The following tables describes the columns of the Decoy PSMs page.
Column | Description |
|---|---|
# Missed Cleavages | Displays the number of cleavage sites in a peptide sequence that a cleavage reagent (enzyme) did not cleave. This number excludes cases where an amino acid such as proline inhibits the cleaving enzyme. For example, if proline resides next to lysine or arginine, trypsin does not cleave the lysine or arginine. The application returns a 0 value for the # Missed Cleavages when all peptides have been completely digested. |
# Protein Groups | Displays the number of identified decoy protein groups containing the peptide. |
# Proteins | Displays the total number of identified proteins in the decoy protein group. |
Annotated Sequence | Displays the flanking residues of a peptide in a protein. |
Charge | Displays the charge state of the peptide. |
Checked | Indicates whether the item is selected. |
Concatenated Rank | Displays the value for the “best” PSM that the search engine found. This value includes the rank of the decoy PSMs for the same spectra. |
Confidence | Indicates a confidence level associated with the peptide sequence at the top level:
|
Decoy Peptides Matched | Displays the number of peptide candidates that fall into the precursor mass tolerance window set for the search. |
File ID | Displays a short identifier of the input file that the fragment spectrum belongs to. |
Identifying Node | Displays the name of the search engine node, the order that the application submitted the search to the job queue, and the number assigned to the node in the workflow. |
Identifying Node No | Displays the number of the workflow node that the application used to identify the peptides composing the protein. |
Identifying Node Type | Displays the name of the search engine node. |
Ions Matched | Displays the number of fragment ions matched by the search engine related to the number of possible fragment ions. |
-Log E-Value | Displays the log transform of the ProSightPC e-value. |
m/z [Da] | Displays the mass-to-charge ratio of the precursor ion, in daltons. |
Matched Ions | Displays the number of ions matched by the search engine. This column is only displayed when peptides are ungrouped. |
MH+ [Da] | Displays the protonated monoisotopic mass of the peptides, in daltons. It is the measured mass, as opposed to the expected mass in the Theo. MH+ [Da] column. |
Modifications | Displays the static and dynamic modifications identified in the peptide. |
Original Precursor Charge | Displays the charge state of the precursor as stored in the scan header of the raw data file. |
Percolator PEP | Displays the posterior error probability (PEP) for the identified peptide group. This column appears when the processing workflow includes the Percolator node. For information on how this node calculates the posterior error probability, see Percolator node. |
Percolator q-value | Displays the q-value for the identified peptide group. This column appears when the processing workflow includes the Percolator node. For information on how this node calculates the q-value, see Percolator node. |
Percolator SVMScore | Displays the maximum Percolator score for the identified decoy PSM. |
Protein Accessions | Displays the unique identifiers (accessions) of all decoy proteins from all decoy protein groups that include the given peptide sequence. The identifiers displayed in the Protein Group Accessions column are the same as those displayed in the Accession column on the Proteins and PSMs pages. |
Protein Descriptions | Describes the proteins associated with the peptide. This description is taken from the FASTA file. |
PSM Ambiguity | Displays the grouping status of the PSM from the following categories:
For more information on the protein group inference process that the application uses to assign the grouping status of PSMs, see Understanding protein grouping. |
Rank | Displays the ordering of peptides by rank. |
Search Engine Rank | Displays the original rank that the search engine assigned for all PSMs and peptide groups. |
Search ID | Displays the order that the application submitted the search to the job queue. |
Sequence | Displays the sequence of amino acids that compose a peptide. Modified amino acids are shown in lowercase letters. In the Unmodified Sequence column, the sequence is displayed in capital letters. |
Spectral angle | The correlation between the theoretical and experimental spectra calculated by the INFERYS Rescoring node. |
Spectrum File | Displays the name of the file containing the spectra. |
Theo. MH+ [Da] | Displays the MH+ mass, in daltons, calculated from the amino acid sequence, including the modifications. It is the expected mass, as opposed to the measured mass in the MH+ [Da] column. |
Total Ions | Displays the total possible number of ions. |
XCorr (Sequest HT searches only) | Scores the number of fragment ions that are common to two different peptides with the same precursor mass and calculates the cross-correlation score for all candidate peptides queried from the database. |
DCn | Displays the normalized score difference between the currently selected PSM and the highest-scoring PSM for that spectrum. |
DM [ppm] | Displays the difference between the theoretical mass of the peptide and the experimental mass of the precursor ion. |
Dm/z [Da] | Displays the difference between the measured charged mass (m/z [Da]) and the theoretical mass of the same charge (z). |