spc

Documentation

Index

• type AlternativeProtein
• type AminoacidModification
• type AnalysisResult
• type AnalysisSummary
• type Annotation
• type DataFormat
• type DistributionPoint
• type IndistinguishablePeptide
• type IndistinguishableProtein
• type InterProphetResult
• type ModAminoAcidProbability
• type ModAminoacidMass
• type ModificationInfo
• type MsmsPipelineAnalysis
• type MsmsRunSummary
• type PTMProphetResult
• type PTMResult
• type Parameter
• type PepXML
  • func (p *PepXML) Parse(f string)
• type Peptide
• type PeptideParentProtein
• type PeptideProphetResult
• type PeptideprophetSummary
• type ProgramDetails
• type ProphetModel
• type ProtXML
  • func (p *ProtXML) Parse(f string)
• type Protein
• type ProteinGroup
• type ProteinProphetDetails
• type ProteinSummary
• type ProteinSummaryHeader
• type SearchDatabase
• type SearchHit
• type SearchResult
• type SearchScore
• type SearchScoreSummary
• type SearchSummary
• type Specificity
• type SpectrumQuery
• type TerminalModification

Types

type AlternativeProtein

type AlternativeProtein struct {
	Protein   []byte `xml:"protein,attr"`
	PepPrevAA []byte `xml:"peptide_prev_aa,attr"`
	PepNextAA []byte `xml:"peptide_next_aa,attr"`
}

AlternativeProtein tag

type AminoacidModification

type AminoacidModification struct {
	AminoAcid []byte  `xml:"aminoacid,attr"`
	MassDiff  float64 `xml:"massdiff,attr"`
	Mass      float64 `xml:"mass,attr"`
	Variable  []byte  `xml:"variable,attr"`
}

AminoacidModification tag

type AnalysisResult

type AnalysisResult struct {
	Analysis             []byte               `xml:"analysis,attr"`
	PeptideProphetResult PeptideProphetResult `xml:"peptideprophet_result"`
	InterProphetResult   InterProphetResult   `xml:"interprophet_result"`
	PTMProphetResult     []PTMProphetResult   `xml:"ptmprophet_result"`
}

AnalysisResult tag

type AnalysisSummary

type AnalysisSummary struct {
	Analysis              []byte                `xml:"analysis,attr"`
	PeptideprophetSummary PeptideprophetSummary `xml:"peptideprophet_summary"`
}

AnalysisSummary struct

type Annotation

type Annotation struct {
	ProteinDescription []byte `xml:"protein_description,attr"`
}

Annotation tag

type DataFormat

type DataFormat interface {
	Parse()
}

DataFormat defines different types of data formats from the SPC

type DistributionPoint

type DistributionPoint struct {
	Fvalue         float64 `xml:"fvalue,attr"`
	Obs1Distr      float64 `xml:"obs_1_distr,attr"`
	Model1PosDistr float64 `xml:"model_1_pos_distr,attr"`
	Model1NegDistr float64 `xml:"model_1_neg_distr,attr"`
	Obs2Distr      float64 `xml:"obs_2_distr,attr"`
	Model2PosDistr float64 `xml:"model_2_pos_distr,attr"`
	Model2NegDistr float64 `xml:"model_2_neg_distr,attr"`
	Obs3Distr      float64 `xml:"obs_3_distr,attr"`
	Model3PosDistr float64 `xml:"model_3_pos_distr,attr"`
	Model3NegDistr float64 `xml:"model_3_neg_distr,attr"`
	Obs4Distr      float64 `xml:"obs_4_distr,attr"`
	Model4PosDistr float64 `xml:"model_4_pos_distr,attr"`
	Model4NegDistr float64 `xml:"model_4_neg_distr,attr"`
	Obs5Distr      float64 `xml:"obs_5_distr,attr"`
	Model5PosDistr float64 `xml:"model_5_pos_distr,attr"`
	Model5NegDistr float64 `xml:"model_5_neg_distr,attr"`
	Obs6Distr      float64 `xml:"obs_6_distr,attr"`
	Model6PosDistr float64 `xml:"model_6_pos_distr,attr"`
	Model6NegDistr float64 `xml:"model_6_neg_distr,attr"`
	Obs7Distr      float64 `xml:"obs_7_distr,attr"`
	Model7PosDistr float64 `xml:"model_7_pos_distr,attr"`
	Model7NegDistr float64 `xml:"model_7_neg_distr,attr"`
}

DistributionPoint ...

type IndistinguishablePeptide

type IndistinguishablePeptide struct {
	XMLName            xml.Name `xml:"indistinguishable_peptide"`
	PeptideSequence    []byte   `xml:"peptide_sequence,attr"`
	Charge             uint8    `xml:"charge,attr"`
	CalcNeutralPepMass float32  `xml:"calc_neutral_pep_mass,attr"`
}

IndistinguishablePeptide tag

type IndistinguishableProtein

type IndistinguishableProtein struct {
	ProteinName string `xml:"protein_name,attr"`
}

IndistinguishableProtein tag

type InterProphetResult

type InterProphetResult struct {
	Probability float64 `xml:"probability,attr"`
}

InterProphetResult tag

type ModAminoAcidProbability

type ModAminoAcidProbability struct {
	Position    int     `xml:"position,attr"`
	Probability float32 `xml:"probability,attr"`
}

ModAminoAcidProbability tag

type ModAminoacidMass

type ModAminoacidMass struct {
	Position int     `xml:"position,attr"`
	Mass     float64 `xml:"mass,attr"`
}

ModAminoacidMass tag

type ModificationInfo

type ModificationInfo struct {
	ModNTermMass     float64            `xml:"mod_nterm_mass,attr"`
	ModCTermMass     float64            `xml:"mod_cterm_mass,attr"`
	ModifiedPeptide  []byte             `xml:"modified_peptide,attr"`
	ModAminoacidMass []ModAminoacidMass `xml:"mod_aminoacid_mass"`
}

ModificationInfo tag

type MsmsPipelineAnalysis

type MsmsPipelineAnalysis struct {
	Date            []byte            `xml:"date,attr"`
	SummaryXML      []byte            `xml:"summary_xml,attr"`
	AnalysisSummary []AnalysisSummary `xml:"analysis_summary"`
	MsmsRunSummary  MsmsRunSummary    `xml:"msms_run_summary"`
}

MsmsPipelineAnalysis tag

type MsmsRunSummary

type MsmsRunSummary struct {
	BaseName       []byte          `xml:"base_name,attr"`
	SearchEngine   []byte          `xml:"search_engine,attr"`
	MsmsRunRummary []byte          `xml:"msms_run_summary,attr"`
	MsManufacturer []byte          `xml:"msManufacturer,attr"`
	MsModel        []byte          `xml:"msModel,attr"`
	MsIonization   []byte          `xml:"msIonization,attr"`
	MsMassAnalyzer []byte          `xml:"msMassAnalyzer,attr"`
	MsDetector     []byte          `xml:"msDetector,attr"`
	RawDataType    []byte          `xml:"raw_data_type,attr"`
	RawData        []byte          `xml:"raw_data,attr"`
	SearchSummary  SearchSummary   `xml:"search_summary"`
	SpectrumQuery  []SpectrumQuery `xml:"spectrum_query"`
}

MsmsRunSummary tag

type PTMProphetResult

type PTMProphetResult struct {
	PTM                     []byte                    `xml:"ptm,attr"`
	PTMPeptide              []byte                    `xml:"ptm_peptide,attr"`
	ModAminoAcidProbability []ModAminoAcidProbability `xml:"mod_aminoacid_probability"`
}

PTMProphetResult tag

type PTMResult

type PTMResult struct {
	ScoreBestPosition        string `xml:"score_best_position,attr"`
	IonsBestPosition         string `xml:"ions_best_position,attr"`
	ScoreSecondBestPosition  string `xml:"score_second_best_position,attr"`
	IonsSecondBestPosition   string `xml:"ions_second_best_position,attr"`
	ScoreAllUnshifted        string `xml:"score_all_unshifted,attr"`
	IonsAllUnshifted         string `xml:"ions_all_unshifted,attr"`
	LocalizationPeptide      string `xml:"localization_peptide,attr"`
	PositionScores           string `xml:"position_scores,attr"`
	ScoreShiftedAllPositions string `xml:"score_shifted_all_positions,attr"`
	IonsShiftedAllPositions  string `xml:"ions_shifted_all_positions,attr"`
	ScoreShiftedBestPosition string `xml:"score_shifted_best_position,attr"`
	IonsShiftedBestPosition  string `xml:"ions_shifted_best_position,attr"`
	ShiftedOnlyScores        string `xml:"shifted_only_position_scores,attr"`
	ShiftedOnlyIons          string `xml:"shifted_only_position_ions,attr"`
	BestPositions            string `xml:"best_positions,attr"`
	NumberBestPositions      string `xml:"number_best_positions,attr"`
}

PTMResult tag

type Parameter

type Parameter struct {
	Name  string `xml:"name,attr"`
	Value string `xml:"value,attr"`
}

Parameter tag

type PepXML

type PepXML struct {
	Name                 string
	MsmsPipelineAnalysis MsmsPipelineAnalysis
}

PepXML is the root tag

func (*PepXML) Parse

func (p *PepXML) Parse(f string)

type Peptide

type Peptide struct {
	PeptideSequence         []byte                 `xml:"peptide_sequence,attr"`
	Charge                  uint8                  `xml:"charge,attr"`
	InitialProbability      float64                `xml:"initial_probability,attr"`
	Weight                  float64                `xml:"weight,attr"`
	GroupWeight             float64                `xml:"group_weight,attr"`
	IsNondegenerateEvidence []byte                 `xml:"is_nondegenerate_evidence,attr"`
	NEnzymaticTermini       uint8                  `xml:"n_enzymatic_termini,attr"`
	CalcNeutralPepMass      float64                `xml:"calc_neutral_pep_mass,attr"`
	ModificationInfo        ModificationInfo       `xml:"modification_info"`
	PeptideParentProtein    []PeptideParentProtein `xml:"peptide_parent_protein"`
}

Peptide tag

type PeptideParentProtein

type PeptideParentProtein struct {
	ProteinName []byte `xml:"protein_name,attr"`
}

PeptideParentProtein tag

type PeptideProphetResult

type PeptideProphetResult struct {
	Probability float64 `xml:"probability,attr"`
}

PeptideProphetResult tag

type PeptideprophetSummary

type PeptideprophetSummary struct {
	DistributionPoint []DistributionPoint `xml:"distribution_point"`
}

PeptideprophetSummary struct

type ProgramDetails

type ProgramDetails struct {
	Analysis              []byte                `xml:"analysis,attr"`
	Time                  []byte                `xml:"time,attr"`
	Version               []byte                `xml:"version,attr"`
	ProteinProphetDetails ProteinProphetDetails `xml:"proteinprophet_details"`
}

ProgramDetails tag

type ProphetModel

type ProphetModel struct {
	Charge uint8
	Points map[string]uint8
}

ProphetModel tag

type ProtXML

type ProtXML struct {
	Name           string
	ProteinSummary ProteinSummary
}

ProtXML is the root tag

func (*ProtXML) Parse

func (p *ProtXML) Parse(f string)

Parse is the main function for parsing pepxml data

type Protein

type Protein struct {
	ProteinName                     []byte                     `xml:"protein_name,attr"`
	UniqueStrippedPeptides          []byte                     `xml:"unique_stripped_peptides,attr"`
	GroupSiblingID                  []byte                     `xml:"group_sibling_id,attr"`
	NumberIndistinguishableProteins int32                      `xml:"n_indistinguishable_proteins,attr"`
	TotalNumberPeptides             int                        `xml:"total_number_peptides,attr"`
	TotalNumberIndPeptides          int                        `xml:"total_number_distinct_peptides,attr"`
	PercentCoverage                 float32                    `xml:"percent_coverage,attr"`
	PctSpectrumIDs                  float32                    `xml:"pct_spectrum_ids,attr"`
	Probability                     float64                    `xml:"probability,attr"`
	Parameter                       Parameter                  `xml:"parameter"`
	Annotation                      Annotation                 `xml:"annotation"`
	IndistinguishableProtein        []IndistinguishableProtein `xml:"indistinguishable_protein"`
	Peptide                         []Peptide                  `xml:"peptide"`
}

Protein tag

type ProteinGroup

type ProteinGroup struct {
	GroupNumber uint32    `xml:"group_number,attr"`
	Probability float64   `xml:"probability,attr"`
	Protein     []Protein `xml:"protein"`
}

ProteinGroup tag

type ProteinProphetDetails

type ProteinProphetDetails struct {
	XMLName               xml.Name `xml:"proteinprophet_details"`
	OccamFlag             []byte   `xml:"occam_flag,attr"`
	GroupsFlag            []byte   `xml:"groups_flag,attr"`
	DegenFlag             []byte   `xml:"degen_flag,attr"`
	NSPFlag               []byte   `xml:"nsp_flag,attr"`
	FPKMFlag              []byte   `xml:"fpkm_flag,attr"`
	InitialPeptideWtIters []byte   `xml:"initial_peptide_wt_iters,attr"`
	NspDistributionIters  []byte   `xml:"nsp_distribution_iters,attr"`
	FinalPeptideWtIters   []byte   `xml:"final_peptide_wt_iters,attr"`
	RunOptions            []byte   `xml:"run_options,attr"`
}

ProteinProphetDetails tag

type ProteinSummary

type ProteinSummary struct {
	ProteinSummaryHeader ProteinSummaryHeader `xml:"protein_summary_header"`
	ProteinGroup         []ProteinGroup       `xml:"protein_group"`
}

ProteinSummary tag is the root level

type ProteinSummaryHeader

type ProteinSummaryHeader struct {
	MinPeptideProbability       float32        `xml:"min_peptide_probability,attr"`
	MinPeptideWeight            float32        `xml:"min_peptide_weight,attr"`
	NumPredictedCorrectProteins float32        `xml:"num_predicted_correct_prots,attr"`
	TotalNumberSpectrumIDs      float32        `xml:"total_no_spectrum_ids,attr"`
	NumInput1Spectra            uint32         `xml:"num_input_1_spectra,attr"`
	NumInput2Spectra            uint32         `xml:"num_input_2_spectra,attr"`
	NumInput3Spectra            uint32         `xml:"num_input_3_spectra,attr"`
	NumInput4Spectra            uint32         `xml:"num_input_4_spectra,attr"`
	NumInput5Spectra            uint32         `xml:"num_input_5_spectra,attr"`
	ProgramDetails              ProgramDetails `xml:"program_details"`
}

ProteinSummaryHeader tag

type SearchDatabase

type SearchDatabase struct {
	XMLName   xml.Name `xml:"search_database"`
	LocalPath []byte   `xml:"local_path,attr"`
	Type      []byte   `xml:"type,attr"`
}

SearchDatabase tag

type SearchHit

type SearchHit struct {
	HitRank             uint8                `xml:"hit_rank,attr"`
	Peptide             []byte               `xml:"peptide,attr"`
	PrevAA              []byte               `xml:"peptide_prev_aa,attr"`
	NextAA              []byte               `xml:"peptide_next_aa,attr"`
	Protein             []byte               `xml:"protein,attr"`
	Class               []byte               `xml:"group,attr"`
	TotalTerm           uint8                `xml:"num_tol_term,attr"`
	MissedCleavages     uint8                `xml:"num_missed_cleavages,attr"`
	IsRejected          uint8                `xml:"is_rejected,attr"`
	TotalProteins       uint32               `xml:"num_tot_proteins,attr"`
	MatchedIons         uint16               `xml:"num_matched_ions,attr"`
	TotalIons           uint16               `xml:"tot_num_ions,attr"`
	MatchedPeptides     uint32               `xml:"num_matched_peptides,attr"`
	CalcNeutralPepMass  float64              `xml:"calc_neutral_pep_mass,attr"`
	Massdiff            float64              `xml:"massdiff,attr"`
	ModificationInfo    ModificationInfo     `xml:"modification_info"`
	Score               []SearchScore        `xml:"search_score"`
	AnalysisResult      []AnalysisResult     `xml:"analysis_result"`
	AlternativeProteins []AlternativeProtein `xml:"alternative_protein"`
	PTMResult           PTMResult            `xml:"ptm_result"`
}

SearchHit tag

type SearchResult

type SearchResult struct {
	SearchHit []SearchHit `xml:"search_hit"`
}

SearchResult tag

type SearchScore

type SearchScore struct {
	Name  []byte `xml:"name,attr"`
	Value string `xml:"value,attr"`
}

SearchScore tag

type SearchScoreSummary

type SearchScoreSummary struct {
	XMLName   xml.Name    `xml:"search_score_summary"`
	Parameter []Parameter `xml:"parameter"`
}

SearchScoreSummary tag

type SearchSummary

type SearchSummary struct {
	SearchID               uint16                  `xml:"search_id,attr"`
	BaseName               []byte                  `xml:"base_name,attr"`
	SearchEngine           []byte                  `xml:"search_engine,attr"`
	SearchEngineVersion    []byte                  `xml:"search_engine_version,attr"`
	SearchDatabase         SearchDatabase          `xml:"search_database"`
	AminoAcidModifications []AminoacidModification `xml:"aminoacid_modification"`
	TerminalModifications  []TerminalModification  `xml:"terminal_modification"`
	Parameter              []Parameter             `xml:"parameter"`
}

SearchSummary tag

type Specificity

type Specificity struct {
	Xmlname xml.Name `xml:"specificity"`
	Cut     []byte   `xml:"cut,attr"`
	NoCut   []byte   `xml:"no_cut,attr"`
	Sense   []byte   `xml:"sense,attr"`
}

Specificity tag

type SpectrumQuery

type SpectrumQuery struct {
	CompensationVoltage              string       `xml:"compensation_voltage,attr"`
	Spectrum                         []byte       `xml:"spectrum,attr"`
	StartScan                        int          `xml:"start_scan,attr"`
	EndScan                          int          `xml:"end_scan,attr"`
	AssumedCharge                    uint8        `xml:"assumed_charge,attr"`
	Index                            uint32       `xml:"index,attr"`
	RetentionTimeSec                 float64      `xml:"retention_time_sec,attr"`
	IonMobility                      float64      `xml:"ion_mobility,attr"`
	UncalibratedPrecursorNeutralMass float64      `xml:"uncalibrated_precursor_neutral_mass,attr"`
	PrecursorNeutralMass             float64      `xml:"precursor_neutral_mass,attr"`
	SearchResult                     SearchResult `xml:"search_result"`
}

SpectrumQuery tag

type TerminalModification

type TerminalModification struct {
	MassDiff float64 `xml:"massdiff,attr"`
	Mass     float64 `xml:"mass,attr"`
	Terminus []byte  `xml:"terminus,attr"`
	Variable []byte  `xml:"variable,attr"`
}

TerminalModification tag