infer charge state of features in ramclustR object.
assign.z(
ramclustObj = NULL,
chargestate = c(1:5),
mzError = 0.02,
nEvents = 2,
minPercentSignal = 10,
assume1 = TRUE
)returns a ramclustR object. new slots holding:
zmax. vector with length equal to number of compounds. max charge state detected for that compound
fm. vector of inferred 'm', m/z value * z value
fz. vector of inferred 'z' values based on analysis of isotopes in spectrum.
ramclustR object to annotate
integer vector. vector of integers of charge states to look for. default = c(1:5)
numeric. the error allowed in charge state m/z filtering. absolute mass units
integer. the number of isotopes necessary to assign a charnge state > 1. default = 2.
numeric. the ratio of isotope signal (all isotopes) divided by total spectrum signal * 100 much be greater than minPercentSignal to evaluate charge state. Value should be between 0 and 100.
logical. when TRUE, m/z values for which no isotopes are found are assumed to be at z = 1.
Corey Broeckling
Annotation of ramclustR spectra. looks at isotope spacing for clustered features to infer charge state for each feature and a max charge state for each compound
Broeckling CD, Afsar FA, Neumann S, Ben-Hur A, Prenni JE. RAMClust: a novel feature clustering method enables spectral-matching-based annotation for metabolomics data. Anal Chem. 2014 Jul 15;86(14):6812-7. doi: 10.1021/ac501530d. Epub 2014 Jun 26. PubMed PMID: 24927477.
Broeckling CD, Ganna A, Layer M, Brown K, Sutton B, Ingelsson E, Peers G, Prenni JE. Enabling Efficient and Confident Annotation of LC-MS Metabolomics Data through MS1 Spectrum and Time Prediction. Anal Chem. 2016 Sep 20;88(18):9226-34. doi: 10.1021/acs.analchem.6b02479. Epub 2016 Sep 8. PubMed PMID: 7560453.