nontarget (version 1.9)

homol.search: Homologue series extraction from LC-MS data.

Description

Dynamic programming algorithm for unsupervised detection of homologue series in LC-(HR)MS data.

Usage

homol.search(peaklist,isotopes,	elements=c("C","H","O"),use_C=FALSE,minmz=5,
maxmz=120,minrt=-2,maxrt=2,ppm=TRUE,mztol=3.5,rttol=0.5,minlength=5,
mzfilter=FALSE,vec_size=3E6,mat_size=3,R2=.98,spar=.45,plotit=FALSE,deb=0)

Arguments

peaklist

Dataframe of picked LC-MS peaks with three numeric columns for (a) m/z, (b) intensity and (c) retention time, such as peaklist.

isotopes

Dataframe isotopes

elements

FALSE or chemical elements in the changing units of the homologue series, e.g. c("C","H") for alkane chains. Used to restrict search.

use_C

For elements: take element ratio to C-atoms into account? Used to restrict search.

minmz

Defines the lower limit of the m/z window to search homologue series peaks, relative to the m/z of the one peak to search from. Absolute m/z value [u].

maxmz

Defines the upper limit of the m/z window to search homologue series peaks, relative to the m/z of the one peak to search from. Absolute m/z value [u].

minrt

Defines the lower limit of the retention time (RT) window to look for other homologue peaks, relative to the RT of the one peak to search from, i.e., RT+minrt. For decreasing RT with increasing HS mass, use negative values of minrt.

maxrt

Defines the upper limit of the RT window to look for other homologue peaks, relative to the RT of the one peak to search from, i.e., RT+maxrt. See minrt.

ppm

Should mztol be set in ppm (TRUE) or in absolute m/z [u] (FALSE)?

mztol

m/z tolerance setting: +/- value by which the m/z of a peak may vary from its expected value. If parameter ppm=TRUE (see below) given in ppm, otherwise, if ppm=FALSE, in absolute m/z [u].

rttol

Retention time (RT) tolerance by which the RT between two adjacent pairs of a homologue series is allowed to differ. Units as given in column 3 of peaklist argument, e.g. [min].

minlength

Minimum number of peaks in a homologue series.

mzfilter

Vector of numerics to filter for homologue series with specific m/z differences of their repeating units, given the tolerances in mztol. Mind charge z!

vec_size

Vector size. Ignore unless a relevant error message is printed (then try to increase size).

mat_size

Matrix size for recombining, multiple of input tuples. Ignore unless a relevant error message is printed (then try to increase size).

R2

FALSE or 0smooth.spline.

spar

Smoothing parameter, typically (but not necessarily) in (0,1]. See smooth.spline.

plotit

Logical FALSE or 0=minlength, clustered HS pairs, etc .

deb

Debug returns, ignore.

Value

List of type homol with 6 entries

Warning

The rttol argument of homol.search must not be mixed with that of pattern.search or pattern.search2.

Details

A dynamic programming approach is used to extract series of peaks that differ in constant m/z units and smooth changes in their retention time within bounds of mass defect changes. First, a nearest neighbour path through a kd-tree representation of the data is used to extract all feasible peak triplets. These triplets are then combined to all plausible n-tupels in n-3 steps. At each such step, each newly formed n-tupel is checked for smooth changes of RT with increasing m/z of the homologues, using cubic splines and a R2-based threshold of the model fit.

See Also

rm.sat isotopes peaklist plothomol

Examples

data(peaklist);
data(isotopes)
homol<-homol.search(
	peaklist,
	isotopes,	
	elements=c("C","H","O"),
	use_C=TRUE,
	minmz=5,
	maxmz=120,
	minrt=-.5,
	maxrt=2,
	ppm=TRUE,
	mztol=3.5,
	rttol=0.5,
	minlength=5,
	mzfilter=FALSE,
	vec_size=3E6,
	mat_size=3,
	spar=.45,
	R2=.98,
	plotit=FALSE
)	
plothomol(homol);