OpenSwathLibraryPreparation.h File Reference

#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/DATASTRUCTURES/Param.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/config.h>
#include <string>
#include <utility>
#include <vector>

Go to the source code of this file.

Classes
class	OpenSwathLibraryPreparation
	Shared spectral-library preparation helper for OpenSWATH-family workflows. More...
struct	OpenSwathLibraryPreparation::LibraryStats
struct	OpenSwathLibraryPreparation::AssayGeneratorParameters
struct	OpenSwathLibraryPreparation::PredictedLibraryParameters
struct	OpenSwathLibraryPreparation::DecoyGeneratorParameters

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

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Class Documentation

OpenMS::OpenSwathLibraryPreparation::AssayGeneratorParameters

struct OpenMS::OpenSwathLibraryPreparation::AssayGeneratorParameters

Class Members
vector< size_t >	allowed_fragment_charges {1, 2, 3, 4}
vector< string >	allowed_fragment_types {"b", "y"}
bool	disable_decoy_transitions = false
bool	enable_detection_specific_losses = false
bool	enable_detection_unspecific_losses = false
bool	enable_identification_ms2_precursors = true
bool	enable_identification_specific_losses = true
bool	enable_identification_unspecific_losses = false
bool	enable_ipf = false
bool	enable_swath_specifity = false
int	ipf_decoy_seed = 1
size_t	max_num_alternative_localizations = 10000
Int	max_transitions = 6
Int	min_transitions = 6
double	precursor_lower_mz_limit = 400.0
double	precursor_mz_threshold = 0.025
double	precursor_upper_mz_limit = 1200.0
double	product_lower_mz_limit = 350.0
double	product_mz_threshold = 0.025
double	product_upper_mz_limit = 2000.0
bool	reuse_existing_modifications_db = false
vector< pair< double, double > >	swathes
bool	test_mode = false
string	unimod_file

OpenMS::OpenSwathLibraryPreparation::PredictedLibraryParameters

struct OpenMS::OpenSwathLibraryPreparation::PredictedLibraryParameters

Class Members
string	ccs_model_path
bool	clip_nterm_methionine {}
string	enzyme
vector< string >	fixed_modifications
Int	inference_threads {}
Int	instrument_index {}
Size	max_peptide_length {}
Size	max_variable_modifications {}
Size	min_peptide_length {}
Size	missed_cleavages {}
string	ms2_model_path
double	nce {}
vector< Int >	precursor_charges
bool	predict_ccs {}
Size	prediction_batch_size {}
string	rt_model_path
vector< string >	variable_modifications

OpenMS::OpenSwathLibraryPreparation::DecoyGeneratorParameters

struct OpenMS::OpenSwathLibraryPreparation::DecoyGeneratorParameters

Class Members
double	aim_decoy_fraction = 1.0
vector< size_t >	allowed_fragment_charges {1, 2, 3, 4}
vector< string >	allowed_fragment_types {"b", "y"}
string	decoy_tag = "DECOY_"
bool	enable_detection_specific_losses = false
bool	enable_detection_unspecific_losses = false
string	method = "shuffle"
double	min_decoy_fraction = 0.8
double	product_mz_threshold = 0.025
bool	separate = false
double	shift_precursor_mz_shift = 0.0
double	shift_product_mz_shift = 20.0
Int	shuffle_max_attempts = 30
Int	shuffle_seed = 1	Shuffle RNG seed: 1 gives reproducible decoys, -1 uses the current time.
double	shuffle_sequence_identity_threshold = 0.5
bool	switch_kr = true