Calculating Precursor Purity for MS2 spectra

MS instruments generally collect precursor ions in a discrete m/z isolation window before fragmenting them and recording the respective fragment (MS2) spectrum. Ideally, only a single ion species is fragmented, depending also on the size of the isolation window, different ions (with slightly different m/z) might be fragmented. The resulting MS2 spectrum might thus contain fragments from different ions and hence be less pure.

The precursorPurity() function calculates the precursor purity of MS2 (fragment) spectra expressed as the ratio between the itensity of the highest signal in the isolation window to the sum of intensities of all MS1 peaks in the isolation window. This is similar to the calculation performed in the msPurity Bioconductor package.

The peak intensities within the isolation window is extracted from the last MS1 spectrum before the respective MS2 spectrum. The spectra are thus expected to be ordered by retention time. For the isolation window either the isolation window reported in the Spectra object is used, or it is calculated based on the MS2 spectra's precursor m/z. By default, the isolation window is calculated based on the precursor m/z and parameters tolerance and ppm: precursorMz +/- (tolerance + ppm(precursorMz, ppm)). If the actually used precursor isolation window is defined and available in the Spectra object, it can be used instead by setting useReportedIsolationWindow = TRUE (default is useReportedIsolationWindow = FALSE). Note that parameters tolerance and ppm are ignored for useReportedIsolationWindow = TRUE.

Usage

precursorPurity(
  object,
  tolerance = 0.05,
  ppm = 0,
  useReportedIsolationWindow = FALSE,
  BPPARAM = SerialParam()
)

Arguments

object: Spectra() object with LC-MS/MS data.
tolerance: numeric(1) defining an absolute value (in Da) to be used to define the isolation window. For the precursor purity calculation of an MS2 spectrum, all MS1 peaks from the previous MS1 scan with an m/z between the fragment spectrum's precursorMz +/- (tolerance + ppm(precursorMz, ppm)) are considered.
ppm: numeric(1) defining the m/z dependent acceptable difference in m/z. See documentation of parameter tolerance for more information.
useReportedIsolationWindow: logical(1) whether the reported isolation window, defined by spectra variables isolationWindowLowerMz and isolationWindowUpperMz in the input Spectra object, should be used instead of calculating the isolation window from the reported precursor m/z and parameters tolerance and ppm. Only few manufacturers report the isolation window with the spectra variables isolationWindowLowerMz and isolationWindowTargetMz, thus the default for this parameter is FALSE.
BPPARAM: parallel processing setup. Defaults to BPPARAM = SerialParam(). See BiocParallel::SerialParam() for more information.

Value

numeric vector of length equal to the number of spectra in object, with values representing the calculated precursor purity for each spectrum. For MS1 spectra, NA_real_ is returned. For MS2 spectra, the purity is defined as the proportion of maximum signal to the total ion current within the isolation window that is attributable to the selected precursor ion. If no matching MS1 scan is found or the precursor peak is missing, NA_real_ is returned.

Note

This approach is applicable only when fragment spectra are obtained through data-dependent acquisition (DDA), as it assumes that the peak with the highest intensity within the given isolation m/z window (from the previous MS1 spectrum) corresponds to the precursor ion.

The spectra in object have to be ordered by their retention time.

Author

Ahlam Mentag, Johannes Rainer

Examples