Classes
class	AlignmentMethod

class	CborOutputStream

class	JsonInput

class	MbrPeptideMeasurements

class	MsRun

class	MsRunGroup

class	MsRunPeptideList

class	Peptide

class	PeptideBase

class	PeptideLabel

class	PeptideMeasurements

class	PeptideMeasurementsBase

class	PeptideObservation

class	Precursor
	A Precursor object represents the parent/precursor of the MS level 2 scan with number _scan_num in the mzxml file. More...

class	PrecursorParser

class	Protein

class	QuantificationMethod

class	Utils

Typedefs
typedef std::shared_ptr< AlignmentMethod >	AlignmentMethodSp

typedef std::shared_ptr< MbrPeptideMeasurements >	MbrPeptideMeasurementsSp

typedef std::shared_ptr< MsRun >	MsRunSp

typedef std::shared_ptr< MsRunGroup >	MsRunGroupSp

typedef std::shared_ptr< MsRunPeptideList >	MsRunPeptideListSp

typedef std::shared_ptr< Peptide >	PeptideSp

typedef std::shared_ptr< PeptideLabel >	PeptideLabelSp

typedef std::shared_ptr< PeptideObservation >	PeptideObservationSp

typedef std::shared_ptr< PeptideMeasurements >	PeptideMeasurementsSp

typedef std::shared_ptr< Precursor >	PrecursorSp

typedef std::shared_ptr< Protein >	ProteinSp

typedef std::shared_ptr< QuantificationMethod >	QuantificationMethodSp

Enumerations
enum class	PeakQualityCategory : std::int8_t { nomatch , aa , a , ab , zaa , za , zab , b , c , d , post_matching , missed , last }

Variables
class PMSPP_LIB_DECL	AlignmentMethod

Typedef Documentation

◆ AlignmentMethodSp

typedef std::shared_ptr<AlignmentMethod> pappso::masschroq::AlignmentMethodSp

Definition at line 42 of file alignmentmethod.h.

◆ MbrPeptideMeasurementsSp

typedef std::shared_ptr<MbrPeptideMeasurements> pappso::masschroq::MbrPeptideMeasurementsSp

Definition at line 44 of file mbrpeptidemeasurements.h.

◆ MsRunGroupSp

typedef std::shared_ptr<MsRunGroup> pappso::masschroq::MsRunGroupSp

Definition at line 42 of file msrungroup.h.

◆ MsRunPeptideListSp

typedef std::shared_ptr<MsRunPeptideList> pappso::masschroq::MsRunPeptideListSp

Definition at line 47 of file msrunpeptidelist.h.

◆ MsRunSp

typedef std::shared_ptr<MsRun> pappso::masschroq::MsRunSp

Definition at line 44 of file msrun.h.

◆ PeptideLabelSp

typedef std::shared_ptr<PeptideLabel> pappso::masschroq::PeptideLabelSp

Definition at line 52 of file peptide.h.

◆ PeptideMeasurementsSp

typedef std::shared_ptr<PeptideMeasurements> pappso::masschroq::PeptideMeasurementsSp

Definition at line 50 of file peptidemeasurements.h.

◆ PeptideObservationSp

typedef std::shared_ptr< PeptideObservation > pappso::masschroq::PeptideObservationSp

Definition at line 45 of file peptidemeasurements.h.

◆ PeptideSp

typedef std::shared_ptr<Peptide> pappso::masschroq::PeptideSp

Definition at line 46 of file peptide.h.

◆ PrecursorSp

typedef std::shared_ptr<Precursor> pappso::masschroq::PrecursorSp

Definition at line 39 of file precursor.h.

◆ ProteinSp

typedef std::shared_ptr<Protein> pappso::masschroq::ProteinSp

Definition at line 39 of file protein.h.

◆ QuantificationMethodSp

typedef std::shared_ptr<QuantificationMethod> pappso::masschroq::QuantificationMethodSp

Definition at line 46 of file quantificationmethod.h.

Enumeration Type Documentation

◆ PeakQualityCategory

enum class pappso::masschroq::PeakQualityCategory : std::int8_t

strong

Enumerator
nomatch	there is no category, because no matching is done (mz list for example)
aa	best possible : more than one direct MS2 fragmentation in same MSRUN
a	peak detected using a single direct MS2 observation
ab	peak detected using direct MS2 observation... but the peak is fragmented. all MS2 retention times are not givins the same peak
zaa
za
zab
b	less good : match between run, peak found at the aligned retention time
c	less good : match between run, peak found at the aligned retention time, but multiple choice
d	less good : match between run, peak found but in the margin of peak (second chance)
post_matching	post matching category : new retention times are computed using real XIC, and aligned rt give a match
missed	no peak found at all
last

Definition at line 41 of file types.h.

{
  nomatch, ///< there is no category, because no matching is done (mz list for
           ///< example)
  aa,  ///< best possible : more than one direct MS2 fragmentation in same MSRUN
  a,   ///< peak detected using a single direct MS2 observation
  ab,  ///< peak detected using direct MS2 observation... but the peak is
       ///< fragmented. all MS2 retention times are not givins the same peak
  zaa, ///<
  za,  ///<
  zab, ///<
  b,   ///< less good : match between run, peak found at the aligned retention
       ///< time
  c,   ///< less good : match between run, peak found at the aligned retention
       ///< time, but multiple choice
  d,   ///< less good : match between run, peak found but in the margin of peak
       ///< (second chance)
  post_matching, ///< post matching category : new retention times are computed
                 ///< using real XIC, and aligned rt give a match
  missed,        ///< no peak found at all
  last
};

Variable Documentation

◆ AlignmentMethod

class PMSPP_LIB_DECL pappso::masschroq::AlignmentMethod

Definition at line 40 of file alignmentmethod.h.

Classes

Typedefs

Enumerations

Variables