ProteinGroup-class: ProteinGroup objects

In isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

Description

The ProteinGroup class is a container for identified peptides and proteins, and groups them to distinguish proteins with specific peptides.

Usage

ProteinGroup(from,template=NULL,proteinInfo=data.frame())

protein.ac(x, protein.g)
protein.g(x, pattern, variables=c("AC","name"), ...)

Arguments

from	data.frame object to create a ProteinGroup from. See Details from column specifications
template	'template' ProteinGroup object for grouping.
x	ProteinGroup object
protein	character string
proteinInfo	data.frame for proteinInfo slot
protein.g	character string, denoting a 'protein group'.
pattern	character string, see grep for details.
variables	AC maps a protein accession code to a protein group. name maps using protein information from proteinInfo.
...	Passed on to grep.

Details

The ProteinGroup class stores spectrum to peptide to protein mapping.

The proteins are grouped by their evidence, i. e. peptides:

• Peptides with changes only from Leucin to Isoleucin are considered the same, as they cannot be distinguished by MS.

• Proteins which are detected with the same peptides are grouped together to a 'indistinguishable protein'- normally these are splice variants.

• Proteins with specific peptides are 'reporters'.

• Proteins with no specific peptides are grouped under these 'reporters.

This information is stored in six slots:

spectra.n.peptides

a named 'character' vector, names being spectrum identifier and values are peptides.

peptide.n.proteins

a 'data.frame' containing the number of proteins the peptides could derive from.

peptide.n.protein

a character 'matrix' linking peptides to proteins.

indistinguishable.proteins

a 'matrix' contain.

Constructor

ProteinGroup(tbl.prot.pep,template=NULL): Creates a ProteinGroup object.

tbl.prot.pep

A 'data.frame' with three columns: 1. Protein, 2. Peptide, 3. Spectrum.

template

Optional ProteinGroup object the grouping is based upon.

Coercion

In the code snippets below, x is a ProteinGroup object.

as(from, "ProteinGroup"):

Creates a ProteinGroup object from a data.frame.

as.data.frame(x, row.names = NULL, optional = FALSE):

Creates a data.frame with columns protein (character), peptide (character), spectrum.

as.concise.data.frame(from):

Creates a 'concise' data.frame with one spectrum per row, and protein ACs combined

Accessors

In the following code snippets, x is a ProteinGroup object.

spectrumToPeptide(x):

Gets spectrum to peptide assignment.

peptideInfo(x):

Peptide information such as protein start position.

peptideSpecificity(x):

Gets a 'data.frame' containing the peptide specificity: they can be reporter-specific, group-specific, or non-specific.

peptideNProtein(x):

Gets peptide to protein assignment.

indistinguishableProteins(x):

Gets the proteins which cannot be distinguished based on peptide evidence.

proteinGroupTable:

Gets the protein grouping, listing reporters and group members.

peptides(x,protein=NULL,specificity=c("reporter-specific", "group-specific","unspecific"),columns="peptide",set=union):

Gets all peptides detected, or just those for a protein with the defined specificity. columns might define multiple columns of peptideSpecificity(x). set=union returns the union of peptides of all proteins defined, set=intersect returns the intersection.

Author(s)

Florian P. Breitwieser

See Also

IBSpectra

Examples

tbl <- data.frame(spectrum=1:14,peptide=c(rep(letters[1:3],4),"a","x"),
                  modif=":",start.pos=1,
                  protein=c(rep(c("A","B"),each=6),"C","D"))
pg <- ProteinGroup(tbl)
pg
proteinGroupTable(pg)

data(ibspiked_set1)
pg <- proteinGroup(ibspiked_set1)
ceru.proteins <- protein.g(pg,"CERU")

## all ceru peptides
peptides(pg,ceru.proteins)

## peptides shared by all ceru proteins
peptides(pg,ceru.proteins, set=intersect) 

isobar documentation built on Nov. 8, 2020, 7:48 p.m.