OpenSearchModificationAnalysis.h File Reference

#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <map>
#include <vector>
#include <unordered_map>
#include <unordered_set>

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Classes
class	OpenSearchModificationAnalysis
	Utility class for analyzing modification patterns in open search results. More...
struct	OpenSearchModificationAnalysis::ModificationPattern
	Stores details of a modification pattern found in the data. More...
struct	OpenSearchModificationAnalysis::ModificationSummary
	Data structure for modification summary output. More...
struct	OpenSearchModificationAnalysis::DeltaMassEntry
	Statistics for a single delta mass bin in the histogram. More...
struct	OpenSearchModificationAnalysis::PTMEntry
	Statistics for a mapped PTM. More...
struct	OpenSearchModificationAnalysis::DeltaMassStatistics
	Container for delta mass statistics table. More...
struct	OpenSearchModificationAnalysis::PTMStatistics
	Container for PTM statistics table. More...
struct	OpenSearchModificationAnalysis::OpenSearchAnalysisResult
	Combined result of open search modification analysis. More...
struct	OpenSearchModificationAnalysis::FuzzyDoubleComparator
	Comparator for approximate comparison of double values. More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

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Class Documentation

OpenMS::OpenSearchModificationAnalysis::ModificationPattern

struct OpenMS::OpenSearchModificationAnalysis::ModificationPattern

Stores details of a modification pattern found in the data.

Collaboration diagram for OpenSearchModificationAnalysis::ModificationPattern:

Class Members
double	count = 0.0	Number of peptides with this modification.
vector< double >	masses	Masses associated with the modification.
int	num_charge_states = 0	Number of different charge states observed.

OpenMS::OpenSearchModificationAnalysis::ModificationSummary

struct OpenMS::OpenSearchModificationAnalysis::ModificationSummary

Data structure for modification summary output.

Collaboration diagram for OpenSearchModificationAnalysis::ModificationSummary:

Class Members
int	count	Modification rate (number of occurrences)
vector< double >	masses	Masses associated with the modification.
String	name	Modification name.
int	num_charge_states	Number of charge states.

OpenMS::OpenSearchModificationAnalysis::DeltaMassEntry

struct OpenMS::OpenSearchModificationAnalysis::DeltaMassEntry

Statistics for a single delta mass bin in the histogram.

Collaboration diagram for OpenSearchModificationAnalysis::DeltaMassEntry:

Class Members
int	count = 0	Number of PSMs with this delta mass.
double	delta_mass = 0.0	Central delta mass value.
bool	is_known_modification = false	Whether this maps to a known modification.
String	mapped_modification = ""	Name of mapped modification (if any)
int	num_charge_states = 0	Number of different charge states observed.
double	percentage = 0.0	Percentage of total PSMs.
int	unique_peptides = 0	Number of unique peptide sequences.

OpenMS::OpenSearchModificationAnalysis::PTMEntry

struct OpenMS::OpenSearchModificationAnalysis::PTMEntry

Statistics for a mapped PTM.

Collaboration diagram for OpenSearchModificationAnalysis::PTMEntry:

Class Members
int	count = 0	Number of PSMs with this modification.
double	mass_deviation = 0.0	Deviation between theoretical and observed.
String	name	Modification name (e.g., "Oxidation (M)")
int	num_charge_states = 0	Number of different charge states observed.
double	observed_mass = 0.0	Mean observed delta mass.
double	percentage = 0.0	Percentage of total modified PSMs.
map< char, int >	residue_counts	Count per amino acid residue.
String	target_residues	Target residues for this modification.
double	theoretical_mass = 0.0	Theoretical mass shift from ModificationsDB.
int	unique_peptides = 0	Number of unique peptide sequences.

OpenMS::OpenSearchModificationAnalysis::DeltaMassStatistics

struct OpenMS::OpenSearchModificationAnalysis::DeltaMassStatistics

Container for delta mass statistics table.

Collaboration diagram for OpenSearchModificationAnalysis::DeltaMassStatistics:

Class Members
vector< DeltaMassEntry >	entries	All delta mass entries.
double	mean_delta_mass = 0.0	Mean delta mass (excluding unmodified)
double	median_delta_mass = 0.0	Median delta mass (excluding unmodified)
int	modified_psms = 0	PSMs with non-zero delta mass.
int	total_psms = 0	Total number of PSMs analyzed.
int	unmodified_psms = 0	PSMs with ~zero delta mass.

OpenMS::OpenSearchModificationAnalysis::PTMStatistics

struct OpenMS::OpenSearchModificationAnalysis::PTMStatistics

Container for PTM statistics table.

Collaboration diagram for OpenSearchModificationAnalysis::PTMStatistics:

Class Members
vector< PTMEntry >	entries	All PTM entries.
int	num_unique_modifications = 0	Number of distinct modifications found.
int	total_modified_psms = 0	Total PSMs with mapped modifications.
int	unknown_modification_psms = 0	PSMs with unknown modifications.

OpenMS::OpenSearchModificationAnalysis::OpenSearchAnalysisResult

struct OpenMS::OpenSearchModificationAnalysis::OpenSearchAnalysisResult

Combined result of open search modification analysis.

Collaboration diagram for OpenSearchModificationAnalysis::OpenSearchAnalysisResult:

Class Members
DeltaMassStatistics	delta_mass_stats	Delta mass histogram statistics.
PTMStatistics	ptm_stats	Mapped PTM statistics.
vector< ModificationSummary >	summaries	Legacy modification summaries.