README.md
In nathaniel-mahieu/mz.unity: Detection of Complex Relationships In Mass Spectra

mz.unity

mz.unity is an R package for detecting and exploring complex relationships in accurate-mass mass spectrometry data. Mz.unity implements a combiunatorial search which can be tailored to many specific relationships. These include simple relationships like isotopes, charge carriers, and common neutral losses but also complex relationships such as distal fragments, mers, and background mers.

For more detailed information please see the forthcoming publication.

mz.unity is available as an R package on GitHub: nathaniel-mahieu/mz.unity

#install.packages("devtools")
devtools::install_github("nathaniel-mahieu/mz.unity")

library(mz.unity)
relationships = mz.unity.search(A, B, M, ppm, BM.limits)

A, B, M: matrices with accurate mass, charge, and direction (denoting gain or loss). A is searched for in combinations of B and M.
ppm: the maximum mass error allowed
BM.limits: The combinatorial depth with which to search.

Toy data and more examples can be found in the /inst directory. Examples are copied from there.

pIso2 = mz.unity.search(A = ps, 
                        B = ps, 
                        M = M.iso, ppm = 1, 
                        BM.limits = cbind(M.min = c(1), M.max = c(1), B.n = c(1)))
head(pIso2)

##      A        ppm M.1 B.1
## 1   25 -0.1904717   1   5
## 2   10  0.1236177   1  25
## 3   57  0.3110863   1  48
## 4   94 -0.8560973   1  57
## 5 1015  0.3189293   1 921
## 6 1083  0.3035952   1 938

Below we annotate and plot some simple relationships:

rels = mz.unity.search(A = ps, 
                       B = ps, 
                       M = M.z, ppm = 10, 
                       BM.limits = cbind(M.min = c(2), M.max = c(2), B.n = c(1))
                       )

df = subset(rels, rel %in% c("z", "pol", "nl"))
df = reindex(df, '^A$|^A.|^B$|^B.', mzz$id)

vertices = c(unique(subset(mzz, monoiso & source %in% c("psn", "psp"))[,"id"]))
vertices = unique(c(vertices, unlist(expandGraph(df)[,1:2])))

g = graph.data.frame(expandGraph(df)[,1:2], vertices = data.frame(v=as.character(vertices)))
plot(g, asp = .4, vertex.size = 2, edge.arrow.mode=1, edge.arrow.size = 0.3, vertex.label.cex=.6, vertex.frame.color='transparent', vertex.label.color = "transparent")

plot of chunk unnamed-chunk-22

Complex relationship plot

This plot is of the relationships involving glutamate, NAD and their dimer. Aggregation of compound groups was performed with aggregate.self under the assumption that all fragments were mers. This assumption is incorrect but necessary because more information is needed to distinguish fragments from mers. plot of chunk unnamed-chunk-26