library_messar: Substructure recommendation for unknown spectrum

In daniellyz/MergeION2: Merging and Networking Scans from Multiple LC-MS/MS Raw Data Files

Substructure recommendation for unknown spectrum

Description

The function recommends substructures for an unknown spectrum

Usage

library_messar(
  query_spectrum = NULL,
  params.search = list(mz_search = 0.01, tops = 5),
  params.query.sp = list(prec_mz = 100, use_prec = T, compound.type = "Metabolite")
)

Arguments

query_spectrum	Two-column data matrix. Two columns represent m/z and intensity of query tandem spectrum. At least 3 valid peaks should be provided
params.search	General parameters for matching fragments to mz_search: Numeric. Absolute mass tolerance in Da for fragment match. tops: Integer. Top n substructures recommended.
params.query.sp	Parameters for matching an unknown spectra prec_mz: Numeric. Precursor mass of query spectrum. please put the correct value of precursor mass. use_prec: Boolean. If set to TRUE, precursor mass is used to calculate the neutral loss. compound.type: Character. Either "Metabolite" or "Drug". Different models are applied to Metabolite or Drug.

Value

Recommended substructures (ordered) as a two-column matrix: SMILES code and score

Author(s)

Youzhong Liu, [e-mail]

Examples

## Not run:  url_test = "https://raw.githubusercontent.com/daniellyz/MergeION2/master/inst/spectra/caffeine.txt"

test = read.table(url_test, header = FALSE, sep=" ")

results = library_messar(query_spectrum = test, params.query.sp = list(prec_mz = 195.088, use_prec = T, compound.type = "Drug"))
## End(Not run)

daniellyz/MergeION2 documentation built on Jan. 26, 2024, 6:24 a.m.