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PAW_table_descriptions_9.txt
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PAW_table_descriptions_9.txt
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Column header keys for PAW tables:
** PAW TMT reporter ion text files (msn_files folder) ** Reporter ion peak values by scan number
lc-name RAW file basename
ms2_scan Peptide MS2 scan number
ms3_scan Associated MS3 scan number for SPS (or MS2 scan number)
* cent_ * Centroid of data within each narrow window for each channel
* area_ * AUC of reporter ion peak for each channel (probably all zero)
* height_ * Reporter ion peak height (maximum value in narrow window) for each channel
** Top-hit text files (msn_files folder) ** Summaries of Comet top-hits (redundant by loci)
start Beginning scan number
end Ending scan number
Z Peptide charge state
expM Measured MH+ mass
SpRank Ranking from preliminary scoring
theoM Calculated MH+ mass for sequence
deltaCN Delta CN score (gap score)
Xcorr Cross correlation score
Sequence Peptide sequence string
Loci Protein accession (FASTA database key)
NewDeltaCN More robust gap score
ISBDisc Peptide prophet discriminant function (no longer used)
NewDisc New discriminant function score
ntt Number of peptide termini consistent with enzymatic cleavage
ForR F if target match, R if decoy match
Sp Preliminary score or expectation value (depends on Comet settings)
[* height_ *] [optional] Reporter ion peak heights
** Filtered top-hit summaries (filtered_files folder) ** Top hits passing score thresholds
start Beginning scan number
end Ending scan number
Z Peptide charge state
expM Measured MH+ mass
SpRank Ranking from preliminary scoring
theoM Calculated MH+ mass for sequence
deltaCN Delta CN score (gap score)
Xcorr Cross correlation score
Sequence Peptide sequence string
Loci Protein accession (FASTA database key)
NewDeltaCN More robust gap score
ISBDisc Peptide prophet discriminant function (no longer used)
NewDisc New discriminant function score
ntt Number of peptide termini consistent with enzymatic cleavage
ForR F if target match, R if decoy match
Sp Preliminary score or expectation value (depends on Comet settings)
[* height_ *] [optional] Reporter ion peak heights
TxtIdx Text file index
dmassDa Delta mass in Daltons
dmassPPM Delta mass in PPM
Length Peptide sequence length
NumMods Total number of variable modifications in peptide
ModsStr String summarizing peptide modifications (space for unmod)
IndexTuple Tuple with score index values
TestValue NewDisc threshold value for peptide class
** Protein_summary table (results_files folder) ** Redundant inferred proteins summary
ProtGroup Arbitrary integral protein group number (redundant by groups)
Counter Column of ones for visible row counting
Accession FASTA database keys
Filter Text flag column to denote contaminant and decoy matches
Coverage Protein sequence coverage (%)
SeqLength Number of amino acids in protein sequence
MW Calculated molecular weight of FASTA protein sequence
Description FASTA sequence header line (after key)
CountsTot Total spectral counts (SpC) for all samples in experiment
UniqueTot Total unique SpC for all samples in experiment
UniqFrac Fraction of SpC that are unique (map to single FASTA entry)
* Total_ * Total SpC for respective sample
* Unique_ * Total unique SpC for respective sample
* Corrected_ * Corrected SpC (shared peptide counts fractionally split) for respective sample
OtherLoci Union of all accessions having any common shared peptides for respective protein
** Peptide_summary table (results_files folder) ** Peptide summary for proteins
ProtGroup Arbitrary protein group number (keyed to protein table)
Accession FASTA database keys
Sequence Peptide sequence string
Begin Beginning amino acid residue number (in FASTA sequence)
End Ending amino acid residue number (in FASTA sequence)
Unique TRUE if peptide only matches to one FASTA entry/group, FALSE if shared
NTT Number of peptide termini consistent with enzymatic cleavage
Z Peptide charge state
TotCount Total spectral count for peptide across all samples
* sample names * Total spectral counts for peptide in respective sample
OtherLoci Union of all accessions having any common shared peptides for respective protein
** Per-sample peptide results files (results_files folder) ** Detailed peptide results
ProtGroup Arbitrary protein group number (keyed to protein table)
Accession FASTA database keys
Sequence Peptide sequence string
Unique TRUE if peptide only matches to one FASTA entry/group, FALSE if shared
TotCount Total spectral count for peptide
NTT Number of peptide termini consistent with enzymatic cleavage
Xcorr Cross correlation score
DeltaCN Delta CN score (gap score)
SpRank Ranking from preliminary scoring
NewDisc New discriminant function score
Z Peptide charge state
Delta_Mass Delta mass in Daltons
Exp_Mass Measured MH+ mass
Calc_Mass Calculated MH+ mass for sequence
DTA_filename SEQUEST-style DTA name (contains scan numbers and charge state)
** Grouped_protein_summary table (results_files folder) ** Grouped non-redundant protein summary
ProtGroup Arbitrary integral protein group number (redundant by groups)
Counter Column of ones for visible row counting
Accession FASTA database keys (for primary proteins)
Identical Accessions of other indistinguishable proteins
Similar Accessions of homologous proteins that were grouped into families
OtherLoci Union of all accessions having any common shared peptides for respective protein
Filter Text flag column to denote contaminant and decoy matches
Coverage Protein sequence coverage (%)
SeqLength Number of amino acids in protein sequence
MW Calculated molecular weight of FASTA protein sequence
Description FASTA sequence header line (after key)
CountsTot Total spectral counts (SpC) for all samples in experiment
UniqueTot Total unique SpC for all samples in experiment
UniqFrac Fraction of SpC that are unique (map to single FASTA entry)
* Total_ * Total SpC for respective sample
* Unique_ * Total unique SpC for respective sample
* Corrected_ * Corrected SpC (shared peptide counts fractionally split) for respective sample
** Grouped_peptide_summary table (results_files folder) ** Peptide summary for grouped proteins
ProtGroup Arbitrary protein group number (keyed to protein table)
Accession FASTA database keys
Sequence Peptide sequence string
Begin Beginning amino acid residue number (in FASTA sequence)
End Ending amino acid residue number (in FASTA sequence)
Unique TRUE if peptide only matches to one FASTA entry/group, FALSE if shared
NTT Number of peptide termini consistent with enzymatic cleavage
Z Peptide charge state
TotCount Total spectral count for peptide across all samples
* sample names * Total spectral counts for peptide in respective sample
OtherLoci Union of all accessions having any common shared peptides for respective protein