Glossary of Terminology

AA

AAsInCommon

quantificationIntensity -- The maximum value (apex intensity) in the extracted ion chromatogram for the most abundant isotopic form of the quantified peptide. For TMT quantification, this will be 10 numbers separated by a "|", each representing a plex (see quantification page for details).

quantificationRT -- The retention time of the extracted ion chromatogram apex peak for the quantified peptide (for LFQ). For TMT quantification, this is just the MS2 scan retention time.

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 score. 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 score. 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 -- Number of predicted fragment ions observed in the experimental spectrum.

matched ions -- The predicted fragment ions observed in the experimental spectrum are listed.

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

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 -- (Protein Groups Output) -- Number of unique+shared peptides observed that match to the specified protein group.

Number of proteins in group -- (Protein Groups Output) -- The number of proteins in the protein group. Multiple proteins are associated with a peptide identification when parsimony cannot distinguish between the options.

Number of PSMs -- (Protein Groups Output) -- The number of peptide spectral matches below 1% FDR observed for all peptides assigned to the protein group.

Number of unique peptides -- (Protein Groups Output) -- Number of unique proteins for the protein group. See Unique Peptides definition.

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 -- (Protein Groups Output) -- Displays amino acids in the protein observed in any peptide spectral match with a Q value > 0.01 for each protein in the group, with the "|" character as the delimiter. Lowercase residues were not observed. Uppercase residues were observed.

Sequence coverage % -- (Protein Groups Output) -- The fraction of amino acids in the protein observed in any peptide spectral match with a Q value > 0.01.

Shared peptides -- (Protein Groups Output) -- Peptides that are shared between multiple proteins in the protein database(s) used for the search are listed.

Start and End ResidueInProtein

Summed MetaMorpheus Score -- (Protein Groups Output) -- The highest-scoring PSM per peptide base sequence, summed for all observed peptide base sequences. The list of protein groups are ordered by score.

terminal localization

totalIonCurrent

UnimodDiffs

UnimodFormulas

UnimodID

Uniprot

Unique peptides -- (Protein Groups Output) -- Peptides that are unique to the listed protein (they can only come from that one protein, based on the database in silico digestion). Currently, peptides that are unique to the group are not listed here; i.e., a protein group with >1 protein will always have 0 unique peptides because they are shared between all proteins in the group.