Find all library spectra10 above a cosine threshold for each imaging peak, restricting to a global precursor-mz range.

Find all library spectra10 above a cosine threshold for each imaging peak, restricting to a global precursor-mz range.

Usage

Pseudo_msms(
  raw_mz,
  counts,
  spectra10_list,
  ppm_tol = 10,
  frag_tol_da = 0.01,
  cos_threshold = 0.7,
  min_precursor = 0,
  max_precursor = Inf
)

Arguments

raw_mz

Numeric vector of length n_peaks

counts

Numeric matrix n_peaks × n_pixels

spectra10_list

List of Spectrum2 objects (length N_lib)

ppm_tol

Precursor‐matching tolerance in ppm (default 10)

frag_tol_da

Fragment‐matching tolerance in Da (default 0.01)

cos_threshold

Minimum cosine similarity to report (default 0.7)

min_precursor

Minimum allowed precursor m/z (default = 0, i.e. no lower bound)

max_precursor

Maximum allowed precursor m/z (default = Inf, i.e. no upper bound)

Value

A list of length n_peaks. Each element is an integer vector giving the indices in spectra10_list of all library spectra10 with cosine ≥ cos_threshold (or integer(0) if none).