diff --git a/404.html b/404.html index d0a68c38..24b8b796 100644 --- a/404.html +++ b/404.html @@ -31,7 +31,7 @@ Spectra - 1.13.7 + 1.13.8 + + + + + +
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+

Estimating precursor m/z valus for DDA data

+ Source: R/Spectra-estimatePrecursorMz.R +
estimatePrecursorMz.Rd
+
+ +
+

MS data from Waters instruments are calibrated through the Lock Mass, but, +while all m/z values of mass peaks in each spectrum will be calibrated by +this method, the reported precursor m/z might not. The precursor m/z in the +converted mzML file will have m/z values from quadrupole isolation windows +instead of accurate m/z values. See also the +GNPS documentation +for more information.

+

The estimatePrecursorMz function estimates/adjusts the reported precursor +m/z of a fragment spectrum using the following approach: in data dependent +acquisition (DDA) mode, the MS instrument will select ions with the highest +intensities in one MS scan for fragmentation. Thus, for each fragment +spectrum, this method identifies in the previous MS1 spectrum the peak with +the highest intensity and an m/z value similar to the fragment spectrum's +reported precursor m/z (given parameters tolerance and ppm). This m/z +value is then reported. Since the fragment spectrum's potential MS1 mass +peak is selected based on its intensity, this method should only be used +for DDA data.

+
+ +
+

Usage

+ 
estimatePrecursorMz(object, tolerance = 0.3, ppm = 10, BPPARAM = SerialParam())
+
+ +
+

Arguments

+
object
+

Spectra() object with DDA data.

+ + +
tolerance
+

numeric(1) defining an absolute acceptable difference in +m/z between the fragment spectra's reported precursor m/z and the +MS1 peaks considered as the precursor peak. 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.

+ + +
BPPARAM
+

parallel processing setup. Defaults to +BPPARAM = SerialParam(). See SerialParam() for more information.

+ +
+
+

Value

+ + +

numeric of length equal to the number of spectra in object with +the fragment spectra's estimated precursor m/z values. For MS1 spectra +NA_real_ values are returned. The original precursor m/z is reported +for MS2 spectra for which no matching MS1 peak was found.

+
+
+

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.

+

Users of this function should evaluate and compare the estimated precursor +m/z values with the originally reported one and only consider adjusted values +they feel comfortable with.

+
+
+

Author

+

Mar Garcia-Aloy, Johannes Rainer

+
+ +
+

Examples

+ 

+## Load a DDA test data set. For the present data set no large differences
+## between the reported and the *actual* precursor m/z are expected.
+fl <- system.file("TripleTOF-SWATH", "PestMix1_DDA.mzML", package = "msdata")
+s <- Spectra(fl)
+
+pmz <- estimatePrecursorMz(s)
+
+## plot the reported and estimated precursor m/z values against each other
+plot(precursorMz(s), pmz)
+abline(0, 1)
+
+
+## They seem highly similar, but are they identical?
+identical(precursorMz(s), pmz)
+#> [1] FALSE
+all.equal(precursorMz(s), pmz)
+#> [1] "Mean relative difference: 1.654551e-05"
+
+## Plot also the difference of m/z values against the m/z value
+plot(precursorMz(s), precursorMz(s) - pmz, xlab = "precursor m/z",
+    ylab = "difference reported - estimated precursor m/z")
+
+
+## we could then replace the reported precursor m/z values
+s$precursorMz <- pmz
+
+
+
+ + +
+

Developed by RforMassSpectrometry Package Maintainer, Laurent Gatto, Johannes Rainer, Sebastian Gibb, Philippine Louail.

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+ +
+

Site built with pkgdown 2.0.7.9000.

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+ +
+ + + + + + + diff --git a/reference/filterFourierTransformArtefacts.html b/reference/filterFourierTransformArtefacts.html index 09f8dd0c..8faeab92 100644 --- a/reference/filterFourierTransformArtefacts.html +++ b/reference/filterFourierTransformArtefacts.html @@ -32,7 +32,7 @@ Spectra - 1.13.7 + 1.13.8