Data review before sending to ExperimentHub

[cvanderaa]

We should simplify and curate the rowData of the specht2019v2 dataset. These are the current fields:

• Sequence
• Length
• Modifications
• Modified.sequence
• Deamidation..N..Probabilities
• Oxidation..M..Probabilities
• Deamidation..N..Score.Diffs
• Oxidation..M..Score.Diffs
• Acetyl..Protein.N.term.
• Deamidation..N.
• Oxidation..M.
• Missed.cleavages
• Proteins: should be renamed to ProteinGroup
• Leading.proteins
• protein: should be renamed to Protein
• Gene.names: names of all genes associated to Proteins, should be associated to protein instead
• Protein.names: names of all proteins associated to Proteins, should be associated to protein instead
• Type
• Set
• MS.MS.m.z
• Charge
• m.z
• Mass
• Resolution
• Uncalibrated...Calibrated.m.z..ppm.
• Uncalibrated...Calibrated.m.z..Da.
• Mass.error..ppm.
• Mass.error..Da.
• Uncalibrated.mass.error..ppm.
• Uncalibrated.mass.error..Da.
• Max.intensity.m.z.0
• Retention.time
• Retention.length
• Calibrated.retention.time
• Calibrated.retention.time.start
• Calibrated.retention.time.finish
• Retention.time.calibration
• Match.time.difference
• Match.m.z.difference
• Match.q.value: all NA because no MBR was performed
• Match.score: all NA because no MBR was performed
• Number.of.data.points
• Number.of.scans
• Number.of.isotopic.peaks
• PIF
• Fraction.of.total.spectrum
• Base.peak.fraction
• PEP: deprecated after DART-ID update
• MS.MS.count
• MS.MS.scan.number
• Score
• Delta.score
• Combinatorics
• Intensity
• Reporter.intensity.corrected.0
• Reporter.intensity.corrected.1
• Reporter.intensity.corrected.2
• Reporter.intensity.corrected.3
• Reporter.intensity.corrected.4
• Reporter.intensity.corrected.5
• Reporter.intensity.corrected.6
• Reporter.intensity.corrected.7
• Reporter.intensity.corrected.8
• Reporter.intensity.corrected.9
• Reporter.intensity.corrected.10
• Reporter.intensity.count.0
• Reporter.intensity.count.1
• Reporter.intensity.count.2
• Reporter.intensity.count.3
• Reporter.intensity.count.4
• Reporter.intensity.count.5
• Reporter.intensity.count.6
• Reporter.intensity.count.7
• Reporter.intensity.count.8
• Reporter.intensity.count.9
• Reporter.intensity.count.10
• Reporter.PIF
• Reporter.fraction
• Reverse
• Potential.contaminant
• id
• Protein.group.IDs
• Peptide.ID
• Mod..peptide.ID
• MS.MS.IDs
• Best.MS.MS
• AIF.MS.MS.IDs
• Deamidation..N..site.IDs
• Oxidation..M..site.IDs
• remove: generated by DART-ID
• dart_PEP: generated by DART-ID, should be renamed PEP
• dart_qval: generated by DART-ID
• razor_protein_fdr: generated by DART-ID
• Deamidation..NQ..Probabilities
• Deamidation..NQ..Score.Diffs
• Deamidation..NQ.
• Reporter.intensity.corrected.11
• Reporter.intensity.corrected.12
• Reporter.intensity.corrected.13
• Reporter.intensity.corrected.14
• Reporter.intensity.corrected.15
• Reporter.intensity.corrected.16
• Reporter.intensity.count.11
• Reporter.intensity.count.12
• Reporter.intensity.count.13
• Reporter.intensity.count.14
• Reporter.intensity.count.15
• Reporter.intensity.count.16
• Deamidation..NQ..site.IDs
• input_id: generated by DART-ID
• rt_minus: generated by DART-ID
• rt_plus: generated by DART-ID
• mu: generated by DART-ID
• muij: generated by DART-ID
• sigmaij: generated by DART-ID
• pep_new: generated by DART-ID
• exp_id: generated by DART-ID
• peptide_id: generated by DART-ID
• stan_peptide_id: generated by DART-ID
• exclude: generated by DART-ID
• residual: generated by DART-ID
• participated: generated by DART-ID
• peptide: peptide sequence + charge

Description of most fields is given on the MaxQuant website.

The fields in bold are the ones I think must stay.