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Commit 6f613afd authored by michele's avatar michele
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Merge branch 'april2013hackfest' of https://github.com/meowcat/RMassBank into april2013hackfest

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NAMESPACE
+ 6
− 6
View file @ 6f613afd
export(CTS.externalIdSubset)
export(CTS.externalIdTypes)
export(RmbDefaultSettings)
export(RmbSettingsTemplate)
export(add.formula)
export(addMB)
export(addPeaks)
......@@ -16,6 +12,8 @@ export(cleanElnoise)
export(combineMultiplicities)
export(compileRecord)
export(createMolfile)
export(CTS.externalIdSubset)
export(CTS.externalIdTypes)
export(dbe)
export(deprofile)
export(deprofile.fwhm)
......@@ -85,6 +83,8 @@ export(recalibrateSingleSpec)
export(recalibrateSpectra)
export(resetInfolists)
export(resetList)
export(RmbDefaultSettings)
export(RmbSettingsTemplate)
export(smiles2mass)
export(to.limits.rcdk)
export(toMassbank)
......@@ -93,9 +93,9 @@ export(validate)
exportClasses(mbWorkspace)
exportClasses(msmsWorkspace)
exportMethods(show)
import(RCurl)
import(XML)
import(mzR)
import(RCurl)
import(rjson)
import(XML)
importClassesFrom(mzR)
importMethodsFrom(mzR)
R/settings_example.R
+ 89
− 13
View file @ 6f613afd
......@@ -13,12 +13,14 @@
#' Describes all settings for the RMassBank settings file.
#'
#' \itemize{
#' \item{\code{deprofile}}{Whether and how to deprofile input raw files. Leave the
#' \item{\code{deprofile}}{
#' Whether and how to deprofile input raw files. Leave the
#' setting empty if your raw files are already in "centroid" mode. If your
#' input files are in profile mode, you have the choice between algorithms
#' \code{\link{deprofile}.spline, deprofile.fwhm, deprofile.localMax}; refer to
#' the individual manpages for more information.}
#' \item{\code{rtMargin, rtShift}}{The allowed retention time deviation relative to the
#' \item{\code{rtMargin, rtShift}}{
#' The allowed retention time deviation relative to the
#' values specified in your compound list (see \code{\link{loadList}}), and the systematic
#' shift (due to the use of, e.g., pre-columns or other special equipment.}
#' \item{\code{babeldir}}{
......@@ -28,16 +30,18 @@
#' have explicit hydrogen atoms.
#' The path should point to the directory where babel.exe (or the Linux "babel" equivalent) lies.
#' }
#' \item{\code{use_version}}{Which MassBank record format to use; version 2 is strongly advised,
#' \item{\code{use_version}}{
#' Which MassBank record format to use; version 2 is strongly advised,
#' version 1 is considered outdated and should be used only if for some reason you are running
#' old servers and an upgrade is not feasible.}
#' \item{\code{use_rean_peaks}}{Whether to include peaks from reanalysis (see
#' \item{\code{use_rean_peaks}}{
#' Whether to include peaks from reanalysis (see
#' \code{\link{reanalyzeFailpeaks}}) in the MassBank records. Boolean, TRUE or FALSE.
#' }
#' \item{\code{annotations}}{
#' A list of constant annotations to use in the MassBank records. The entries
#' \code{authors, copyright, license, instrument, instrument_type, compound_class}
#' correspond to the MassBank entries \code{AUTHORS, COPYRIGHT, LICENSE, AC$INSTRUMENT,
#' correspond to the MassBank entries \code{AUTHORS, COPYRIGHT, PUBLICATION, LICENSE, AC$INSTRUMENT,
#' AC$INSTRUMENT_TYPE, CH$COMPOUND_CLASS}. The entry \code{confidence_comment} is added as
#' \code{COMMENT: CONFIDENCE} entry.
#'
......@@ -58,28 +62,100 @@
#' Entries under \code{ms_dataprocessing} are added as \code{MS$DATA_PROCESSING:} entries,
#' in addition to the default \code{WHOLE: RMassBank}.
#' }
#' \item{\code{spectraList}}{This setting describes the experimental annotations for the single
#' \item{\code{annotator}}{
#' For advanced users: option to select your own custom annotator.
#' Check \code{\link{annotator.default}} and the source code for details.}
#' \item{\code{spectraList}}{
#' This setting describes the experimental annotations for the single
#' data-dependent scans. For every data-dependent scan event, a \code{spectraList} entry with
#' \code{mode, ces, ce, res} denoting collision mode, collision energy in short and verbose
#' notation, and FT resolution.}
#' \item{\code{accessionNumberShifts}}{This denotes the starting points for accession numbers
#' \item{\code{accessionNumberShifts}}{
#' This denotes the starting points for accession numbers
#' for different ion types. For example, \code{pH: 0, mH: 50} means that [M+H]+ spectra will
#' start at \code{XX123401} (\code{XX} being the \code{entry_prefix} and \code{1234} the compound
#' id) and [M-H]- will start at \code{XX123451}.}
#' \item{\code{electronicNoise, electronicNoiseWidth}}{Known electronic noise peaks and the window
#' \item{\code{electronicNoise, electronicNoiseWidth}}{
#' Known electronic noise peaks and the window
#' to be used by \code{\link{cleanElnoise}}}
#' \item{\code{recalibrateBy}}{\code{dppm} or \code{dmz} to recalibrate either by delta ppm or by
#' \item{\code{recalibrateBy}}{
#' \code{dppm} or \code{dmz} to recalibrate either by delta ppm or by
#' delta mz.}
#' \item{\code{recalibrateMS1}}{\code{common} or \code{separate} to recalibrate MS1 data points together
#' \item{\code{recalibrateMS1}}{
#' \code{common} or \code{separate} to recalibrate MS1 data points together
#' or separately from MS2 data points.}
#' \item{\code{recalibrator: MS1, MS2}}{The functions to use for recalibration of MS1 and MS2 data points.
#' \item{\code{recalibrator: MS1, MS2}}{
#' The functions to use for recalibration of MS1 and MS2 data points.
#' Note that the \code{MS1} setting is only meaningful if \code{recalibrateMS1: separate}, otherwise
#' the \code{MS2} setting is used for a common recalibration curve. See \code{\link{recalibrate.loess}}
#' for details.
#' }
#' for details.}
#' \item{\code{multiplicityFilter}}{
#' Define the multiplicity filtering level. Default is 2, a value of 1
#' is off (no filtering) and >2 is harsher filtering.}
#' \item{\code{titleFormat}}{
#' The title of MassBank records is a mini-summary
#' of the record, for example "Dinotefuran; LC-ESI-QFT; MS2; CE: 35%; R=35000; [M+H]+".
#' By default, the first compound name \code{CH$NAME}, instrument type
#' \code{AC$INSTRUMENT_TYPE}, MS/MS type \code{AC$MASS_SPECTROMETRY: MS_TYPE},
#' collision energy \code{RECORD_TITLE_CE}, resolution \code{AC$MASS_SPECTROMETRY: RESOLUTION}
#' and precursor \code{MS$FOCUSED_ION: PRECURSOR_TYPE} are used. If alternative
#' information is relevant to differentiate acquired spectra, the title should be adjusted.
#' For example, many TOFs do not have a resolution setting.
#' See MassBank documentation for more.}
#' \item{\code{filterSettings}}{
#' A list of settings that affect the MS/MS processing. The entries
#' \code{ppmHighMass, ppmLowMass, massRangeDivision} set values for
#' pre-processing, prior to recalibration. \code{ppmHighMass} defines the
#' ppm error for the high mass range (default 10 ppm for Orbitraps),
#' \code{ppmLowMass} is the error for the low mass range (default 15 ppm
#' for Orbitraps) and \code{massRangeDivision} is the m/z value defining
#' the split between the high and low mass range (default m/z = 120).
#'
#' The entry \code{ppmFine} defines the ppm cut-off post recalibration.
#' The default value of 5 ppm is recommended for Orbitraps. For other
#' instruments this can be interpreted from the recalibration plot.
#' All ppm limits are one-sided (e.g. this includes values to +5 ppm or -5 ppm
#' deviation from the exact mass).
#'
#' The entries \code{prelimCut, prelimCutRatio} define the intensity cut-off and
#' cut-off ratio (in % of the most intense peak) for pre-processing. This affects
#' the peak selection for the recalibration only. Careful: the default value
#' 1e4 for Orbitrap LTQ positive mode could remove all peaks for TOF data
#' and will remove too many peaks for Orbitrap LTQ negative mode spectra!
#'
#' The entry \code{specOKLimit} defines the intensity limit to include MS/MS spectra.
#' MS/MS spectra must have at least one peak above this limit to proceed through
#' the workflow.
#'
#' \code{dbeMinLimit} defines the minimum allowable ring and double bond equivalents (DBE)
#' allowed for assigned formulas. This assumes maximum valuences for elements with
#' multiple valence states. The default is -0.5 (accounting for fragments being ions).
#'
#' The entries \code{satelliteMzLimit, satelliteIntLimit} define the cut-off m/z and
#' intensity values for satellite peak removal (an artefact of Fourier Transform
#' processing). All peaks within the m/z limit (default 0.5) and intensity ratio
#' (default 0.05 or 5 %) of the respective peak will be removed. Applicable to
#' Fourier Transform instruments only (e.g. Orbitrap).
#' }
#' \item{\code{filterSettings}}{
#' Parameters for adjusting the raw data retrieval.
#' The entry \code{ppmFine} defines the ppm error to look for the precursor in
#' the MS1 (parent) spectrum. Default is 10 ppm for Orbitrap.
#'
#' \code{mzCoarse} defines the error to search for the precursor specification
#' in the MS2 spectrum. This is often only saved to 2 decimal places and thus
#' can be quite inaccurate. The accuracy also depends on the isolation window used.
#' The default settings (for e.g. Orbitrap) is 0.5 (Da, or Th for m/z).
#'
#' The entry \code{fillPrecursorScan} is largely untested. The default value
#' (FALSE) assumes all necessary precursor information is available in the mzML file.
#' A setting ot TRUE tries to fill in the precursor data scan number if it is missing.
#' Only tested on one case study so far - feedback welcome!
#' }
#' }
#'
#'
#' @author Michael Stravs, Emma Schymanski
#' @seealso \code{\link{loadRmbSettings}}
#' @rdname RmbSettings
#' @name RmbSettings
......
man/RmbDefaultSettings.Rd
+ 2
− 2
View file @ 6f613afd
\name{RmbDefaultSettings}
\alias{RmbDefaultSettings}
\alias{RmbSettingsTemplate}
\alias{loadRmbSettings}
\alias{loadRmbSettingsFromEnv}
\alias{RmbDefaultSettings}
\alias{RmbSettingsTemplate}
\title{RMassBank settings}
\usage{
loadRmbSettings(file_or_list)
......
man/RmbSettings.Rd
+ 112
− 28
View file @ 6f613afd
......@@ -5,14 +5,14 @@
Describes all settings for the RMassBank settings file.
}
\details{
\itemize{ \item{\code{deprofile}}{Whether and how to
\itemize{ \item{\code{deprofile}}{ Whether and how to
deprofile input raw files. Leave the setting empty if
your raw files are already in "centroid" mode. If your
input files are in profile mode, you have the choice
between algorithms \code{\link{deprofile}.spline,
deprofile.fwhm, deprofile.localMax}; refer to the
individual manpages for more information.}
\item{\code{rtMargin, rtShift}}{The allowed retention
\item{\code{rtMargin, rtShift}}{ The allowed retention
time deviation relative to the values specified in your
compound list (see \code{\link{loadList}}), and the
systematic shift (due to the use of, e.g., pre-columns or
......@@ -24,11 +24,11 @@
OpenBabel; the CACTUS structures have explicit hydrogen
atoms. The path should point to the directory where
babel.exe (or the Linux "babel" equivalent) lies. }
\item{\code{use_version}}{Which MassBank record format to
use; version 2 is strongly advised, version 1 is
\item{\code{use_version}}{ Which MassBank record format
to use; version 2 is strongly advised, version 1 is
considered outdated and should be used only if for some
reason you are running old servers and an upgrade is not
feasible.} \item{\code{use_rean_peaks}}{Whether to
feasible.} \item{\code{use_rean_peaks}}{ Whether to
include peaks from reanalysis (see
\code{\link{reanalyzeFailpeaks}}) in the MassBank
records. Boolean, TRUE or FALSE. }
......@@ -36,10 +36,10 @@
to use in the MassBank records. The entries
\code{authors, copyright, license, instrument,
instrument_type, compound_class} correspond to the
MassBank entries \code{AUTHORS, COPYRIGHT, LICENSE,
AC$INSTRUMENT, AC$INSTRUMENT_TYPE, CH$COMPOUND_CLASS}.
The entry \code{confidence_comment} is added as
\code{COMMENT: CONFIDENCE} entry.
MassBank entries \code{AUTHORS, COPYRIGHT, PUBLICATION,
LICENSE, AC$INSTRUMENT, AC$INSTRUMENT_TYPE,
CH$COMPOUND_CLASS}. The entry \code{confidence_comment}
is added as \code{COMMENT: CONFIDENCE} entry.
The entry \code{internal_id_fieldname} is used to name
the MassBank entry which will keep a reference to the
......@@ -63,32 +63,116 @@
Entries under \code{ms_dataprocessing} are added as
\code{MS$DATA_PROCESSING:} entries, in addition to the
default \code{WHOLE: RMassBank}. }
\item{\code{spectraList}}{This setting describes the
experimental annotations for the single data-dependent
scans. For every data-dependent scan event, a
\code{spectraList} entry with \code{mode, ces, ce, res}
denoting collision mode, collision energy in short and
verbose notation, and FT resolution.}
\item{\code{accessionNumberShifts}}{This denotes the
\item{\code{annotator}}{ For advanced users: option to
select your own custom annotator. Check
\code{\link{annotator.default}} and the source code for
details.} \item{\code{spectraList}}{ This setting
describes the experimental annotations for the single
data-dependent scans. For every data-dependent scan
event, a \code{spectraList} entry with \code{mode, ces,
ce, res} denoting collision mode, collision energy in
short and verbose notation, and FT resolution.}
\item{\code{accessionNumberShifts}}{ This denotes the
starting points for accession numbers for different ion
types. For example, \code{pH: 0, mH: 50} means that
[M+H]+ spectra will start at \code{XX123401} (\code{XX}
being the \code{entry_prefix} and \code{1234} the
compound id) and [M-H]- will start at \code{XX123451}.}
\item{\code{electronicNoise, electronicNoiseWidth}}{Known
electronic noise peaks and the window to be used by
\code{\link{cleanElnoise}}}
\item{\code{recalibrateBy}}{\code{dppm} or \code{dmz} to
recalibrate either by delta ppm or by delta mz.}
\item{\code{recalibrateMS1}}{\code{common} or
\code{separate} to recalibrate MS1 data points together
or separately from MS2 data points.}
\item{\code{recalibrator: MS1, MS2}}{The functions to use
for recalibration of MS1 and MS2 data points. Note that
the \code{MS1} setting is only meaningful if
\item{\code{electronicNoise, electronicNoiseWidth}}{
Known electronic noise peaks and the window to be used by
\code{\link{cleanElnoise}}} \item{\code{recalibrateBy}}{
\code{dppm} or \code{dmz} to recalibrate either by delta
ppm or by delta mz.} \item{\code{recalibrateMS1}}{
\code{common} or \code{separate} to recalibrate MS1 data
points together or separately from MS2 data points.}
\item{\code{recalibrator: MS1, MS2}}{ The functions to
use for recalibration of MS1 and MS2 data points. Note
that the \code{MS1} setting is only meaningful if
\code{recalibrateMS1: separate}, otherwise the \code{MS2}
setting is used for a common recalibration curve. See
\code{\link{recalibrate.loess}} for details. } }
\code{\link{recalibrate.loess}} for details.}
\item{\code{multiplicityFilter}}{ Define the multiplicity
filtering level. Default is 2, a value of 1 is off (no
filtering) and >2 is harsher filtering.}
\item{\code{titleFormat}}{ The title of MassBank records
is a mini-summary of the record, for example
"Dinotefuran; LC-ESI-QFT; MS2; CE: 35%; R=35000; [M+H]+".
By default, the first compound name \code{CH$NAME},
instrument type \code{AC$INSTRUMENT_TYPE}, MS/MS type
\code{AC$MASS_SPECTROMETRY: MS_TYPE}, collision energy
\code{RECORD_TITLE_CE}, resolution
\code{AC$MASS_SPECTROMETRY: RESOLUTION} and precursor
\code{MS$FOCUSED_ION: PRECURSOR_TYPE} are used. If
alternative information is relevant to differentiate
acquired spectra, the title should be adjusted. For
example, many TOFs do not have a resolution setting. See
MassBank documentation for more.}
\item{\code{filterSettings}}{ A list of settings that
affect the MS/MS processing. The entries
\code{ppmHighMass, ppmLowMass, massRangeDivision} set
values for pre-processing, prior to recalibration.
\code{ppmHighMass} defines the ppm error for the high
mass range (default 10 ppm for Orbitraps),
\code{ppmLowMass} is the error for the low mass range
(default 15 ppm for Orbitraps) and
\code{massRangeDivision} is the m/z value defining the
split between the high and low mass range (default m/z =
120).
The entry \code{ppmFine} defines the ppm cut-off post
recalibration. The default value of 5 ppm is recommended
for Orbitraps. For other instruments this can be
interpreted from the recalibration plot. All ppm limits
are one-sided (e.g. this includes values to +5 ppm or -5
ppm deviation from the exact mass).
The entries \code{prelimCut, prelimCutRatio} define the
intensity cut-off and cut-off ratio (in % of the most
intense peak) for pre-processing. This affects the peak
selection for the recalibration only. Careful: the
default value 1e4 for Orbitrap LTQ positive mode could
remove all peaks for TOF data and will remove too many
peaks for Orbitrap LTQ negative mode spectra!
The entry \code{specOKLimit} defines the intensity limit
to include MS/MS spectra. MS/MS spectra must have at
least one peak above this limit to proceed through the
workflow.
\code{dbeMinLimit} defines the minimum allowable ring and
double bond equivalents (DBE) allowed for assigned
formulas. This assumes maximum valuences for elements
with multiple valence states. The default is -0.5
(accounting for fragments being ions).
The entries \code{satelliteMzLimit, satelliteIntLimit}
define the cut-off m/z and intensity values for satellite
peak removal (an artefact of Fourier Transform
processing). All peaks within the m/z limit (default 0.5)
and intensity ratio (default 0.05 or 5 %) of the
respective peak will be removed. Applicable to Fourier
Transform instruments only (e.g. Orbitrap). }
\item{\code{filterSettings}}{ Parameters for adjusting
the raw data retrieval. The entry \code{ppmFine} defines
the ppm error to look for the precursor in the MS1
(parent) spectrum. Default is 10 ppm for Orbitrap.
\code{mzCoarse} defines the error to search for the
precursor specification in the MS2 spectrum. This is
often only saved to 2 decimal places and thus can be
quite inaccurate. The accuracy also depends on the
isolation window used. The default settings (for e.g.
Orbitrap) is 0.5 (Da, or Th for m/z).
The entry \code{fillPrecursorScan} is largely untested.
The default value (FALSE) assumes all necessary precursor
information is available in the mzML file. A setting ot
TRUE tries to fill in the precursor data scan number if
it is missing. Only tested on one case study so far -
feedback welcome! } }
}
\author{
Michael Stravs, Emma Schymanski
}
\seealso{
\code{\link{loadRmbSettings}}
......
vignettes/RMassBank.Rnw
+ 81
− 10
View file @ 6f613afd
......@@ -29,9 +29,10 @@ options(width=74)
\parskip 1em
\begin{document}
\SweaveOpts{concordance=TRUE}
\title{RMassBank: The workflow by example}
\author{Michael Stravs}
\author{Michael Stravs, Emma Schymanski}
\maketitle
\tableofcontents
\newpage
......@@ -40,7 +41,7 @@ options(width=74)
\Rpackage{RMassBank} is a two-part computational mass spectrometry workflow:
\begin{itemize}
\item In a first step, MSMS spectra of compounds are extracted from raw LC-MS data files,
\item In the first step, MSMS spectra of compounds are extracted from raw LC-MS data files,
the MSMS spectra are recalibrated using assigned fragment formulas, and effectively
denoised by using only annotated peaks (plus peaks which can be manually added.)
\item In the second step, the processed, recalibrated, cleaned data is prepared for
......@@ -59,7 +60,7 @@ message board hosted by the Metabolomics-Forum:
\section{Installation and loading}
The library is available from Bioconductor (\url{http://www.bioconductor.org}).
In addition to the library itself, it is required to install the OpenBabel
In addition to the library itself, it is recommended to install the OpenBabel
chemical toolkit, available from \url{http://www.openbabel.org} for various
platforms (or via Linux package distribution systems).
......@@ -87,7 +88,7 @@ the (mathematical) centroid peak, i.e. the area-weighted mass peak.} or in
profile mode.
Data in the examples was acquired using an LTQ Orbitrap XL instrument in profile
mode, and converted from profile-mode RAW into centroid-mode mzML
using MSConvertGUI from the ProteoWiz toolsuite. The settings were as shown in the
using MSConvertGUI from ProteoWizard. The settings were as shown in the
screenshot below (note the "Peak Picking" filter.)
\begin{figure}[htbp]
......@@ -140,7 +141,7 @@ A settings template file, to be edited by hand, can be generated using
RmbSettingsTemplate("mysettings.ini")
@
where \funcarg{mysettings.ini} is the file which will be generated. This file
where \funcarg{mysettings.ini} is the file that will be generated. This file
should then be edited. Important settings are:
\begin{itemize}
\item \funcarg{deprofile}: Whether to use a deprofiling algorithm to work
......@@ -157,10 +158,10 @@ should then be edited. Important settings are:
\item \funcarg{use\_version}: which MassBank data format to use. The default is the newer version 2; alternatively, the (deprecated) version 1 can be specified for MassBank servers running old versions of the server software.
\item \funcarg{use\_rean\_peaks}: Whether or not peaks from reanalysis should be used (see below for details.)
\item \funcarg{add\_annotation}: Whether or not fragments should be annotated
with the (putative) molecular formula in MassBank records.
with the (tentative) molecular formula in MassBank records.
\item \funcarg{annotations}: A list of annotation data used in the MassBank records.
\begin{itemize}
\item \funcarg{authors}, \funcarg{copyright}, \funcarg{license}, \funcarg{instrument}, \funcarg{instrument\_type}, %
\item \funcarg{authors}, \funcarg{copyright}, \funcarg{publication}, \funcarg{license}, \funcarg{instrument}, \funcarg{instrument\_type}, %
\funcarg{compound\_class}: values for the corresponding MassBank fields
\item \funcarg{confidence\_comment}: A commentary field about "compound confidence" which is added like "COMMENT: CONFIDENCE standard compound" in the MassBank record.
\item \funcarg{internal\_id\_fieldname}: The name for an internal ID field in the MassBank record where to store the compound ID (in the compound list). For \funcarg{internal\_id\_fieldname} = "MY\_ID", the ID will be stored like "COMMENT: MY\_ID 1234".
......@@ -171,7 +172,8 @@ should then be edited. Important settings are:
In addition to the tags specified here, MS\$DATA\_PROCESSING:
WHOLE RMassBank will be added (corresponding to a list("WHOLE" = "RMassBank") entry for this option.)
\end{itemize}
\item \funcarg{spectraList}: The list of data-dependent scans triggered by a MS1 scan in their order; used for annotation of MassBank records. See the template file for description.
\item \funcarg{annotator}: For advanced users: option to select your own custom annotator. Check ?annotator.default and the source code for details.
\item \funcarg{spectraList}: The list of data-dependent scans triggered by a MS1 scan in their order; used for annotation of MassBank records. See the template file for description.
\item \funcarg{accessionNumberShifts}: A list defining the starting points
for generating MassBank record accession numbers. RMassBank generates
2-letter + 6-digit accession numbers. The 2-letter code is defined by
......@@ -203,6 +205,54 @@ should then be edited. Important settings are:
recalibration and appears to work well for pure MS1 datapoints. However,
common recalibration for MS1 and MS2 appears to be the best option in
general.
\item \funcarg{multiplicityFilter}: Define the multiplicity filtering level. Default is 2, a value of 1 is off (no filtering) and >2 is harsher filtering.
\item \funcarg{titleFormat}: The title of MassBank records is a mini-summary
of the record, for example "Dinotefuran; LC-ESI-QFT; MS2; CE: 35\%; R=35000; [M+H]+".
By default, the first compound name \Rvar{CH\$NAME}, instrument type
\Rvar{AC\$INSTRUMENT\_TYPE}, MS/MS type \Rvar{AC\$MASS\_SPECTROMETRY: MS\_TYPE},
collision energy \Rvar{RECORD\_TITLE\_CE}, resolution \Rvar{AC\$MASS\_SPECTROMETRY: RESOLUTION}
and precursor \Rvar{MS\$FOCUSED\_ION: PRECURSOR\_TYPE} are used. If alternative
information is relevant to differentiate acquired spectra, the title should be adjusted.
For example, many TOFs do not have a resolution setting. See MassBank documentation for more.
\item \funcarg{filterSettings}: A list of settings that affect the MS/MS processing.
\begin{itemize}
\item \funcarg{ppmHighMass}, \funcarg{ppmLowMass}: values for pre-processing,
prior to recalibration. The default settings (for e.g. Orbitrap) is 10 ppm
for high mass range, 15 ppm for low mass range (defined by \Rvar{massRangeDivision})
\item \funcarg{massRangeDivision}: The m/z value defining the split between
\Rvar{ppmHighMass} and \Rvar{ppmLowMass} above. The default m/z 120 is
recommended for Orbitraps.
\item \funcarg{ppmFine}: This defines the ppm cut-off post recalibration.
The default value of 5 ppm is recommended for Orbitraps.
\item \funcarg{prelimCut}, \funcarg{prelimCutRatio}: Intensity cut-off and cut-off ratio
(in \% of the most intense peak) for pre-processing. Affects peak selection
for the recalibration only. Careful: the default 1e4 for Orbitrap LTQ positive could
remove all peaks for TOF data and will remove too many peaks for Orbitrap LTQ
negative mode spectra!
\item \funcarg{specOKLimit}: MS/MS must have at least one peak above this limit
present to be processed.
\item \funcarg{dbeMinLimit}: The minimum allowable ring and double bond equivalent (DBE)
allowed for assigned formulas. Assumes maximum valences for elements with multiple
possible valences. Default is -0.5 (accounting for fragment peaks being ions).
\item \funcarg{satelliteMzLimit}, \funcarg{satelliteIntLimit}: Cut-off m/z and
intensity values for satellite peak removal. All peaks within the m/z (default 0.5)
and intensity ratio (default 0.05 or 5 \%) of the respective peak will be removed.
Applicable to Fourier Transform instruments (e.g. Orbitrap).
\end{itemize}
\item \funcarg{findMsMsRawSettings}: Parameters for adjusting the raw data retrieval.
\begin{itemize}
\item \funcarg{ppmFine}: The ppm error to look for the precursor in the MS1 (parent)
spectrum. Default is 10 ppm for Orbitrap.
\item \funcarg{mzCoarse}: The error to search for the precursor specification in the
MS2 spectrum. This is often only saved to 2 decimal places and thus inaccurate and
may also depend on the isolation window.
The default settings (for e.g. Orbitrap) is m/z=0.5 for \Rvar{mzCoarse}.
\item \funcarg{fillPrecursorScan}: The default value (FALSE) assumes all
necessary precursor information was available in the mzML file. A setting of
TRUE tries to fill in the precursor data scan number if it is missing.
Only tested on one case-study so far.
\end{itemize}
\end{itemize}
See also the manpage \Rvar{?RmbSettings} for a description of all RMassBank
......@@ -227,7 +277,7 @@ visually less appealing since they have all hydrogen atoms explicit, and CACTUS
is only a backup solution.)
First, a workspace for the \Rvar{msmsWorkflow} must be created:
First, create a workspace for the \Rvar{msmsWorkflow}:
<<>>=
w <- newMsmsWorkspace()
@
......@@ -299,7 +349,14 @@ w <- msmsWorkflow(w, mode="pH", steps=c(1:4), archivename =
"pH_narcotics")
@
If you are experimenting with novel datasets which might give errors, it is
The recalibration can also be plotted at a later stage:
<<eval=FALSE>>=
plotRecalibration(w)
@
If you are experimenting with new datasets which might give errors, it is
advised to run the workflow step by step. This is because if an error occurs, you will
lose all intermediate results from the workflow, which might complicate
finding the errors. (E.g., if you process steps 2-4 and an error occurs in step
......@@ -311,6 +368,15 @@ finding the errors. (E.g., if you process steps 2-4 and an error occurs in step
# etc.
@
It can be useful to check if any data is retrieved at step 1:
<<eval=FALSE>>=
lapply(w@specs,function(s) s$foundOK)
@
To check the progress through the workflow, call e.g.:
<<eval=FALSE>>=
findProgress(w)
@
Note that usually a recalibration curve should be done which >15 compounds, and
it will become smoother with more compounds. To show the curve found with the
......@@ -410,6 +476,11 @@ which must be fixed by hand: 2 near-identical names in the infolist; a very high
ID where a lower one exists (which is "better"), a ChEBI entry saying "ChEBI" instead of the
actual ChEBI code.
CAUTION: At this stage the compound name is taken from the user-provided
compound list and one IUPAC entry from CTS. Please check your compound list carefully!
The original naming system from CTS
will be reinstated once the scoring system is re-included in the new services.
After fixing the CSV infolist, it should be copied into the infolist folder and the infolist
reloaded:
......
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