@pavel-shliaha Could you please add (by clicking edit) the missing cells? I will add it as man page than.
IdentPeptides.csv
understanding the meaning of some columns will require reading "Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures."
Column
Description
protein.Accession
UniProt Accession Number
protein.Description
Description
protein.dataBaseType
Whether the id originates from forward or reverse database
protein.falsePositiveRate
false DISCOVERY rate for protein level identifications (calculated as the proportion of proteins idetified from the random database at every point). Waters call it false positive rate, which is an error
peptide.matchType
pass 1 (PepFrag1) or pass2 (MissedCleavage; VarMod; InSource; NeutralLoss_H2O; PepFrag2) identifications for more details see the paper above. Note synapter only deals with pepFrag1 or pepFrag2 ids. FDR is calculated separately for pepFrag1 and pepFrag2
peptide.mhp
peptide mz (charge corrected)
peptide.seq
peptide sequence
peptide.score
peptide identification score (see above)
precursor.leID
low energy scan ID
precursor.mhp
precursor mz (charge corrected)
precursor.retT
precursor retention time
precursor.inten
precursor intensity
precursor.z
precursor charge
precursor.mz
precursor mz
precursor.Mobility
precursor ion mobility
errorppm
ppm error of identifications
pval
pvalue of identification calculated by synapter
qval
pvalue corrected by syanpter (qval algorithm)
BH
pvalue corrected by syanpter (BH algorithm)
Bonferroni
pvalue corrected by syanpter (Bonferroni algorithm)
predictedRt
predicted retention time after retention time correction
sdRt
standard deviation of the retention time prediction
MatchedPeptides.csv
Column
Description
protein.Accession
UniProt Accession Number
protein.Description
Description
protein.dataBaseType
protein.falsePositiveRate
peptide.matchType
peptide.mhp
peptide mz (charge corrected)
peptide.seq
peptide sequence
peptide.score
precursor.leID
low energy scan ID
precursor.mhp
precursor mz (charge corrected)
precursor.retT
precursor retention time
precursor.inten
precursor intensity
precursor.z
precursor charge
precursor.mz
precursor mz
precursor.Mobility
precursor ion mobility
errorppm
pval
qval
BH
Bonferroni
predictedRt
predicted retention time after retention time correction
sdRt
standard deviation of the retention time prediction
matchedEMRTs
comma-separated list of matched EMRTs
spectrumID
high energy scan Id (quantitation)
rt_min
retention time in minutes (quantitation)
mwHPlus
mz (quantitation)
charge
charge (quantitation)
Intensity
intensity (quantitation)
Counts
counts (quantitation)
clust_drift
ion mobility (quantitation)
isFid
ion_ID
single ion/fragment ID (quantitation)
ion_z
single ion/fragment charge (quantitation)
ion_iso
single ion/fragment isotop (quantitation)
ion_area
ion_counts
single ion/fragment counts (quantitation)
Model
isotopicDistr
list of isotopic distribution (format: charge_isotope:intensity;)
matched.quant.spectrumIDs
comma-separated list of matched quantitation spectra IDs
precursor.leID.quant
precursor low energy scan ID (quantitation)
idSource
synapterPlgsAgreement
agree/disagree between PLGS and synapter
FragmentMatching
fragment matching result
matchedEMRTs.beforeFilterUniqueMatches
comma-separated list of matched EMRTs before filterUniqueMatches
matchedEMRTs.beforeFilterNonUniqueMatches
comma-separated list of matched EMRTs before filterNonUniqueMatches
matchedMultipleIdentEMRTs
matches multiple identification EMRTs TRUE/FALSE
intensityCorrectionFactor
applied intensity correction factor (generated by intensityModel)
MergedPeptides.csv
Column
Description
peptide.seq
peptide sequence
protein.Accession.ident
UniProt Accession Number (identification)
protein.Description.ident
Description
protein.dataBaseType.ident
protein.falsePositiveRate.ident
peptide.matchType.ident
peptide.mhp.ident
peptide mz (charge corrected) (identification)
peptide.score.ident
precursor.leID.ident
low energy scan ID (identification)
precursor.mhp.ident
precursor mz (charge corrected) (identification)
precursor.retT.ident
precursor retention time (identification)
precursor.inten.ident
precursor intensity (identification)
precursor.z.ident
precursor charge (identification)
precursor.mz.ident
precursor mz (identification)
precursor.Mobility.ident
precursor ion mobility (identification)
errorppm.ident
pval.ident
qval.ident
BH.ident
Bonferroni.ident
protein.Accession.quant
UniProt Accession Number (quantitation)
protein.Description.quant
Description
protein.dataBaseType.quant
protein.falsePositiveRate.quant
peptide.matchType.quant
peptide.mhp.quant
peptide mz (charge corrected) (quantitation)
peptide.score.quant
precursor.leID.quant
low energy scan ID (quantitation)
precursor.mhp.quant
precursor mz (charge corrected) (quantitation)
precursor.retT.quant
precursor retention time (quantitation)
precursor.inten.quant
precursor intensity (quantitation)
precursor.z.quant
precursor charge (quantitation)
precursor.mz.quant
precursor mz (quantitation)
precursor.Mobility.quant
precursor ion mobility (quantitation)
errorppm.quant
pval.quant
qval.quant
BH.quant
Bonferroni.quant
deltaRt
difference between identification and quantitation run in retention time
intenRatio
intensity ratio between identification and quantitation run in retention time
@pavel-shliaha Could you please add (by clicking
edit) the missing cells? I will add it as man page than.IdentPeptides.csv
understanding the meaning of some columns will require reading "Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures."
MatchedPeptides.csv
MergedPeptides.csv
QuantPeptides.csv