Glossary of Terminology

All Scores

BaseSequence -- The peptide amino acid sequence without modifications.

Base Sequences Mapped

Best Peptide Notch QValue

Best Peptide Score

Contaminant

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 Decoy Notch

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 Target Notch

Decoy

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.

Delta Score

Different Peak Matches

eScore

Essential Sequence

eValue

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

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

Full Sequences Mapped

Gene -- The gene name associated with the protein.

Gene Name

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

Intensity

Localized Scores

Mass Diff (Da) -- The absolute mass difference between the observed and theoretical precursor mass. (Calculated as observed-theoretical).

MassDiff (ppm) -- The ppm mass difference between the observed and theoretical precursor mass. (Calculated as observed-theoretical).

Matched Ion Counts -- The number of product ions found for each series.

Matched Ion Series -- The found product ions and their respective charges.

Matched Ion Mass Diff (Da) -- The absolute mass differences between the observed and theoretical product ion masses. (Calculated as observed-theoretical). Order can be found in Matched Ion Series

Matched Ion Mass Diff (Ppm) -- The ppm mass differences between the observed and theoretical product ion masses. (Calculated as observed-theoretical). Order can be found in Matched Ion Series

Matched Ion Mass-To-Charge Ratios -- The theoretical m/zs that were matched to the observed spectrum.

Matched Ion Intensities -- The observed intensities for the matched product ions.

Missed Cleavages -- 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 event.

Modification Info List

Mods

Mods Chemical Formulas

Mods Combined Chemical Formula

MS2 Retention Time

Next Amino Acid -- 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.

Num Charge States Observed

Num Experimental Peaks

Num Variable Mods

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 with a Q-Value <0.01 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.

Organism

Organism Name

Peak Apex Mass Error (ppm)

Peak Charge

Peak Detection Type

Peak intensity

Peak MZ

Peak RT Apex

Peak RT End

Peak RT Start

Peak Split Valley RT

Peptide Description -- Same as Protein Full Name.

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

Peptides Sharing Same Peaks

Precursor Charge

Precursor Mass -- The neutral (uncharged) mass of the peptide.

Precursor MZ

Precursor Scan Number

Previous Amino Acid -- The amino acid in the protein preceding the specified peptide.

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

Protein Cumulative Decoy

Protein Cumulative Target

Protein Decoy/Contaminant/Target

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

Protein Group

Protein Name

Protein QValue

Protein Unmodified Mass

PSMs Mapped

QValue

QValue Notch

Scan Number -- 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.

Scan Retention Time

Score -- MetaMorpheus 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.

Sequence Coverage with Mods

Sequence Variations

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 Residues In Protein

Theoretical MZ

Theoreticals Searched

Total Ion Current

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.