clean_spectrum {msentropy}

Clean a spectrum

Description

Clean a spectrum

This function will clean the peaks by the following steps: 1. Remove empty peaks (mz <= 0 or intensity <= 0). 2. Remove peaks with mz >= max_mz or mz < min_mz. 3. Centroid the spectrum by merging peaks within min_ms2_difference_in_da or min_ms2_difference_in_ppm. 4. Remove peaks with intensity < noise_threshold * max_intensity. 5. Keep only the top max_peak_num peaks. 6. Normalize the intensity to sum to 1.

Note: The only one of min_ms2_difference_in_da and min_ms2_difference_in_ppm should be positive.

Usage

clean_spectrum(
  peaks,
  min_mz,
  max_mz,
  noise_threshold,
  min_ms2_difference_in_da,
  min_ms2_difference_in_ppm,
  max_peak_num,
  normalize_intensity
)

Arguments

peaks

A matrix of spectral peaks, with two columns: mz and intensity

min_mz

The minimum mz value to keep, set to -1 to disable

max_mz

The maximum mz value to keep, set to -1 to disable

noise_threshold

The noise threshold, set to -1 to disable, all peaks have intensity < noise_threshold * max_intensity will be removed

min_ms2_difference_in_da

The minimum mz difference in Da to merge peaks, set to -1 to disable, any two peaks with mz difference < min_ms2_difference_in_da will be merged

min_ms2_difference_in_ppm

The minimum mz difference in ppm to merge peaks, set to -1 to disable, any two peaks with mz difference < min_ms2_difference_in_ppm will be merged

max_peak_num

The maximum number of peaks to keep, set to -1 to disable

normalize_intensity

Whether to normalize the intensity to sum to 1

Value

A matrix of spectral peaks, with two columns: mz and intensity

Examples

mz <- c(100.212, 169.071, 169.078, 300.321)
intensity <- c(0.3716, 7.917962, 100., 66.83)
peaks <- matrix(c(mz, intensity), ncol = 2, byrow = FALSE)
clean_spectrum(peaks, min_mz = 0, max_mz = 1000, noise_threshold = 0.01,
               min_ms2_difference_in_da = 0.02, min_ms2_difference_in_ppm = -1,
               max_peak_num = 100, normalize_intensity = TRUE)