known.table.common.pos: A known feature table based on HMDB.

In yufree/apLCMS: Adaptive processing of LC-MS data

A known feature table based on HMDB.

Description

This table was compiled from HMDB metabolites. It contains only the H+, Na+, K+ and NH4+ derivative of known metabolites. It suites the need for analyzing LC/MS data generated with anion exchange chromatography.

Usage

data(known.table.common.pos)

Format

A data frame containing the known metabolite ions and previously found features. It contains 18 columns: "chemical_formula": the chemical formula if knonw; "HMDB_ID": HMDB ID if known; "KEGG_compound_ID": KEGG compound ID if known; "neutral.mass": the neutral mass if known: "ion.type": the ion form, such as H+, Na+, ..., if known; "m.z": m/z value, either theoretical for known metabolites, or mean observed value for unknown but previously found features; "Number_profiles_processed": the total number of LC/MS profiles that were used to build this database; "Percent_found": in what percentage was this feature found historically amount all data processed in building this database; "mz_min": the minimum m/z value observed for this feature; "mz_max": the maximum m/z value observed for this feature; "RT_mean": the mean retention time observed for this feature; "RT_sd": the standard deviation of retention time observed for this feature; "RT_min": the minimum retention time observed for this feature; "RT_max": the maximum retention time observed for this feature; "int_mean.log.": the mean log intensity observed for this feature; "int_sd.log.": the standard deviation of log intensity observed for this feature; "int_min.log.": the minimum log intensity observed for this feature; "int_max.log.": the maximum log intensity observed for this feature;

Source

Wishart, D. S., et al. (2009). HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res 37, D603-10.

Examples

data(known.table.common.pos)

yufree/apLCMS documentation built on May 19, 2024, 1:22 p.m.