1 Introduction

## 
## Attaching package: 'gplots'
## The following object is masked from 'package:stats':
## 
##     lowess

This vignette assumes you are familiar with the standard usage of RMassBank, which is documented in

vignette("RMassBank")

2 Skipping recalibration

For instances where recalibration is not wanted, e.g. there is not enough data, or the user wants to use non-recalibrated data, recalibration can be deactivated. To do this, the recalibrator entry in the settings must be set to recalibrate.identity. This can be done in the settings file directly (preferred):

recalibrator:
    MS1: recalibrate.identity
    MS2: recalibrate.identity

Or, alternatively, the settings can be adapted directly via R code.

RmbDefaultSettings()
rmbo <- getOption("RMassBank")
rmbo$recalibrator <- list(
        "MS1" = "recalibrate.identity",
        "MS2" = "recalibrate.identity"
    )
options("RMassBank" = rmbo)

To show the results of using a non-recalibrated workflow, we load a workspace with pre-processed data:

w <- loadMsmsWorkspace(system.file("results/pH_narcotics_RF.RData", 
                package="RMassBankData"))
## Warning in .updateObject.RmbWorkspace.1to2(w, ..., verbose): You are
## loading an archive from an old RMassBank version. The aggregate tables are
## not loaded from the original object, but recomputed.
## Warning in .updateObject.RmbWorkspace.1to2(w, ..., verbose): If you hand-
## edited any aggregate table, the information might not be retained in the
## new object.
## Warning in .updateObject.RmbWorkspace.1to2(w, ..., verbose): You are
## loading an archive from an old RMassBank version. The aggregate tables are
## not loaded from the original object, but recomputed.
## Warning in .updateObject.RmbWorkspace.1to2(w, ..., verbose): If you hand-
## edited any aggregate table, the information might not be retained in the
## new object.
## Warning in .updateObject.RmbWorkspace.1to2(w, ..., verbose): You are
## loading an archive from an old RMassBank version. The multiplicity
## filtering results are not loaded from the original object, but recomputed.
## Warning in .updateObject.RmbWorkspace.1to2(w, ..., verbose): If you hand-
## edited any multiplicity filtering results, the information might not be
## retained in the new object.

The recalibration curve:

recal <- makeRecalibration(w@parent,
                recalibrateBy = rmbo$recalibrateBy,
                recalibrateMS1 = rmbo$recalibrateMS1,
                recalibrator = list(MS1="recalibrate.loess",MS2="recalibrate.loess"),
                recalibrateMS1Window = 15)

w@rc <- recal$rc
w@rc.ms1 <- recal$rc.ms1
w@parent <- w
plotRecalibration(w)