msms_search_lipidmaps: Do a MSMS search on the Glycerophospholipid MS/MS Prediction...

In ricoderks/Rcpm: General functions for the Center of Proteomics and Metabolomics (LUMC)

Do a MSMS search on the Glycerophospholipid MS/MS Prediction database from LipidMaps

Description

Search the Glycerophospholipid MS/MS Prediction database from LipidMaps (http://www.lipidmaps.org/).

Usage

msms_search_lipidmaps(
  lipidclass = c("glycerolipids", "phospholipids"),
  intensity_threshold = 10,
  prec_tol = 0.01,
  prod_tol = 0.01,
  headgroup = "",
  ion = "",
  min_matches = 5,
  LIMIT = c("All", "even"),
  peaklist = NULL
)

Arguments

lipidclass	define the lipidclass you want to search, currently available phospholipics and glycerolipids
intensity_threshold	set the intensity threshold
prec_tol	precursor ion mass tolerance (+/- m/z)
prod_tol	product ion mass tolerance (+/- m/z)
headgroup	search all headgroups of a lipidclass, see details for more inforamtion
ion	set the ion type (see details for more info)
min_matches	how many matches should the search at least have
LIMIT	limit the chains to 'even' or 'odd' and 'even' (All)
peaklist	in PKL format See detail section for more information.

Details

This function uses the Programmatic Access functionality of LipidMaps to search the LMSD database.

Phospholipids:

Headgroups are defined as: "Any" or one off "PC", "PA", "PS", "PE", "PG", "PI"

The ion types are defined as: * chloride : [M-H]- / [M+Cl]- * acetate : [M-H]- / [M+Acetate-H]- * formate : [M-H]- / [M+Formate-H]-

Glycerolipids:

Headgroups are defined as: "Any" or one off "MD", "DG", "TG"

The ion types are defined as: * ammonium : [M+NH4]+

Value

The function returns a dataframe with the search results. If there is a connection problem NULL is returned and a warning message showing the status code of the connection.

Author(s)

Rico Derks

Examples

mypeaks <- c("818.59 10000 1\n758.57 20\n687.50 20\n506.33 50\n494.33 15\n488.31 2")

results <- msms_search_lipidmaps(lipidclass = "phospholipids",
                     intensity_threshold = 10,
                     prec_tol = 0.01,
                     prod_tol = 0.01,
                     headgroup = "Any",
                     ion = "formate",
                     min_matches = 2,
                     LIMIT = "All",
                     peaklist = mypeaks)

ricoderks/Rcpm documentation built on May 18, 2022, 7:49 a.m.