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The "MIAPE" Class for Storing Proteomics Experiment Information

MIAPE-class.Rd

The Minimum Information About a Proteomics Experiment. The current implementation is based on the MIAPE-MS 2.4 document.

Slots

title:

Object of class character containing a single-sentence experiment title.

abstract:

Object of class character containing an abstract describing the experiment.

url:

Object of class character containing a URL for the experiment.

pubMedIds:

Object of class character listing strings of PubMed identifiers of papers relevant to the dataset.

samples:

Object of class list containing information about the samples.

preprocessing:

Object of class list containing information about the pre-processing steps used on the raw data from this experiment.

other:

Object of class list containing other information for which none of the above slots applies.

dateStamp:

Object of class character, giving the date on which the work described was initiated; given in the standard 'YYYY-MM-DD' format (with hyphens).

name:

Object of class character containing the name of the (stable) primary contact person for this data set; this could be the experimenter, lab head, line manager, ...

lab:

Object of class character containing the laboratory where the experiment was conducted.

contact:

Object of class character containing contact information for lab and/or experimenter.

email:

Object of class character containing tmail contact information for the primary contact person (see name above).

instrumentModel:

Object of class character indicating the model of the mass spectrometer used to generate the data.

instrumentManufacturer:

Object of class character indicating the manufacturing company of the mass spectrometer.

instrumentCustomisations:

Object of class character describing any significant (i.e. affecting behaviour) deviations from the manufacturer's specification for the mass spectrometer.

softwareName:

Object of class character with the instrument management and data analysis package(s) name(s).

softwareVersion:

Object of class character with the instrument management and data analysis package(s) version(s).

switchingCriteria:

Object of class 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].

isolationWidth:

Object of class 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.

parameterFile:

Object of class 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.

ionSource:

Object of class character describing the ion source (ESI, MALDI, ...).

ionSourceDetails:

Object of class character describing the relevant details about the ion source. See MIAPE-MI docuement for more details.

analyser:

Object of class character describing the analyzer type (Quadrupole, time-of-flight, ion trap, ...).

analyserDetails:

Object of class character describing the relevant details about the analyzer. See MIAPE-MI document for more details.

collisionGas:

Object of class character describing the composition of the gas used to fragment ions in the collision cell.

collisionPressure:

Object of class numeric providing the pressure (in bars) of the collision gas.

collisionEnergy:

Object of class 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 "Spectrum2" instances, and is the preferred way of accessing this data.

detectorType:

Object of class character describing the type of detector used in the machine (microchannel plate, channeltron, ...).

detectorSensitivity:

Object of class character giving and appropriate measure of the sensitivity of the described detector (e.g. applied voltage).

Methods

The following methods as in "MIAME":

abstract(MIAPE):

An accessor function for abstract.

expinfo(MIAPE):

An accessor function for name, lab, contact, title, and url.

notes(MIAPE), notes(MIAPE) <- value:

Accessor functions for other. notes(MIAME) <- character appends character to notes; use notes(MIAPE) <- list to replace the notes entirely.

otherInfo(MIAPE):

An accessor function for other.

preproc(MIAPE):

An accessor function for preprocessing.

pubMedIds(MIAPE), pubMedIds(MIAME) <- value:

Accessor function for pubMedIds.

expemail(MIAPE):

An accessor function for email slot.

exptitle(MIAPE):

An accessor function for title slot.

analyzer(MIAPE):

An accessor function for analyser slot. analyser(MIAPE) is also available.

analyzerDetails(MIAPE):

An accessor function for analyserDetails slot. analyserDetails is also available.

detectorType(MIAPE):

An accessor function for detectorType slot.

ionSource(MIAPE):

An accessor function for ionSource slot.

ionSourceDetails(MIAPE):

An accessor function for ionSourceDetails slot.

instrumentModel(MIAPE):

An accessor function for instrumentModel slot.

instrumentManufacturer(MIAPE):

An accessor function for instrumentManufacturer slot.

instrumentCustomisations(MIAPE):

An accessor function for instrumentCustomisations slot.

as(,"MIAME"):

Coerce the object from MIAPE to MIAME class. Used when converting an MSnSet into an ExpressionSet.

MIAPE-specific methods, including MIAPE-MS meta-data:

show(MIAPE):

Displays the experiment data.

msInfo(MIAPE):

Displays 'MIAPE-MS' information.

Extends

Class "MIAxE", directly. Class "Versioned", by class "MIAxE", distance 2.

References

About MIAPE: 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