makeRecalibration: Recalibrate MS/MS spectra

In sneumann/RMassBank: Workflow to process tandem MS files and build MassBank records

Description

Recalibrates MS/MS spectra by building a recalibration curve of the assigned putative fragments of all spectra in aggregatedSpecs (measured mass vs. mass of putative associated fragment) and additionally the parent ion peaks.

Usage

makeRecalibration(w, mode, 
 	recalibrateBy = getOption("RMassBank")$recalibrateBy,
		recalibrateMS1 = getOption("RMassBank")$recalibrateMS1,
		recalibrator = getOption("RMassBank")$recalibrator,
		recalibrateMS1Window = getOption("RMassBank")$recalibrateMS1Window 
		)

 recalibrateSpectra(mode, rawspec = NULL, rc = NULL, rc.ms1=NULL, w = NULL,
		recalibrateBy = getOption("RMassBank")$recalibrateBy,
		recalibrateMS1 = getOption("RMassBank")$recalibrateMS1)

 recalibrateSingleSpec(spectrum, rc, 
		recalibrateBy = getOption("RMassBank")$recalibrateBy)

Arguments

w	For makeRecalibration: to perform the recalibration with. For recalibrateSpectra: the msmsWorkspace which contains the recalibration curves (alternatively to specifying rc, rc.ms1).
mode	"pH", "pNa", "pM", "mH", "mM", "mFA" for different ions ([M+H]+, [M+Na]+, [M]+, [M-H]-, [M]-, [M+FA]-).
recalibrateBy	Whether recalibration should be done by ppm ("ppm") or by m/z ("mz").
recalibrateMS1	Whether MS1 spectra should be recalibrated separately ("separate"), together with MS2 ("common") or not at all ("none"). Usually taken from settings.
recalibrator	The recalibrator functions to be used. Refer to recalibrate for details. Usually taken from settings.
recalibrateMS1Window	Window width to look for MS1 peaks to recalibrate (in ppm).
spectrum	For recalibrateSingleSpec: a MSnbase Spectrum-derived object, commonly a RmbSpectrum2 for MS2 or Spectrum1 for MS1.
rawspec	For recalibrateSpectra:an RmbSpectraSetList of RmbSpectraSet objects , as the w@spectra slot from msmsWorkspace or any object returned by findMsMsHR. If empty, no spectra are recalibrated, but the recalibration curve is returned.
rc, rc.ms1	The recalibration curves to be used in the recalibration.

Details

Note that the actually used recalibration functions are governed by the general MassBank settings (see recalibrate).

If a set of acquired LC-MS runs contains spectra for two different ion types (e.g. [M+H]+ and [M+Na]+) which should both be processed by RMassBank, it is necessary to do this in two separate runs. Since it is likely that one ion type will be the vast majority of spectra (e.g. most in [M+H]+ mode), and only few spectra will be present for other specific adducts (e.g. only few [M+Na]+ spectra), it is possible that too few spectra are present to build a good recalibration curve using only e.g. the [M+Na]+ ions. Therefore we recommend, for one set of LC/MS runs, to build the recalibration curve for one ion type (msmsWorkflow(mode="pH", steps=c(1:8), newRecalibration=TRUE)) and reuse the same curve for processing different ion types (msmsWorkflow(mode="pNa", steps=c(1:8), newRecalibration=FALSE)). This also ensures a consistent recalibration across all spectra of the same batch.

Value

makeRecalibration: a list(rc, rc.ms1) with recalibration curves for the MS2 and MS1 spectra.

recalibrateSpectra: if rawspec is not NULL, returns the recalibrated spectra as RmbSpectraSetList. All spectra have their mass recalibrated and evaluation data deleted.

recalibrateSingleSpec: the recalibrated Spectrum (same object, recalibrated masses, evaluation data like assigned formulae etc. deleted).

Author(s)

Michael Stravs, Eawag <[e-mail]>

Examples

## Not run:  
			rcCurve <- recalibrateSpectra(w, "pH")
			w@spectra <- recalibrateSpectra(mode="pH", rawspec=w@spectra, w=myWorkspace)
			w@spectra <- recalibrateSpectra(mode="pH", rawspec=w@spectra,	rcCurve$rc, rcCurve$rc.ms1)
			
## End(Not run)

sneumann/RMassBank documentation built on Oct. 20, 2020, 3:19 p.m.