\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
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@@ -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).
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@@ -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]
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@@ -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
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@@ -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.
\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".
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@@ -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
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@@ -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 peaks 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 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
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@@ -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}:
