Parse MzTab files
MzTab-class.RdThe 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 datalist.- mzTabMode
signature(x = "MzTab"): returns the mode (complete or summary) of themzTabdata. A shortcut formetadata(x)$`mzTab-mode`.- mzTabType
signature(x = "MzTab"): returns the type (quantification or identification) of themzTabdata. A shortcut formetadata(x)$`mzTab-type`.- fileName
signature(object = "MzTab"): returns the file name of the originalmzTabfile.- peptides
signature(object = "MzTab"): returns the peptidedata.frame.- proteins
signature(object = "MzTab"): returns the proteinsdata.frame.- psms
signature(object = "MzTab"): returns the PSMsdata.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.
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.
Author
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).
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]]
#> Object of class "MzTab".
#> Description: date of export: Mon Jun 16 10:57:56 BST 2014
#> Mode: Summary
#> Type: Quantification
#> Available data: Proteins PSMs
dim(proteins(mzt[[4]]))
#> [1] 1249 19
dim(psms(mzt[[4]]))
#> [1] 8761 18
prots4 <- proteins(mzt[[4]])
class(prots4)
#> [1] "data.frame"
prots4[1:5, 1:4]
#> accession
#> 1 223462890
#> 2 19855078
#> 3 21450277
#> 4 6978545
#> 5 51315739
#> description
#> 1 Spna2 protein [Mus musculus]
#> 2 RecName: Full=Sodium/potassium-transporting ATPase subunit alpha-3; Short=Na(+)/K(+) ATPase alpha-3 subunit; AltName: Full=Na(+)/K(+) ATPase alpha(III) subunit; AltName: Full=Sodium pump subunit alpha-3
#> 3 sodium/potassium-transporting ATPase subunit alpha-1 precursor [Mus musculus]
#> 4 sodium/potassium-transporting ATPase subunit alpha-2 precursor [Rattus norvegicus]
#> 5 RecName: Full=Protein bassoon
#> taxid species
#> 1 10090 Mus musculus (Mouse)
#> 2 10090 Mus musculus (Mouse)
#> 3 10090 Mus musculus (Mouse)
#> 4 10090 Mus musculus (Mouse)
#> 5 10090 Mus musculus (Mouse)