This function can be used to create an
"MSnSet" by reading and parsing an
mzTab file. The metadata section is always used to populate
the MSnSet's experimentData()@other$mzTab slot.
Usage
readMzTabData(
file,
what = c("PRT", "PEP", "PSM"),
version = c("1.0", "0.9"),
verbose = isMSnbaseVerbose()
)Arguments
- file
A
characterwith themzTabfile to be read in.- what
One of
"PRT","PEP"or"PSM", defining which of protein, peptide PSMs section should be returned as anMSnSet.- version
A
characterdefining the format specification version of the mzTab file. Default is"1.0". Version"0.9"is available of backwards compatibility. SeereadMzTabData_v0.9for details.- verbose
Produce verbose output.
See also
See MzTab and MSnSetList for
details about the inners of readMzTabData.
Examples
testfile <- "https://raw.githubusercontent.com/HUPO-PSI/mzTab/master/examples/1_0-Proteomics-Release/PRIDE_Exp_Complete_Ac_16649.xml-mztab.txt"
prot <- readMzTabData(testfile, "PRT")
prot
#> MSnSet (storageMode: lockedEnvironment)
#> assayData: 1249 features, 4 samples
#> element names: exprs
#> protocolData: none
#> phenoData: none
#> featureData
#> featureNames: X223462890 X19855078 ... X26329627 (1249 total)
#> fvarLabels: accession description ... protein_coverage (15 total)
#> fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> pubMedIds: pubmed:21398567
#> Annotation:
#> - - - Processing information - - -
#> MSnbase version: 2.31.2
head(fData(prot))
#> accession
#> X223462890 223462890
#> X19855078 19855078
#> X21450277 21450277
#> X6978545 6978545
#> X51315739 51315739
#> X117938332 117938332
#> description
#> X223462890 Spna2 protein [Mus musculus]
#> X19855078 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
#> X21450277 sodium/potassium-transporting ATPase subunit alpha-1 precursor [Mus musculus]
#> X6978545 sodium/potassium-transporting ATPase subunit alpha-2 precursor [Rattus norvegicus]
#> X51315739 RecName: Full=Protein bassoon
#> X117938332 spectrin beta chain, brain 1 isoform 1 [Mus musculus]
#> taxid species database database_version
#> X223462890 10090 Mus musculus (Mouse) NCBInr_2010_10 nr_101020.fasta
#> X19855078 10090 Mus musculus (Mouse) NCBInr_2010_10 nr_101020.fasta
#> X21450277 10090 Mus musculus (Mouse) NCBInr_2010_10 nr_101020.fasta
#> X6978545 10090 Mus musculus (Mouse) NCBInr_2010_10 nr_101020.fasta
#> X51315739 10090 Mus musculus (Mouse) NCBInr_2010_10 nr_101020.fasta
#> X117938332 10090 Mus musculus (Mouse) NCBInr_2010_10 nr_101020.fasta
#> search_engine best_search_engine_score[1]
#> X223462890 [MS, MS:1001207, Mascot, ] 6539.67
#> X19855078 [MS, MS:1001207, Mascot, ] 6331.91
#> X21450277 [MS, MS:1001207, Mascot, ] 4577.11
#> X6978545 [MS, MS:1001207, Mascot, ] 4342.81
#> X51315739 [MS, MS:1001207, Mascot, ] 4177.55
#> X117938332 [MS, MS:1001207, Mascot, ] 4001.66
#> search_engine_score[1]_ms_run[1] num_psms_ms_run[1]
#> X223462890 6539.67 157
#> X19855078 6331.91 144
#> X21450277 4577.11 112
#> X6978545 4342.81 108
#> X51315739 4177.55 100
#> X117938332 4001.66 109
#> num_peptides_distinct_ms_run[1] num_peptides_unique_ms_run[1]
#> X223462890 92 NA
#> X19855078 49 NA
#> X21450277 39 NA
#> X6978545 42 NA
#> X51315739 59 NA
#> X117938332 72 NA
#> ambiguity_members
#> X223462890 NA
#> X19855078 NA
#> X21450277 NA
#> X6978545 NA
#> X51315739 NA
#> X117938332 NA
#> modifications
#> X223462890 <NA>
#> X19855078 32-MOD:00425,525-MOD:00425,606-MOD:00425,725-MOD:00425,739-MOD:00425,940-MOD:00425
#> X21450277 42-MOD:00425,616-MOD:00425,749-MOD:00425,950-MOD:00425
#> X6978545 40-MOD:00425,613-MOD:00425,746-MOD:00425,947-MOD:00425
#> X51315739 <NA>
#> X117938332 <NA>
#> protein_coverage
#> X223462890 0
#> X19855078 0
#> X21450277 0
#> X6978545 0
#> X51315739 0
#> X117938332 0
head(exprs(prot))
#> protein_abundance_assay[1] protein_abundance_assay[2]
#> X223462890 1 0.853
#> X19855078 NA NA
#> X21450277 1 0.776
#> X6978545 1 0.784
#> X51315739 NA NA
#> X117938332 1 0.865
#> protein_abundance_assay[3] protein_abundance_assay[4]
#> X223462890 0.864 0.791
#> X19855078 NA NA
#> X21450277 0.819 0.687
#> X6978545 0.848 0.693
#> X51315739 NA NA
#> X117938332 0.861 0.795
psms <- readMzTabData(testfile, "PSM")
psms
#> MSnSet (storageMode: lockedEnvironment)
#> assayData: 8761 features, 0 samples
#> element names: exprs
#> protocolData: none
#> phenoData: none
#> featureData
#> featureNames: X1661 X2280 ... X20346 (8761 total)
#> fvarLabels: sequence PSM_ID ... end (18 total)
#> fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> pubMedIds: pubmed:21398567
#> Annotation:
#> - - - Processing information - - -
#> MSnbase version: 2.31.2
head(fData(psms))
#> sequence PSM_ID accession unique database database_version
#> X1661 QQVLDR 1661 223462890 NA NCBInr_2010_10 nr_101020.fasta
#> X2280 LVQYLR 2280 223462890 NA NCBInr_2010_10 nr_101020.fasta
#> X2281 LVQYLR 2281 223462890 NA NCBInr_2010_10 nr_101020.fasta
#> X2537 LQQLFR 2537 223462890 NA NCBInr_2010_10 nr_101020.fasta
#> X2809 EAGSVSLR 2809 223462890 NA NCBInr_2010_10 nr_101020.fasta
#> X5465 LSILSEER 5465 223462890 NA NCBInr_2010_10 nr_101020.fasta
#> search_engine search_engine_score[1] modifications
#> X1661 [MS, MS:1001207, Mascot, ] 37.76 0-MOD:01499
#> X2280 [MS, MS:1001207, Mascot, ] 44.64 0-MOD:01499
#> X2281 [MS, MS:1001207, Mascot, ] 44.76 0-MOD:01499
#> X2537 [MS, MS:1001207, Mascot, ] 45.41 0-MOD:01499
#> X2809 [MS, MS:1001207, Mascot, ] 55.05 0-MOD:01499
#> X5465 [MS, MS:1001207, Mascot, ] 39.82 0-MOD:01499
#> retention_time charge exp_mass_to_charge calc_mass_to_charge
#> X1661 NA 1 902.4821 902.5181
#> X2280 NA 1 935.5775 935.5800
#> X2281 NA 1 935.5833 935.5800
#> X2537 NA 1 948.5956 948.5753
#> X2809 NA 1 962.5098 962.5393
#> X5465 NA 1 1090.6232 1090.6230
#> spectra_ref pre post start end
#> X1661 ms_run[1]:spectrum=1661 R Y 20 25
#> X2280 ms_run[1]:spectrum=2280 K E 151 156
#> X2281 ms_run[1]:spectrum=2281 K E 151 156
#> X2537 ms_run[1]:spectrum=2537 R D 786 791
#> X2809 ms_run[1]:spectrum=2809 K M 1058 1065
#> X5465 ms_run[1]:spectrum=5465 K T 442 449