\name{MIAPE-class} \Rdversion{1.1} \docType{class} \alias{MIAPE-class} \alias{class:MIAPE} \alias{MIAPE} \alias{show,MIAPE-method} \alias{msInfo,MIAPE-method} \alias{msInfo} \alias{abstract,MIAPE-method} \alias{samples,MIAPE-method} \alias{pubMedIds,MIAPE-method} \alias{pubMedIds<-,MIAPE-method} \alias{otherInfo,MIAPE-method} \alias{expinfo,MIAPE-method} \alias{notes,MIAPE-method} \alias{notes<-,MIAPE-method} \alias{combine,MIAPE,MIAPE-method} \title{The "MIAPE" Class for Storing Proteomics Experiment Information} \description{ The Minimum Information About a Proteomics Experiment. The current implementation is based on the MIAPE-MS 2.4 document. } \section{Slots}{ \describe{ \item{\code{title}:}{Object of class \code{character} containing a single-sentence experiment title. } \item{\code{abstract}:}{Object of class \code{character} containing an abstract describing the experiment. } \item{\code{url}:}{Object of class \code{character} containing a URL for the experiment. } \item{\code{pubMedIds}:}{Object of class \code{character} listing strings of PubMed identifiers of papers relevant to the dataset. } \item{\code{samples}:}{Object of class \code{list} containing information about the samples. } \item{\code{preprocessing}:}{Object of class \code{list} containing information about the pre-processing steps used on the raw data from this experiment. } \item{\code{other}:}{Object of class \code{list} containing other information for which none of the above slots does not applies. } \item{\code{dateStamp}:}{Object of class \code{character}, giving yhe date on which the work described was initiated; given in the standard 'YYYY-MM-DD' format (with hyphens). } \item{\code{name}:}{Object of class \code{character} containing the name of the (stable) primary contact person for this data set; this could be the experimenter, lab head, line manager, \ldots} \item{\code{lab}:}{Object of class \code{character} containing the laboratory where the experiment was conducted. } \item{\code{contact}:}{Object of class \code{character} containing contact information for lab and/or experimenter. } \item{\code{instrumentModel}:}{Object of class \code{character} indicating the model of the mass spectrometer used to generate the data. } \item{\code{instrumentManufacturer}:}{Object of class \code{character} indicating the manufacturing company of the mass spectrometer. } \item{\code{instrumentCustomisations}:}{Object of class \code{character} describing any significant (i.e. affecting behaviour) deviations from the manufacturer's specification for the mass spectrometer. } \item{\code{softwareName}:}{Object of class \code{character} with the instrument management and data analysis package(s) name(s). } \item{\code{softwareVersion}:}{Object of class \code{character} with the instrument management and data analysis package(s) version(s). } \item{\code{ switchingCriteria}:}{Object of class \code{character} describing the list of conditions that cause the switch from survey or zoom mode (MS1) to or tandem mode (MSn where n > 1); e.g. 'parent ion'' mass lists, neutral loss criteria and so on [applied for tandem MS only]. } \item{\code{isolationWidth}:}{Object of class \code{numeric} describing, for tandem instruments, the total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion m/z, provided for all levels or by MS level. } \item{\code{parameterFile}:}{Object of class \code{character} giving the location and name under which the mass spectrometer's parameter settings file for the run is stored, if available. Ideally this should be a URI+filename, or most preferably an LSID, where feasible. } \item{\code{ionSource}:}{Object of class \code{character} describing the ion source (ESI, MALDI, \ldots). } \item{\code{ionSourceDetails}:}{Object of class \code{character} describing the relevant details about the ion source. See MIAPE-MI docuement for more details. } \item{\code{analyser}:}{Object of class \code{character} describing the analyser type (Quadrupole, time-of-flight, ion trap, \ldots). } \item{\code{analyserDetails}:}{Object of class \code{character} describing the relevant details about the analyser. See MIAPE-MI docuement for more details. } \item{\code{collisionGas}:}{Object of class \code{character} describing the composition of the gas used to fragment ions in the collision cell. } \item{\code{collisionPressure}:}{Object of class \code{numeric} providing the pressure (in bars) of the collision gas. } \item{\code{collisionEnergy}:}{Object of class \code{character} specifying for the process of imparting a particular impetus to ions with a given m/z value, as they travel into the collision cell for fragmentation. This could be a global figure (e.g. for tandem TOF's), or a complex function; for example a gradient (stepped or continuous) of m/z values (for quads) or activation frequencies (for traps) with associated collision energies (given in eV). Note that collision energies are also provided for individual \code{"\linkS4class{Spectrum2}"} instances, and is the preferred way of accessing this data. } \item{\code{detectorType}:}{Object of class \code{character} describing the type of detector used in the machine (microchannel plate, channeltron, \ldots). } \item{\code{detectorSensitivity}:}{Object of class \code{character} giving and appropriate measure of the sensitivity of the described detector (e.g. applied voltage). } } } \section{Methods}{ The following methods as in \code{"\linkS4class{MIAME}"}: \describe{ \item{\code{abstract(MIAPE)}:}{An accessor function for \code{abstract}. } \item{\code{expinfo(MIAPE)}:}{An accessor function for \code{name}, \code{lab}, \code{contact}, \code{title}, and \code{url}.} \item{\code{notes(MIAPE), notes(MIAPE) <- value}:}{Accessor functions for \code{other}. \code{notes(MIAME) <- character} \emph{appends} character to notes; use \code{notes(MIAPE) <- list} to replace the notes entirely.} \item{\code{otherInfo(MIAPE)}:}{An accessor function for \code{other}.} \item{\code{preproc(MIAPE)}:}{An accessor function for \code{preprocessing}.} \item{\code{pubMedIds(MIAPE), pubMedIds(MIAME) <- value}:}{Accessor function for \code{pubMedIds}.} \item{\code{samples(MIAPE)}:}{An accessor function for \code{samples}.} } MIAPE-specific methods, including MIAPE-MS meta-data: \describe{ \item{\code{show(MIAPE)}:}{Displays the experiment data.} \item{\code{msInfo(MIAPE)}:}{Displays 'MIAPE-MS' information.} } } \section{Extends}{ Class \code{"\linkS4class{MIAxE}"}, directly. Class \code{"\linkS4class{Versioned}"}, by class "MIAxE", distance 2. } \references{ About MIAPE: \url{http://www.psidev.info/index.php?q=node/91}, and references therein, especially 'Guidelines for reporting the use of mass spectrometry in proteomics', Nature Biotechnology 26, 860-861 (2008). } \author{ Laurent Gatto } % \note{ % This is a temporary implementation, that will most likely be updated % using the AnnotedDataFrame class. MIAPE is currently just a checklist % of items, but may be more formally described later. % } \keyword{classes}