library_manager: Searching and managing the spectral library

In daniellyz/MergeION: Merge Scans from Multiple LC-MS/MS Raw Data Files

Searching and managing the spectral library

Description

The function queries and selects or removes scans from the spectral library that satisfy user-defined conditions (query metadata)

Usage

library_manager(library, query = "", logical = c("AND", "OR"),
  ppm_search = 20, rt_search = 12)

Arguments

library	A list generated by the function library_generator() or the name of mgf spectral library file
query	Vector of characters. Vector of conditions used for querying the library. e.g. c("IONMODE=Positive","PEPMASS=325.19"). The left-hand side must match with the medata items of the searched library.
logical	Character. "AND" for selecting scans that satisfy all conditions, "OR" when selecting records that satisfy at least one condition
ppm_search	Numeric. Mass tolerance in ppm. Only used when searching by precursor mass "PEPMASS=..."
rt_search	Numeric. Retention time tolerance in second (although rt in the query and metadata in min). Only used when searching by retention time "RT=..."

Value

• SELECTED: Library object that only contain selected scans

• ID_SELECTED: IDs of selected scans

• LEFT: Library object that only contain unselected scans

• ID_SELECTED: IDs of unnselected scans

Examples

data(DRUG_THERMO_LIBRARY)

# Search library using query command lines:
query = library_manager(library2,query=c("IONMODE=Positive","RT=1.2"), logical="AND", rt_search=6)

# Create a new library from query:
new_library1 = query$SELECTED

# Summary of found compounds:
library_reporter(new_library1)

# Remove scans from current library according to query:
new_library2 = query$LEFT

# Add another filter:
query = library_manager(new_library1,query=c("IONMODE=Positive","MSLEVEL=2","RT=1.2"))
new_library3 = query$SELECTED

daniellyz/MergeION documentation built on Oct. 19, 2022, 1:56 p.m.