After running MSFinder on .mat or .msp files, import the spectral search results
import.msfinder.mssearch(
ramclustObj = NULL,
mat.dir = NULL,
msp.dir = NULL,
dir.extension = ".mssearch"
)an updated ramclustR object, with new slots at $msfinder.mssearch.details and $msfinder.mssearch.scores
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
optional directory name code specifying subset of results to use. Useful if running MSFinder from the command line for both spectral searching and interpretation.
Corey Broeckling
this function imports the output from the MSFinder program to annotate the ramclustR object
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.