Peptide Groups Page Columns - Proteome Discoverer Software - Peptide Groups Page Columns - Proteome Discoverer Software - Proteome Discoverer Software

# 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 when all peptides have been completely digested.

# Protein Groups

Displays the number of protein groups containing the peptide.

# Proteins

Displays the total number of identified proteins containing the peptide.

# PSMs

Displays the total number of identified PSMs in the peptide group, including those redundantly identified.

Abundance Ratios

Displays the abundance ratios as normal space values.

This column appears when there are sample ratios defined in the analysis setup.

Abundance Ratios (by Bio. Rep.)

Displays the abundance ratios of the biological replicates as normal space values.

Abundance Ratios (log2)

Displays the abundance ratios as log2 ratios.

Abundance Ratios (log2) (by Bio. Rep.)

Displays the abundance ratios of the biological replicates as log2 values.

Abundances

Displays the abundances of the samples before scaling and normalization.

Abundances (by Bio. Rep.)

Displays the abundance values of the biological replicates.

Abundances (by Bio. Rep.) Counts

Displays the number of abundance values used to calculate the abundances of the biological replicates.

Abundances (Grouped)

Displays the abundance values of the sample groups.

A grouped abundance value is calculated as the arithmetic mean of all the replicate abundance values within a sample group. You can specify the sample grouping on the Grouping and Quantification page when you set up an analysis.

This column appears when you group samples in the analysis setup and there is at least one sample group consisting of at least two samples.

Abundances (Grouped) Counts

Displays the number of samples with detected abundance values used to calculate the abundance of the whole sample group.

Abundances (Grouped) Standard Errors [%]

Displays the standard error of the abundance values of the samples in a sample group, normalized to the group’s median abundance.

Abundances (Normalized)

Displays the normalized abundances values of the samples.

This column appears when you set the Normalization Mode parameter of the Precursor Ions Quantifier node or the Reporter Ions Quantifier node to Total Peptide Amount or Specific Protein Amount.

Abundances (Scaled)

Displays the normalized and scaled abundance values of the samples.

This column appears when you set the Scaling Mode parameter of the Precursor Ions Quantifier node or the Reporter Ions Quantifier node to On All Average or On Controls Average.

Abundances Counts

Displays the number of abundance values used to calculate the sample abundance.

Annotated Sequence

Displays the identified peptide sequence with the flanking residues from the master protein.

Charge (by Search Engine)

Displays the charge state of the peptide.

Checked

Indicates whether the item is selected.

Concatenated Rank (by Search Engine)

Displays the value for the “best” PSM found by the search engine. This value includes the rank of the decoy PSMs for the same spectra.

Confidence

Indicates a confidence level associated with the peptide group at the top level:

• Green: High confidence
• Yellow: Medium confidence
• Red: Low confidence

Confidence (by Search Engine)

Indicates a confidence level associated with the peptide group at the top level:

• Green: High confidence
• Yellow: Medium confidence
• Red: Low confidence

Found in Files

Represents the best confidence of the PSMs of the protein that the application identified in the files:

• Green: High confidence
• Yellow: Medium confidence
• Red: Low confidence
• Blue: Found but unidentified PSM. Only the results from precursor ion quantification searches contain blue boxes.

This column appears only when you include the Data Distributions node in the consensus workflow and set its Show Found in Files parameter to True.

Found in Fractions

Represents the best confidence of the PSMs of the protein that the application identified in the fractions. The colors of the boxes represent the following:

• Green: High confidence
• Yellow: Medium confidence
• Red: Low confidence
• Blue: Found but unidentified PSM. Only the results from precursor ion quantification searches contain blue boxes.

This column appears only when you include the Data Distributions node in the consensus workflow and set its Show Found in Fractions parameter to True.

Found in Sample Groups

Represents the best confidence of the PSMs of the protein that the application identified in the sample groups:

• Green: High confidence
• Yellow: Medium confidence
• Red: Low confidence
• Blue: Found but unidentified PSM. Only the results from precursor ion quantification searches contain blue boxes.
• Grey: n/a

This column appears only when you include the Data Distributions node in the consensus workflow and set its Show Found in Sample Groups parameter to True.

Found in Samples

Represents the best confidence of the PSMs of the protein that the application identified in the samples:

• Green: High confidence
• Yellow: Medium confidence
• Red: Low confidence
• Blue: Found but unidentified PSM. Only the results from precursor ion quantification searches contain blue boxes.

This column appears only when you include the Data Distributions node in the consensus workflow and set its Show Found in Samples parameter to True.

m/z [Da] (by Search Engine)

Displays the mass-to-charge ratio of the precursor ion, in daltons.

Master Protein Accessions

Displays the unique identifiers (accessions) of all master proteins from all protein groups that include the given peptide sequence.

This column appears when you use the Protein Grouping node in the consensus workflow.

Master Protein Descriptions

Displays a description of the master proteins.

Modifications

Displays all the PTMs identified for the given peptide. The sites are displayed only for fixed modifications or for variable modifications when the confidence level is above the threshold set by the IMP-ptmRS node. They are indexed to the local sequence of the peptide, not to the master protein.

Modifications (All Possible Sites)

Displays all modifications found in the PSMs of a peptide group. They are indexed to the local sequence of the peptide, not to the master protein.

Modifications in Master Proteins

Displays the positions of the modifications in the master proteins only if the confidence level is above the threshold set by the IMP-ptmRS node.

Channel Occupancy [%}

Displays the percentage of the quan channels that have non-zero abundance for the peptide. This value is calculated by the Reporter Ions Quantifier node.

Modifications in Master Proteins (All Sites)

Displays the positions of the modifications in the master proteins with confidence levels returned by the IMP-ptmRS node.

Percolator PEP (by Search Engine)

Displays the posterior error probability (PEP) of the best PSM of the peptide group that the search node identified.

This column appears when the consensus workflow includes the Percolator node. For information on how this node calculates the posterior error probability, see Posterior Error Probability (PEP).

Percolator q-Value (by Search Engine)

Displays the q-value of the best PSM of the peptide groups that the search node identified.

This column appears when the consensus workflow includes the Percolator node. For information on how this node calculates the q-value, see q-value.

Percolator SVMScore (by Search Engine)

Displays the maximum Percolator score for the identified peptide group.

This column appears when the consensus workflow includes the Peptide Validator node. For information on this node, see Peptide Validator node.

Positions in Master Proteins

Displays the positions of the peptide in the master protein.

Protein Accessions

Displays the unique identifiers (accessions) of all proteins from all 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.

PSM Ambiguity

Displays the grouping status of the PSM in the peptide group. This column can display the following categories:

• Unambiguous: Indicates that this PSM is the only match that the application considered for this spectrum. There is no ambiguity that it needs to resolve.
• Selected: Indicates that the application selected this PSM from a set of two or more matches that it considered for the protein group inference process.
• Rejected: Indicates that the application rejected this PSM from a set of two or more matches that it considered for the protein group inference process.
• Ambiguous: Indicates that the application considered two or more peptide matches to the same spectrum for the protein group inference process. If you set the Apply Strict Maximum Parsimony Principle parameter of the Protein Grouping node to True in the consensus workflow, the application resolves this ambiguity to Selected or to Rejected.
• Unconsidered: Indicates that the application did not consider this PSM for the protein group inference process because it did not meet the requirements specified in the Protein Grouping (Enabled) settings in the Result Filters page.

For more information on the protein group inference process that the application uses to assign the grouping status of PSMs, see Understanding protein grouping.

Quan Info

Indicates why the application used or did not use a peptide in quantification. The possible reasons are:

• No Quan Values: Indicates that there are no usable quantification results.

(For reporter ion quantification)

• No Quan Labels: A label did not modify the peptide.
• Excluded by Method: Either the average S/N value of the peptide is lower than the thresholds set for the method or the precursor interference is higher than the thresholds set..
• Minimum Channel Occupancy Not Reached: The number of missing quantification values for this peptide exceeds the value allowed by the method.

(For precursor ion quantification)

• Inconsistently Labeled: Peptides do not always display the expected amount of isotopic labeling.
• Indistinguishable Channels: The peptide does not have amino acids that can have the specified labels, or it has the specified labels but has defined channels with the same delta masses, rendering the channels indistinguishable.
• Incompatible Labels: Indicates that the composition of a modification is not known.
• Redundant: Indicates that the quantification results of this peptide group are redundantly used.
• Is Not Reliable: Indicates that all PSMs classified as A1 triggers are excluded from the quantification.
• Excluded Modification: Indicates that a peptide group has specified modifications, which are defined by several parameters of the Precursor Ions Quantification node.
• Shared: Indicates that the peptide group is usable for quantification but is shared among different protein groups or proteins, depending on the setting of the Consider Protein Groups for Peptide Uniqueness parameter in the Reporter Ions Quantifier node.

Quality PEP

Displays the posterior error probability (PEP) for the identified peptide group.

This column appears when the consensus workflow includes the Peptide Validator node. For information on this node, see Peptide Validator node.

Quality q-value

Displays the q-value for the identified peptide group.

This column appears when the consensus workflow includes the Peptide Validator node. For information on this node, see Peptide Validator node.

Rank (by Search Engine)

Displays the ordering of peptides by rank.

RT [min] (by Search Engine)

Displays the retention time when the peptide was observed, in minutes.

Search Engine Rank (by Search Engine)

Displays the original rank assigned by the search engine for all PSMs and peptide groups.

Sequence

Displays the sequence of amino acids that compose the peptide in the peptide group.

Sequence Length

Displays the number of amino acids in a sequence.

SVM_Score

Displays the maximum Percolator score for the identified peptide group.

Theo. MH+ [Da]

Displays the mass calculated from the sequence, the amino acid masses, and the defined modification masses, as opposed to the measured mass.

DCn (by Search Engine)

Displays the normalized score difference between the currently selected PSM and the highest-scoring PSM for that spectrum.

DM [ppm] (by Search Engine)

Displays the difference between the theoretical mass of the peptide and the experimental mass of the precursor ion, in parts per million.

Dm/z [Da] (by Search Engine)

Displays the difference between the measured charged mass (m/z [Da]) and the theoretical mass of the same charge (z).

DScore (by Search Engine)

Displays a measure of the difference between the top two scores for the peptides identified by that spectrum. The application calculates this score as follows:

DScore = Score(Rank N Peptide) – Score(Rank 1 Peptide)/Score(Rank 1 Peptide).

For more information about the delta score calculation, see The Delta Score column.

Contaminant

Displays an X symbol next to the proteins marked as contaminants in the searched FASTA file or files.

This column appears when the consensus workflow includes the Protein Marker node. For more information, see Protein Marker node.

Ratio columns

Display the corrected ratio of the intensity of the reporter ion in a sample to the intensity of the reporter ion in the control sample.

XCorr search_engine_number node_number

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 (Sequest HT searches only).

Quan Usage

Shows which peptide abundances are used for protein quantification.

• Used: Indicates that the node used quantification abundances.
• Not Used: Indicates that the node did not use quantification abundances.

Species Map

Extracts from the FASTA database the species names for proteins and displays and annotates them as colored entries in a distribution map.

This column appears only when you include the Protein Marker node in the consensus workflow and set its As Species Map parameter to True.

Species

Extracts from the FASTA database the species names for proteins and displays and annotates them as semicolon-separated text.

This column appears only when you include the Protein Marker node in the consensus workflow and set its As Species Names parameter to True.

P-Value

Displays the p value for the sample group calculated by running the Tukey HSD test (post hoc) after an analysis of variance (ANOVA) test. For more information on p-values, see Calculate p-values and adjusted p-values for quantification results.

The p value is a number between 0 and 1. If the null hypothesis states that there is no difference between the sample groups for the variance tests, one of the following pertains:

• A low P value means there is a low probability that the null hypothesis is false; that is, the sample groups show a significant difference.
• A high P value means there is a high probability that the null hypothesis is true; that is, the sample groups do not show a significant difference.

The color-coding of the p-values is as follows:

Adj. P-Values

Displays the p-values adjusted by using the Benjamini-Hochberg correction for the false discovery rate. For more information on p-values, see Calculate p-values and adjusted p-values for quantification results.

The color-coding of the adjusted p-values is as follows: