import.msfinder.structures: import.MSFinder.structures

Description Usage Arguments Details Value Author(s) References


After running MSFinder on .mat or .msp files, import the structure that were predicted and their scores


import.msfinder.structures(ramclustObj = RC, mat.dir = NULL,
  msp.dir = NULL, MSFinder.dir = "C:\\MSFinder\\MS-FINDER_2.20")



R object - the ramclustR object which was used to write the .mat or .msp files


optional path to .mat directory


optional path to .msp directory


this function imports the output from the MSFinder program to annotate the ramclustR object


an annotated ramclustR object

ramclustR object with new $ slots for:

- msfinder.structure: data frame of one row describing the best structure match for the selected best formula match

- msfinder.structure$fragments: data frame the fragment ion interpretations supporting the best structure match

- msfinder.structure$details: list containing the best structure match for all formulas. Each list element represents one formula (with the formula as the name), and is composed of a list:

- structures: table of most likely structures

- fragments: list of data frames, with one element for each from from 'structures'. names are assigned based on 'id' column from structures.


Corey Broeckling


Broeckling CD, Afsar FA, Neumann S, Ben-Hur A, Prenni JE. RAMClust: a novel feature clustering method enables spectral-matching-based annotation for metabolomics data. Anal Chem. 2014 Jul 15;86(14):6812-7. doi: 10.1021/ac501530d. Epub 2014 Jun 26. PubMed PMID: 24927477.

Broeckling CD, Ganna A, Layer M, Brown K, Sutton B, Ingelsson E, Peers G, Prenni JE. Enabling Efficient and Confident Annotation of LC-MS Metabolomics Data through MS1 Spectrum and Time Prediction. Anal Chem. 2016 Sep 20;88(18):9226-34. doi: 10.1021/acs.analchem.6b02479. Epub 2016 Sep 8. PubMed PMID: 7560453.

Tsugawa H, Kind T, Nakabayashi R, Yukihira D, Tanaka W, Cajka T, Saito K, Fiehn O, Arita M. Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software. Anal Chem. 2016 Aug 16;88(16):7946-58. doi: 10.1021/acs.analchem.6b00770. Epub 2016 Aug 4. PubMed PMID: 27419259.

sneumann/RAMClustR documentation built on May 30, 2019, 5:05 a.m.