Glossary of Terminology

AA

AAsInCommon

apexIntensity -- The maximum value in the extraction ion chromatogram for the most abundant isotopic form of the quantified peptide.

apexMz -- The m/z for the most abundant charge state of the most abundant isotopic form of the peptide.

apexRT -- The retention time of the extracted ion chromatogram peak for the quantified peptide.

Area 0.01t

Area 0.255

BaseSequence -- The peptide amino acid sequence without modifications.

BestMassInPrecursor -- Wide tolerances used for selection of precursor for fragmentation result in the coisolation of multiple peptides. Commonly, peptides are identifed from the MS2 fragmentation with a precursor mass different than the precursor mass specified in the scan header. In this case, the associated MS1 spectrum is queried to identified other precursor masses that may better match to the peptide identified using the MS2 data. The best mass in precursor in then reported.

Combos

Count

CountDecoy

CountLocalizeableTarget

CountNonLocalizeableTarget

CountTarget

Cumulative Decoy -- The target/decoy approach for determination of FDR yields lists of peptides and proteins matching either target or decoy. These commingled lists are sorted by scored. The top scoring decoy match is labeled as 1. Each additional match to decoy is incremented by one. The total count of decoy matches scoring at or above a particular score at any point in the list is reported as Cumulative Decoy. Cumulative Decoy divided by Cumulative Target is the FDR.

Cumulative Target -- The target/decoy approach for determination of FDR yields lists of peptides and proteins matching either target or decoy. These commingled lists are sorted by scored. The top scoring target match is labeled as 1. Each additional match to target is incremented by one. The total count of target matches scoring at or above a particular score at any point in the list is reported as Cumulative Target. Cumulative Decoy divided by Cumulative Target is the FDR.

cumulative_decoy

cumulative_decoy_notch

cumulative_target

cumulative_target_notch

Decoy/Contaminant/Target -- Each peptide spectral match, unique peptide and protein is assigned as decoy (D)/contaminant (C)/or target (T). The preference in assignment is D>C>T.

FDR -- False discovery rate is defined as cumulative decoy divided by cumulative target.

fileName -- The filename and path that contained the scan used in the identification.

FracLocalizeableTarget

FracWithSingle

FullSequence -- The complete peptide sequence containing all variable and localized modifications.

Gene -- The gene name associated with the protein.

improvement -- The increase in the MetaMorpheus score produced by localization of the modification to the position specified in the FullSequence.

localized scores

MassDiff (Da) -- The absolute mass difference between the identified peptide theoretical mass and the mass of the experimental reported as the precursor.

MassDiff (ppm) -- The ppm mass difference between the identified peptide theoretical mass and the mass of the experimental reported as the BestMassInPrecursor.

MassDiffToBestMass (Da) -- The absoulte mass difference between the identified peptide theoretical mass and the mass of the experimental reported as the BestMassInPrecursor.

MassDiffToBestMass (ppm)-- The ppm mass difference between the identified peptide theoretical mass and the mass of the experimental reported as the BestMassInPrecursor.

MassShift

matched ion counts --

matched ions --

MedianLength --

Mine --

MissedCleavages -- Digestion of proteins into peptides by proteases (e.g. trypsin) is occasionally incomplete. Users may specify the number of allowed missed cleavages to compensate for incomplete digestion of proteins. This expands the search space. Commonly, two missed cleavages are allowed. However, observation of missed cleavages should be expected as a rare evenet.

ModsInCommon

mostAbundantMass

NextAminoAcid -- Amino acid in the protein that is next in line on the C-terminal end.

notch -- A narrow mass window in which the is an allowed mass difference between the experimentally observed peptide and the best matching theoretical peptide.

Number of peptides -- Number of unique peptides observed in the run that match to the specified protein.

Number of proteins in group -- Multiple proteins are associated with a peptide identification when parsimony cannot distinguish between the options.

Number of PSMs -- The number of peptide spectral matches observed in the run for all peptides assigned to the protein or protein group.

Number of unique peptides -- The number of different unique peptides observed in the run for all peptides assigned to the protein or protein group.

numVariableMods

OverlappingFrac

pepCtermLocFrac

pepNtermLocFrac

Peptide Description -- Same as Protein Full Name.

PeptideMonoisotopicMass -- The mass of the peptide calculated from atoms in their most abundant isotopic form (12C, 16O, 14N, etc.). This is the uncharged (neutral) mass.

PreviousAminoAcid -- The amino acid in the protein preceding the specified peptide.

protCtermLocFrac

Protein Accession -- The accession number of the protein as specified in the protein database.

Protein Full Name -- The full name of the protein as specified in the protein database.

Protein FullName

protNtermLocFrac

QValue

Q-Value (%)

QValue_notch

Residues

scanExperimentalPeaks

scanNumber -- The scan number is specified in the header of each scan. The scan number reported usually contains the MS2 data used in the peptide spectral match.

scanPrecursorCharge -- Charge state of the precursor specified in the scan header of the MS2 scan used for the peptide spectral match.

scanPrecursorIntensity -- Peak intensity of the precursor in the MS1 scan associated with the specified peptide spectral match.

scanPrecursorMass -- Neutral mass of the specified precursor.

scanPrecursorMZ -- m/z for the selected precursor

scanRetentionTime -- retention time specified in the scan header of the MS2 scan used for peptide spectral matching

score -- MetaMorpheous score is incremented by one for each matching b- and y-ion. c- and z.-ions are used for ETD. The number after the decimal is the fraction of total peak intensity from the MS2 scan that can be assigned to the particular peptide spectral match.

Sequence coverage -- The fraction of amino acids in the protein observed in any peptide spectral match with a Q value > 0.01.

Sequence coverage %

Shared peptides

Start and End ResidueInProtein

Summed MetaMorpheus Score

terminal localization

totalIonCurrent

UnimodDiffs

UnimodFormulas

UnimodID

Uniprot

Unique peptides -- Peptides that are unique in the proteome. These can only be assigned to a single protein. The user can specify if modified peptides can be considered as unique.