MzTab-class: Parse 'MzTab' files

In MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

Description

The MzTab class stores the output of a basic parsing of a mzTab file. It contain the metadata (a list), comments (a character vector), and the at least of of the following data types: proteins, peptides, PSMs and small molecules (as data.frames).

At this stage, the metadata and data are only minimally parsed. The column names are kept as they are defined in the original files and are thus not all going to be valid colnames. To access them using the dollar operator, use backticks. More specific data extraction and preparation are delegated to more specialised functions, such as the as(., to = "MSnSetList") and readMzTabData for proteomics data.

Note that no attempts are made to verify the validitiy of the mzTab file.

Objects from the Class

Objects can be created by calls the the constructor MzTab that takes a single mzTab file as input.

The objects can subsequently be coerced to MSnSetList instances with as(object, "MSnSetList"). The resulting MSnSetList contains possibly empty MSnSet instances for proteins, peptide and PSMs, respectively named "Proteins", "Peptides" and "PSMs".

The assaydata slots of the two former are populated with the protein_abundance_assay[1-n] and peptide_abundance_assay[1-n] columns in the mzTab file. No abundance values are defined for the latter. The respective feature names correspond to protein accessions, peptide sequences and PSM identifiers, possibly made unique as by appending sequence numbers to duplicates.

Slots

Metadata:

Object of class "list" storing the metadata section.

Filename:

Object of class "character" storing the orginal file name.

Proteins:

Object of class "data.frame" storing the protein data.

Peptides:

Object of class "data.frame" storing the peptide data.

PSMs:

Object of class "data.frame" storing the PSM data.

SmallMolecules:

Object of class "data.frame" storing the small molecules data.

MoleculeFeatures:

Object of class "data.frame" storing the molecule features.

MoleculeEvidence:

Object of class "data.frame" storing the molecule evidence.

Comments:

Object of class "character" storing the comments that were present in the file.

Accessors

metadata

signature(x = "MzTab"): returns the meta data list.

mzTabMode

signature(x = "MzTab"): returns the mode (complete or summary) of the mzTab data. A shortcut for metadata(x)$`mzTab-mode`.

mzTabType

signature(x = "MzTab"): returns the type (quantification or identification) of the mzTab data. A shortcut for metadata(x)$`mzTab-type`.

fileName

signature(object = "MzTab"): returns the file name of the original mzTab file.

peptides

signature(object = "MzTab"): returns the peptide data.frame.

proteins

signature(object = "MzTab"): returns the proteins data.frame.

psms

signature(object = "MzTab"): returns the PSMs data.frame.

smallMolecules

signature(object = "MzTab"): returns the small molecules (SML) data.frame.

moleculeFeatures

signature(object = "MzTab"): returns the small molecules features (SMF) data.frame.

moleculeEvidence

signature(object = "MzTab"): returns the small molecule identification evidence (SME) data.frame.

comments

signature(object = "MzTab"): returns the comments.

Author(s)

Laurent Gatto, with contributions from Richard Cotton (see https://github.com/lgatto/MSnbase/issues/41) and Steffen Neuman (see https://github.com/lgatto/MSnbase/pull/500).

References

The mzTab format is a light-weight, tab-delimited file format for proteomics data. Version mzTab 1.0 is aimed at proteomics, mzTab-M 2.0 was adapted to metabolomics. See https://github.com/HUPO-PSI/mzTab for details and specifications.

Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, Del Toro N, Perez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaino JA, Hermjakob H. The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. Mol Cell Proteomics. 2014 Oct;13(10):2765-75. doi: 10.1074/mcp.O113.036681. Epub 2014 Jun 30. PubMed PMID: 24980485; PubMed Central PMCID: PMC4189001.

Hoffmann N, Rein J, Sachsenberg T, et al. mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics. Anal Chem. 2019;91(5):3302‐3310. doi:10.1021/acs.analchem.8b04310 PubMed PMID: 30688441; PubMed Central PMCID: PMC6660005.

Examples

## Test files from the mzTab developement repository
fls <- c("Cytidine.mzTab", "MTBLS2.mztab", 
         "PRIDE_Exp_Complete_Ac_1643.xml-mztab.txt", 
         "PRIDE_Exp_Complete_Ac_16649.xml-mztab.txt", 
         "SILAC_CQI.mzTab", "SILAC_SQ.mzTab", 
         "iTRAQ_CQI.mzTab", "iTRAQ_SQI.mzTab", 
         "labelfree_CQI.mzTab", "labelfree_SQI.mzTab", 
         "lipidomics-HFD-LD-study-PL-DG-SM.mzTab", 
         "lipidomics-HFD-LD-study-TG.mzTab")

baseUrl <- "https://raw.githubusercontent.com/HUPO-PSI/mzTab/master/examples/1_0-Proteomics-Release/"

## a list of mzTab objects
mzt <- sapply(file.path(baseUrl, fls), MzTab)
stopifnot(length(mzt) == length(fls))
mzt[[4]]

dim(proteins(mzt[[4]]))
dim(psms(mzt[[4]]))

prots4 <- proteins(mzt[[4]])
class(prots4)
prots4[1:5, 1:4]

MSnbase documentation built on Jan. 23, 2021, 2 a.m.