MIAPE-class {MSnbase} | R Documentation

## 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.

### 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.

### Author(s)

Laurent Gatto <lg390@cam.ac.uk>

### 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).

[Package MSnbase version 2.6.4 Index]