Proteins File

Checked - boolean checkbox
Master - boolean for whether or not the protein assigned is the master protein of a protein group
*Accession - gi# (in some cases, multiple numbers)
*Description - Protein description from fasta
Coverage - # coverage as a function of the gene product assigned in the fasta
# Peptides - number of different peptides assigned
*# PSMs - number of spectra assigned to peptides from this protein
# Unique Peptides - number of peptides only assignable to this protein
# Protein Groups - number of protein groups this protein belongs to
# AAs - length of the sequence
MW (kDa) - mass of protein
calc. pI - Isoelectric point of the protein
*Ratios - TMT label ratios relative to the control channel (in this case, relative to sample 1, replicate 1)
*Ratio Standard Errors [%] - normalized errors of the assigned ratios
Everything with an A2 relates to a Byonic output specific information. The most important one there is the Log Prob, which is the probability of correct assignemnt.

PSMs File (where different than above)

Confidence - color coded confidence based on Log Probability at a peptide level
Identifying Node - What algorithm observed the peptide (should be Byonic)
PSM Ambiguity - a boolean reporter of the difference between the assigned peptide and other possible assignments
Annotated Sequence - Peptide sequence assigned; lower case indicates modification
Modifications - Type and location of post translational modifications
# Protein Groups - Number of groups to which the peptide could have been assigned
# Proteins - number of proteins to which the peptide could have been assigned
Master Protein Accession - gi# of the assigned master protein
Protein Accessions - gi#(s) of the possible assigned proteins
Protein Description - as above
#Missed Cleavages - number of tryptic sites that were not cleaved
Charge - z of the ion
delScore, delCn, Rank, and Search Engine Rank - All refer to how much the algorithm prefers this peptide assignment over its nearest other possible assignments
m/z  - Thomsons of the ion selected for fragmentation
MH+ - mass of the protonated ion
delM - deviation from the expected theoretical mass in ppm
delm/z - deviation from the expected theoretical mass in thomsons
Activation Type - type of MS/MS used to generate peptide fragmentation
MS Order - the order at which MS/MS was assigned to a peptide (generally, this will be MS2, although MS3 is possible)
Isolation Interference (%) - estimated of # of ion signal in the isolation window that is not directly assignable to the peptide of interest
Ion Inject Time (ms) - how long ions were collected before meeting the AGC ion load limit
RT (min) - retention time of the peptide when sampled
First Scan - Scan number when sampled
Spectrum File - source file from which the spectrum was obtained
Ions Matched - no idea, I'll look into its
Log Prob - Peptide level assignment probability
Byonic Score - Peptide level assignment score
delByonic Score - next best assignment score delta
Del Mod Score - Next best assignment score allowing for mods
PEP 2D - 2 dimensional posterior error probability of the peptide assignment (Protein aware)
q-Value 2D - estimated FDR for the full list of PSMs thresholded at this PSM by PEP 2D
FDR 2D - # of decoys/# of PSMs in ranked list
Peptide Group FDR 2D - as above, but with groups
PEP 1D, q-value 1D, FDR 1D, Peptide Group FDR 1D - protein oblivious versions of above
Off by X - 1 dalton shifts of the precursor ion relative to the expected mass
Position in Protein - first residue of the peptide as a function of the protein sequence
Reporter Quan Result ID - unique identifier
Quan Info  - whether or not the peptide was unique and or had useable quan values (TMT reporter ions)
Quan Usage - was it used for quan values
Ratios - as above, peptide level
Ungrouped Ratios - Ratios as a function of the offline fractionation
126, 127, 128, 129, 130, 131 - the raw reporter ion intensities
