View source: R/msms_search_lipidmaps.R
msms_search_lipidmaps | R Documentation |
Search the Glycerophospholipid MS/MS Prediction database from LipidMaps (http://www.lipidmaps.org/).
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 )
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. |
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]+
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.
Rico Derks
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)
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