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GNPS-like similarity between two MS/MS spectra

Source: R/score_ms2_methods.R
modified_cosine_params.Rd

modified_cosine_params() generates a parameter list to perform GNPS-like cosine similarity score calculation between two MS2 spectra.

Usage

modified_cosine_params(frag_tolerance)

Arguments

frag_tolerance

The mz fragment tolerance threshold for aligning fragment peaks from two ms2 spectra. GNPS default = 0.5.

Value

A parameters list for similarity scoring method "gnps"

Details

modified_cosine_params() will initiate cosine scoring based on the Python code by Wang et al. (2016), which is currently used for cosine scoring in GNPS, to calculate similarity between two MS2 spectra. This scoring method will compare peaks data, apply a square root normalization to peak intensities, align peaks both with and without correction for mass shifts, and calculate similarity.

References

Mingxun Wang, Jeremy J. Carver, Vanessa V. Phelan, Laura M. Sanchez, Neha Garg, Yao Peng, Don Duy Nguyen et al. "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking." Nature biotechnology 34, no. 8 (2016): 828. PMID: 27504778

Examples

modified_cosine_params(0.5)
#> $tolerance
#> [1] 0.5
#> 
#> $method
#> [1] "gnps"
#> 
#> attr(,"class")
#> [1] "parameters"