This function annotates spectra
Usage
annotate_spectra(
input = get_params(step = "annotate_spectra")$files$spectral$raw,
library = get_params(step = "annotate_spectra")$files$libraries$spectral$exp,
polarity = get_params(step = "annotate_spectra")$ms$polarity,
output = get_params(step = "annotate_spectra")$files$annotations$raw$spectral$spectral,
threshold = get_params(step =
"annotate_spectra")$annotations$thresholds$ms2$similarity$annotation,
ppm = get_params(step = "annotate_spectra")$ms$tolerances$mass$ppm$ms2,
dalton = get_params(step = "annotate_spectra")$ms$tolerances$mass$dalton$ms2,
qutoff = get_params(step = "annotate_spectra")$ms$thresholds$ms2$intensity,
approx = get_params(step = "annotate_spectra")$annotations$ms2approx
)
Arguments
- input
Query file containing spectra. Currently an '.mgf' file
- library
Library containing spectra to match against. Can be '.mgf' or '.sqlite' (Spectra formatted)
- polarity
MS polarity. Must be 'pos' or 'neg'.
- output
Output file.
- threshold
Minimal similarity to report
- ppm
Relative ppm tolerance to be used
- dalton
Absolute Dalton tolerance to be used
- qutoff
Intensity under which ms2 fragments will be removed.
- approx
Perform matching without precursor match