Peakpicking - adelabriere/SLAW GitHub Wiki

Peakpicking

Peakpicking in SLAW is done using three different algorithms, one is the rest of the data workflow is done using the ADAP peakpicking algorithm (DOI) implemented in the MZmine2 software (DOI), the FeatureFinderMetabo algorithm implemented in openMS (DOI) and CentWave as implemented in XCMS (DOI). You can change the selected peakpicking by setting the peakpicking/algorithm to ADAP, openMS or CENTWAVE

Both peak picking includes two main steps, the construction of mass traces which detect peaks with a close mass in consecutive scans (traces_constructions section in parameters.txt) and chromatograms deconvolutions which detect chromatographic peaks along the mass traces (peaks_deconvolution section in parameters.txt). A lot of parameters are conceptually similar between the three algorithms.

As peakpicking algorithm typically includes a lot of parameters, SLAW includes parameter optimization. More details is given here

Parameters:

Common:

  • noise_level_ms1: (Integer). An absolute noise threshold (Count or intensity) to be used on MS1. Any points in a RAW file below this file will be discarded. This should not be too high, as low intensity part can still occurs at the border of a peak. Typically 150 for TOF and 15000 for Orbitrap.

  • noise_level_ms2: (Integer). An absolute noise threshold to be used on MS2. Any points in a RAW file below this file will be discarded. This should not be too high, as low intensity fragment can still be informative.

  • trace_construction/ppm: (Float). The maximum deviation between peaks in consecutives scans in to build a mass trace.
  • trace_construction/min_scan: (Integer). The minimum number of points in a mass trace.
  • peaks_deconvolution/SN: (Float). The Signal-to-Noise threshold used. This quantity should be optimized generally as their values is very different depending from the algorithms.
  • peaks_deconvolution/peak_width: (Float,Float). The peakwidth of the chromatographic peaks in minutes. This is also used in the FeatureFinderMetabo algorithm to determine wavelet ranges.
  • peaks_deconvolution/noise_level: (Float). The minimum feature height for a feature to be kept. It is different from noise_level_ms1 as it is a threshold applied to the detected peaks after the peakpicking is finished.
  • peaks_deconvolution/ms2_mz_tol: (Float). The tolerance in Dalton to map a an MS2 precursor to a peak.
  • peaks_deconvolution/ms2_rt_tol: (Float). The tolerance in minutes to map an MS2 precursor to a peak.

FeatureFinderMetabo only:

  • trace_construction/num_outliers: (Integer). The maximum number of outliers allowed in a mass trace.

ADAP only:

  • peaks_deconvolution/rt_wavelet: (Float,Float). The wavelet range used by the ADAP algorithm.
  • peaks_deconvolution/coefficient_area_threshold: (Float). The coefficient area threshold used to filter the peaks.

XCMS only:

  • None