xcms lcms

XCMS for LCMS

• xcms provides 2 main algorithms for peak picking:

1. MatchedFilter for profile or centroid low resolution MS data
2. centwave for centroid high resolution MS data

• centwave aims to detect regions of interest with less than a defined deviation of m/z in consecutive scans. This deviation must be lower than the value of the parameter ppm.
• The value has to be set according the mass spec machine accuracy.

Params

These are the non-trivial parameters for CentWaveParams object in xcms. The information here is either as comprehensive as, or more comprehensive than, CentWaveParams documentation from xcms.

• ppm - related to m/z. Fluctuation of m/z values from scan to scan. Depends on mass spec accuracy.
• peakwidth (min, max) - related to RT. Range of chromatographic peak widths (in seconds). c(20, 50) for HPLC, c(5, 12) for UPLC. The main purpose of peakwidth is to roughly estimate the peak width range; it is not a threshold. Wavelets used for peak detection are calculated from this parameter. Do not choose minimum peak width to be "too small"; this will not increase sensitivity, but cause peaks to be split.
• mzdiff - related to m/z and RT. Minimum difference of mz for peaks with overlapping retention time (coeluting peak). Must be negative to allow overlap. e.g. -0.001 or 0.05.
• Prefilter c(k,I) - related to intensity. A peak must be present in k scans with an intensity greater than I.
• snthresh - related to intensity. Ratio signal/noise threshold.
• noise - related to intensity. Each centroid must be greater than this value.
• integrate - Integration method. For ‘integrate = 1’ peak limits are found through descent on the mexican hat filtered data, for ‘integrate = 2’ the descent is done on the real data. The latter method is more accurate but prone to noise, while the former is more robust, but less exact.
• mzCenterFun - Name of the function to calculate the m/z center of the chromatographic peak. Allowed are:
  • ‘"wMean"’: intensity-weighted mean of the peak's m/z values,
  • ‘"mean"’: mean of the peak's m/z values,
  • ‘"apex"’: use the m/z value at the peak apex,
  • ‘"wMeanApex3"’: intensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it
  • ‘"meanApex3"’: mean of the m/z value of the peak apex and the m/z values left and right of it.