .FT2 file

header <- readFTheader("demo.ft2")
ft2 <- readAllScanMS2("demo.ft2")
writeAllScanMS2(header,ft2[1:10],"demo10.ft2")

Calculate theorotic peak

Precursor

a <- getSipPrecursorSpectra("KHRIPCDRK", "C13", 0.25, 2)
plot(a)

Peak

B Y ions

a <- getSipBYionSpectra("KHRIPCDRK", "C13", 0.25, 1:2, 2)
plot(a)

BY

PSM visualization

a <- getSipBYionSpectra("KHRIPCDRK", "C13", 0.25, 1:2)
p <- plot(a)
p <- p + plotSipBYionLabel(a)
b <- readAllScanMS2("demo.FT2")
c <- getRealScan(18, b)
p <- p + plotRealScan(c)
p

PSM

TIC visualization

a <- readAllScanMS2("demo.FT2")
b <- getTIC(a)
plotTIC(b)

TIC