This class encapsulates a peptide from the mascot results file. More...

#include <ms_peptide.hpp>

Public Types
enum	PSM { PSM_COMPLETE = 0 , PSM_CROSSLINK_ALPHA = 1 , PSM_CROSSLINK_BETA = 2 }
	Type of data to return from accessor methods. More...

enum	PSM_TYPE { PSM_STANDARD = 0 , PSM_DECOY = 1 , PSM_ERRTOL = 2 , PSM_ERRTOLDECOY = 3 , PSM_LIBRARY = 4 , PSM_CROSSLINK = 5 , N_PSM_TYPES = 6 }
	Specifies the search pass and origin of the peptide match. More...

Public Member Functions
	ms_peptide ()
	Default constructor.

	ms_peptide (const int query, const int rank, const SEARCH_PHASE searchPhase, const double delta, const double observed, const int charge, const int numIonsMatched, const int peaksUsedFromIons1, const double ionsScore, const std::string &seriesUsedStr, const int peaksUsedFromIons2, const int peaksUsedFromIons3, const ms_peptide &pepAlpha, const ms_peptide &pepBeta, const ms_linker_site &linkerSite, const ms_mascotresults *pResults=0, const bool storeReloadableInfo=true)
	Constructor to initialise a crosslinked peptide.

	ms_peptide (const int query, const int rank, const SEARCH_PHASE searchPhase, const int missedCleavages, const double mrCalc, const double delta, const double observed, const int charge, const int numIonsMatched, const std::string &peptideStr, const int peaksUsedFromIons1, const std::string &varModsStr, const std::string &summedModsStr, const std::string &localModsStr, const std::string &monoLinkStr, const ms_linker_site_vector &loopLinks, const double ionsScore, const std::string &seriesUsedStr, const int peaksUsedFromIons2, const int peaksUsedFromIons3, const std::string &primaryNlStr, const std::string &summedModsNlStr, const std::string &localModsNlStr, const std::string &substStr, const std::string &componentStr, const ms_mascotresults *pResults=0, const bool storeReloadableInfo=true)
	Constructor to initialise all values.

	ms_peptide (const ms_peptide &src)
	Copying constructor.

	ms_peptide (int query, int rank, int missedCleavages, double mrCalc, double delta, double observed, int charge, int numIonsMatched, std::string peptideStr, int peaksUsedFromIons1, std::string varModsStr, double ionsScore, std::string seriesUsedStr, int peaksUsedFromIons2, int peaksUsedFromIons3, const ms_mascotresults *pResults=0, bool storeReloadableInfo=true)
	Constructor to initialise most commonly used values.

	~ms_peptide ()
	Destructor.

bool	anyPercolatorResults () const
	Return true if there are percolator results for this peptide.

bool	clearReloadableInfo ()
	To save on memory, may need to call this function.

void	copyFrom (const ms_peptide *src)
	Copies all content from another instance of the class.

std::string	getAmbiguityString (const PSM psmComponent=PSM_COMPLETE) const
	Used for X, B and Z residues in source databases where Mascot then substitutes for a residue.

bool	getAnyMatch () const
	Returns true if there was a peptide match to this spectrum.

void	getAnyProteinTermination (bool &isNterminus, bool &isCterminus, const PSM psmComponent=PSM_COMPLETE) const
	Determines if the Mascot search matched the peptide as a C or N terminus.

int	getCharge () const
	Returns the charge state for the parent mass.

std::string	getComponentStr (const PSM psmComponent=PSM_COMPLETE) const
	Returns the quantitation method component name used for the peptide match.

double	getDelta () const
	Returns the difference between the calculated and experimental relative masses.

double	getExpectationValue () const
	Returns the expectation value.

int	getFirstProtAppearedIn () const
	Returns the hit numberof the first protein that contains this peptide.

ms_linker_site_vector	getIntactLinks () const
	Returns a vector of links between crosslinked peptides.

void	getIntactLinks (ms_linker_site_vector &vec) const
	Returns a vector of links between crosslinked peptides.

double	getIonsIntensity () const
	Returns the total intensity of all of the ions in the spectrum.

double	getIonsScore () const
	Returns the ions score.

bool	getIsFromErrorTolerant () const
	Returns true if this peptide came from the error tolerant search.

bool	getIsFromLibrary () const
	Returns true if this peptide came from the library search.

bool	getLessThanMinPepLen () const
	Returns true if the length of the peptide sequence is less than the minimum used for grouping.

std::string	getLocalModsNlStr (const PSM psmComponent=PSM_COMPLETE) const
	Returns neutral loss information associated with any query-level modification for the peptide.

std::string	getLocalModsStr (const PSM psmComponent=PSM_COMPLETE) const
	Query-level variable modifications as a string of digits.

ms_linker_site_vector	getLoopLinks (const PSM psmComponent=PSM_COMPLETE) const
	Returns a vector of looplinks.

void	getLoopLinks (ms_linker_site_vector &vec, const PSM psmComponent=PSM_COMPLETE) const
	Returns a vector of looplinks.

int	getMissedCleavages (const PSM psmComponent=PSM_COMPLETE) const
	Returns the number of missed cleavages.

std::string	getMonoLinkStr (const PSM psmComponent=PSM_COMPLETE) const
	Returns monolink information associated with a linker used as a variable modification.

double	getMrCalc (const PSM psmComponent=PSM_COMPLETE) const
	Returns the calculated relative mass for this peptide .

double	getMrExperimental () const
	Returns the observed mz value as a relative mass.

int	getNum13C (const double tol, const std::string tolu, const std::string mass_type) const
	Returns the number of 13C peaks offset required to get a match with the supplied tolerance.

int	getNumberOfLinkedPeptides () const
	Returns the number of peptides in this peptide-spectrum match.

int	getNumIonsMatched () const
	Returns the number of ions matched.

int	getNumProteins () const
	Returns the number of proteins that contains this peptide.

double	getObserved () const
	Returns the observed mass / charge value.

int	getPeaksUsedFromIons1 () const
	Returns number of peaks used from `ions1`.

int	getPeaksUsedFromIons2 () const
	Returns number of peaks used from `ions2`.

int	getPeaksUsedFromIons3 () const
	Returns number of peaks used from `ions3`.

int	getPeptideLength (const PSM psmComponent=PSM_COMPLETE) const
	Returns the length in residues of the sequence found for the peptide.

std::string	getPeptideStr (bool substituteAmbiguous=true, const PSM psmComponent=PSM_COMPLETE) const
	Returns the sequence found for the peptide.

void	getPercolatorScores (double posteriorErrorProbability, double qValue, double internalPercolatorScore, double mascotIonsScore) const
	Returns the percolator scores and original Mascot ions score.

int	getPrettyRank () const
	Similar to getRank() except that equivalent scores get the same rank.

std::string	getPrimaryNlStr (const PSM psmComponent=PSM_COMPLETE) const
	Returns neutral loss information associated with any modification for the peptide.

const ms_protein *	getProtein (int num) const
	Returns a pointer to a protein that contains this peptide.

const std::vector< int >	getProteins () const
	Return a list of hit numbers for the proteins that contain this peptide.

int	getQuery () const
	Each peptide is associate with a query.

int	getRank () const
	Return the 'rank' of the peptide match.

std::string	getSeriesUsedStr () const
	Returns the series used as a string.

std::string	getSummedModsNlStr (const PSM psmComponent=PSM_COMPLETE) const
	Returns neutral loss information associated with any summed modification for the peptide.

std::string	getSummedModsStr (const PSM psmComponent=PSM_COMPLETE) const
	Summed variable modifications as a string of digits.

std::string	getVarModsStr (const PSM psmComponent=PSM_COMPLETE) const
	Variable modifications as a string of digits.

bool	isSamePeptideStr (ms_peptide *peptide, bool substituteAmbiguous=true) const
	Returns true if the two peptides are identical.

bool	isSameSummedModsStr (ms_peptide *peptide) const
	Returns true if the two summed variable modifications are identical.

bool	isSameVarModsStr (ms_peptide *peptide) const
	Returns true if the two variable modifications are identical.

ms_peptide &	operator= (const ms_peptide &right)
	C++ assignment operator.

void	setLocalModsStr (const std::string str, const PSM psmComponent=PSM_COMPLETE)
	Query-level variable modifications as a string of digits.

void	setSummedModsStr (const std::string str, const PSM psmComponent=PSM_COMPLETE)
	Summed variable modifications as a string of digits.

void	setVarModsStr (const std::string str, const PSM psmComponent=PSM_COMPLETE)
	Variable modifications as a string of digits.

Detailed Description

This class encapsulates a peptide from the mascot results file.

This class is used for protein summary and peptide summary results. There is generally no need to create an object of this class. Simply open the results file as ms_proteinsummary or ms_peptidesummary and call ms_proteinsummary::getPeptide() or ms_peptidesummary::getPeptide().

To create an ms_peptide object that is not in a Mascot results file, use ms_aahelper::createPeptide().

Examples: peptide_list.cpp, repeat_search.cpp, resfile_summary.cpp, and tools_aahelper.cpp.

Member Enumeration Documentation

◆ PSM

enum PSM

Type of data to return from accessor methods.

Mascot 2.7 and later can identify intact crosslinked peptides. The ms_peptide object contains data for both the peptide sequence(s) and the spectrum match.

The PSM flag specifies the type of data returned from accessor methods. It is used as an optional argument with, for example, getPeptideStr().

See Using enumerated values and static const ints in Perl, Java, Python and C# and Crosslinked search results.

Enumerator
PSM_COMPLETE	Peptide-spectrum match, also linear peptide in a non-crosslinked match.
PSM_CROSSLINK_ALPHA	Alpha peptide in a crosslinked match.
PSM_CROSSLINK_BETA	Beta peptide in a crosslinked match.

◆ PSM_TYPE

enum PSM_TYPE

Specifies the search pass and origin of the peptide match.

Mascot 3.0 and later stores the value of this enum in the psm_type columns of the MSR files for each peptide match.

Enumerator
PSM_STANDARD	Standard (FASTA search of target database)
PSM_DECOY	Decoy (FASTA search of decoy database)
PSM_ERRTOL	Error tolerant (second pass search, target database)
PSM_ERRTOLDECOY	Error tolerant decoy (second pass search, decoy database)
PSM_LIBRARY	Spectral library (SL search of target library)
PSM_CROSSLINK	Crosslink (FASTA search of intact crosslinks of proteins specified in the crosslinking method)

Constructor & Destructor Documentation

◆ ms_peptide() [1/2]

ms_peptide ( )

Default constructor.

The constructor should generally only be used from within the library.

◆ ms_peptide() [2/2]

ms_peptide	(	int	query,
		int	rank,
		int	missedCleavages,
		double	mrCalc,
		double	delta,
		double	observed,
		int	charge,
		int	numIonsMatched,
		std::string	peptideStr,
		int	peaksUsedFromIons1,
		std::string	varModsStr,
		double	ionsScore,
		std::string	seriesUsedStr,
		int	peaksUsedFromIons2,
		int	peaksUsedFromIons3,
		const ms_mascotresults *	pResults = `0`,
		bool	storeNonPersistantInfo = `true`
	)

Constructor to initialise most commonly used values.

This constructor should generally only used from within the library.

Not all values can be initialised from this constructor, but this constructor will remain available in future versions of the library.

Consider using ms_aahelper::createPeptide or ms_mascotresults::getPeptide(const int, const int) const instead of this constructor.

Parameters

query	is the query number in the range 1..ms_mascotresfilebase::getNumQueries()
rank	is the rank number. See getRank() for details
missedCleavages	is the number of missed cleavages, or -1 if there was no match
mrCalc	is the relative mass of the peptide. See getMrCalc()
delta	is the difference between the calculated and experimental relative masses
observed	is the observed mass / charge value. See getObserved()
charge	is the charge state for the parent mass
numIonsMatched	is the number of ions matched. See getNumIonsMatched()
peptideStr	is the peptide sequence
peaksUsedFromIons1	is the number of peaks used from ions1. See getPeaksUsedFromIons1()
varModsStr	is the variable modifications as a string of digits. See getVarModsStr()
ionsScore	is the ions score. See getIonsScore()
seriesUsedStr	is the ions series used as a string. See getSeriesUsedStr()
peaksUsedFromIons2	is the number of peaks used from ions2. See getPeaksUsedFromIons2()
peaksUsedFromIons3	is the number of peaks used from ions2. See getPeaksUsedFromIons3()
pResults	is a pointer to the results object and should be supplied where possible
storeNonPersistantInfo	should be set to true

Member Function Documentation

◆ anyPercolatorResults()

bool anyPercolatorResults ( ) const

Return true if there are percolator results for this peptide.

See Using Percolator scores for further information.

Returns: Should always return true if ms_peptidesummary::MSPEPSUM_PERCOLATOR has been specified.

◆ getAmbiguityString()

std::string getAmbiguityString ( const PSM psmComponent = PSM_COMPLETE ) const

Used for X, B and Z residues in source databases where Mascot then substitutes for a residue.

Mascot 2.0 and later will try and substitute ambiguous 'residues' with a residue to get a match. Specifically:

'X' can be substituted with any residue
'B' can be substituted with an Asparagine (N) or Aspartic acid (D)
'Z' can be substituted with a Glutamic acid (E) or a Glutamine(Q)

This string is read from the h1_q1_subst= line of the results file for the protein summary, and from the q1_p1_subst line of the results file for the peptide summary.

Calling getPeptideStr(true) will return the substituted string.

Calling this function will return a string with the format:

   pos1,ambig1,matched1...,posn,ambigm,matchedn

For example:

getAmbiguityString() returns 3,B,N,4,X,A
getPeptideStr(false) returns AFBXK
getPeptideStr(true) returns AFNAK

If the peptide match is a crosslinked peptide, you must specify psmComponent. PSM_CROSSLINK_ALPHA returns the alpha peptide ambiguity string, and PSM_CROSSLINK_BETA returns the beta peptide ambiguity string. If you pass PSM_COMPLETE, the method returns the empty string.

Parameters

psmComponent Type of data to return: complete molecule, alpha peptide or beta peptide.

Returns: ambiguity string for this peptide

◆ getAnyMatch()

bool getAnyMatch ( ) const

Returns true if there was a peptide match to this spectrum.

Internally (and in the results file) this is signified by the first value on the line, which is the number of missed cleavages. See also getMissedCleavages().

Returns: true if there was a peptide match to this spectrum.

Examples: resfile_summary.cpp.

◆ getAnyProteinTermination()

void getAnyProteinTermination	(	bool &	isNterminus,
		bool &	isCterminus,
		const PSM	psmComponent = `PSM_COMPLETE`
	)		const

Determines if the Mascot search matched the peptide as a C or N terminus.

This is determined from the residues string . The residues string is a series of residues sepearated by colons (':'). If an individual residue starts with a hyphen ('-') then the peptide is an N-terminus for a protein. If an individual residue ends with a one ('1') then the peptide is a C-terminus for a protein.

If the peptide match is a crosslinked peptide, you must specify psmComponent. PSM_CROSSLINK_ALPHA returns the values for the alpha peptide, and PSM_CROSSLINK_BETA for the beta peptide. If you pass PSM_COMPLETE, the returned values are false.

Parameters

isNterminus	Set to true if the peptide was matched as an N-terminus, otherwise false.
isCterminus	Set to true if the peptide was matched as a C-terminus, otherwise false.
psmComponent	Type of data to return: complete molecule, alpha peptide or beta peptide.

◆ getCharge()

int getCharge ( ) const

Returns the charge state for the parent mass.

This will be 0 for an Mr value, or 1,2,3,4 etc. If an error has occurred, then the charge will be -100.

Thread safe: This method is safe to use from multiple threads. See also Using Parser in multithreaded applications.

Returns: The charge state for the parent mass.

Examples: resfile_summary.cpp.

◆ getComponentStr()

std::string getComponentStr ( const PSM psmComponent = PSM_COMPLETE ) const

Returns the quantitation method component name used for the peptide match.

If a search was performed using a 'precursor' quantitation method, then peptide hits may have a quantitation method component name associated with them.

The entry in the results file might be, for example:

   q1_p2_comp=light

Component strings are only saved in the results file for methods with 'Isotopes' defined. For example, with the 15N Metabolic [MD] method. In other cases, for example with the SILAC methods, the component needs to be determined from the modifications assigned to the peptide.

To determine if a method has isotopes, use the following code (error handling omitted to make it more readable):

 my $resfile = msparser::ms_mascotresfile_msr->new($filename);
 my $qfile = new msparser::ms_quant_configfile;
 $qfile->setSchemaFileName(
        "http://www.matrixscience.com/xmlns/schema/quantitation_2"
        . " ../html/xmlns/schema/quantitation_2/quantitation_2.xsd"
        . " http://www.matrixscience.com/xmlns/schema/quantitation_1"
        . " ../html/xmlns/schema/quantitation_1/quantitation_1.xsd"
 );

 my $numIsotopes = 0;
 if ($resfile->getQuantitation($qfile)) {
   my $method = $qfile->getMethodByNumber(0);
   for (my $idx= 0; $idx < $method->getNumberOfComponents(); $idx++) {
     my $comp = $method->getComponentByNumber($idx);
     $numIsotopes += $comp->getNumberOfIsotopes();
   }
 }
 if ($numIsotopes > 0) {
   ... expect getComponentStr to return values...
 }

If the match is an intact crosslinked peptide, you must specify psmComponent. PSM_CROSSLINK_ALPHA returns the alpha component and PSM_CROSSLINK_BETA the beta component. If you pass PSM_COMPLETE, the method returns either the alpha component (if alpha component == beta component) or the empty string.

Parameters

psmComponent Type of data to return: complete molecule, alpha peptide or beta peptide.

Returns: a component name or an empty string.

◆ getDelta()

double getDelta ( ) const

Returns the difference between the calculated and experimental relative masses.

Returns: The delta in daltons.

Examples: resfile_summary.cpp.

◆ getExpectationValue()

double getExpectationValue ( ) const

Returns the expectation value.

Returns: The expectation value.

◆ getFirstProtAppearedIn()

int getFirstProtAppearedIn ( ) const

Returns the hit numberof the first protein that contains this peptide.

Returns: The hit number (1..n) or 0 if the peptide is not in any of the proteins in the ms_peptidesummary list.

◆ getIntactLinks() [1/2]

ms_linker_site_vector getIntactLinks ( ) const

Returns a vector of links between crosslinked peptides.

In Mascot 2.7, the number of links between crosslinked peptides is limited to 1.

Returns: A vector of links, or the empty vector if getNumberOfLinkedPeptides() == 0.

◆ getIntactLinks() [2/2]

void getIntactLinks ( ms_linker_site_vector & vec ) const

Returns a vector of links between crosslinked peptides.

In Mascot 2.7, the number of links between crosslinked peptides is limited to 1.

Parameters

vec	is vector of links, or the empty vector if getNumberOfLinkedPeptides() == 0.

◆ getIonsIntensity()

double getIonsIntensity ( ) const

Returns the total intensity of all of the ions in the spectrum.

This value is only guaranteed to be valid for ms_peptidesummary when sorting unassigned by intensity and using the ms_peptide object returned by the ms_mascotresults::getUnassigned() function.

The same value is returned by ms_inputquery::getTotalIonsIntensity()

Returns: The total intensity of all of the ions in the spectrum.

◆ getIonsScore()

double getIonsScore ( ) const

Returns the ions score.

Note that ms_protein::getPeptideIonsScore() returns the ions score in the context of the protein match and will generally be slightly lower than the return value from this function. The Mascot results pages display the score returned from this function because results from similar proteins are displayed together.

Returns: The ions score.

Examples: peptide_list.cpp, repeat_search.cpp, and resfile_summary.cpp.

◆ getIsFromErrorTolerant()

bool getIsFromErrorTolerant ( ) const

Returns true if this peptide came from the error tolerant search.

This peptide may have been found as a result of a standard error tolerant or an integrated error tolerant search. See Error tolerant searches.

Returns: true if this peptide is from an error tolerant search

◆ getIsFromLibrary()

bool getIsFromLibrary ( ) const

Returns true if this peptide came from the library search.

This peptide may have been found as a result of a library or an integrated library search. See Spectral libraries.

Returns: true if this peptide is from a spectral library search

◆ getLessThanMinPepLen()

bool getLessThanMinPepLen ( ) const

Returns true if the length of the peptide sequence is less than the minimum used for grouping.

If the function returns true, this peptide has not been considered when grouping proteins.

In a crosslinked search, if the match is crosslinked, either alpha or beta sequence must be longer than MinPepLenInPepSummary for the match to be considered in protein grouping. The test for a standard (linear) match is to compare its sequence length, as before.

See also: ms_mascotresults::getMinPepLenInPepSummary()

Returns: true if the peptide length is less than the minimum specified in MinPepLenInPepSummary in the options section of mascot.dat.

◆ getLocalModsNlStr()

std::string getLocalModsNlStr ( const PSM psmComponent = PSM_COMPLETE ) const

Returns neutral loss information associated with any query-level modification for the peptide.

Neutral loss information is encoded in the same way as variable modification neutral losses (getPrimaryNlStr()). The neutral loss string is a string of digits, one digit for the N terminus, one for each residue and one for the C terminus. Each digit specifies the modification used to obtain the match: 0 indicates no modification, while numbers from 1 onwards are indices to the neutral loss vector of the modification, ms_modification::getNeutralLoss().

For example, suppose the peptide match has a query-level modification at residue 6, so that the query-level mods string is 000000100 and the neutral loss string is 000000200. To find the value of neutral loss 2, load the query-level modification object 1 (see getLocalModsStr()) and get the neutral loss vector with ms_modification::getNeutralLoss(). The neutral loss vector is 0-based, so neutral loss 2 is the second element of the vector, at index 1.

See also: getLocalModsStr()

Parameters

psmComponent Type of data to return: complete molecule, alpha peptide or beta peptide.

Returns: A string with neutral loss information, or an empty string.

◆ getLocalModsStr()

std::string getLocalModsStr ( const PSM psmComponent = PSM_COMPLETE ) const

Query-level variable modifications as a string of digits.

One digit is used for the N terminus, one for each residue and one for the C terminus. Each digit specifies the modification used to obtain the match: 0 indicates no modification, while digits and letters 1..9 and A..W indicate the corresponding modification in the IT_MODS array of the input query. The digits can be used to look up the modification name using ms_inputquery::getLocalVarModName().

For example, suppose the query-level mods string of a peptide match is 000000100 (residue 6 modified). To load the modification object:

Look up the name with ms_inputquery::getLocalVarModName(1).
Load the Unimod section of the results file with ms_mascotresfilebase::getUnimod()
Populate the ms_modification object from the Unimod section with ms_modification::getFromUnimod().

Note that query-level modifications can never include error tolerant modifications, so the string never contains an 'X'.

See also: ms_mascotresults::getReadableVarMods()

Parameters

psmComponent Type of data to return: complete molecule, alpha peptide or beta peptide.

Returns: Query-level variable modifications as a string of digits.

◆ getLoopLinks() [1/2]

ms_linker_site_vector getLoopLinks ( const PSM psmComponent = PSM_COMPLETE ) const

Returns a vector of looplinks.

If this is a linear peptide match, psmComponent is ignored.

If this is a crosslinked peptide match, psmComponent chooses between the alpha or the beta peptide. If psmComponent is PSM_COMPLETE, looplinks for both peptides are returned.

Parameters

psmComponent One of ms_peptide::PSM.

Returns: A vector of looplinks, which could be empty.

◆ getLoopLinks() [2/2]

void getLoopLinks	(	ms_linker_site_vector &	vec,
		const PSM	psmComponent = `PSM_COMPLETE`
	)		const

Returns a vector of looplinks.

If this is a linear peptide match, psmComponent is ignored.

If this is a crosslinked peptide match, psmComponent chooses between the alpha or the beta peptide. If psmComponent is PSM_COMPLETE, looplinks for both peptides are returned.

Parameters

vec	is vector of looplinks, which could remain empty.
psmComponent	One of ms_peptide::PSM.

◆ getMissedCleavages()

int getMissedCleavages ( const PSM psmComponent = PSM_COMPLETE ) const

Returns the number of missed cleavages.

◆ getMonoLinkStr()

std::string getMonoLinkStr ( const PSM psmComponent = PSM_COMPLETE ) const

Returns monolink information associated with a linker used as a variable modification.

Monolink information is encoded in a similar way to variable modifications. If the variable modification at position i is a linker (e.g. Xlink:DSS), the value at position i of the monolink string records the index of the monolink (e.g. "neutral loss" element 1 of Xlink:DSS (K)).

Use the relevant number from this function as an argument to ms_mascotresfilebase::getMonoLinkModification() to determine the monolink delta used for scoring.

Parameters

psmComponent Type of data to return: complete molecule, alpha peptide or beta peptide.

Returns: A string with monolink index information, or an empty string if no monolinks were searched.

◆ getMrCalc()

double getMrCalc ( const PSM psmComponent = PSM_COMPLETE ) const

Returns the calculated relative mass for this peptide .

Takes into account any modifications.

In a crosslinked search, the peptide-spectrum match may contain one linear peptide or the complete crosslinked peptide (alpha and beta).

The psmComponent argument is optional in a non-crosslinked search. For a crosslinked match, it chooses the type of data to return. With PSM_COMPLETE, the method returns the mass of the intact molecule: alpha Mr + beta Mr + linker mass. With PSM_CROSSLINK_ALPHA or PSM_CROSSLINK_BETA, the method returns the alpha or beta value, respectively, without the linker.

See Crosslinked search results.

Thread safe: This method is safe to use from multiple threads. See also Using Parser in multithreaded applications.

Parameters

psmComponent Type of data to return: complete molecule, alpha peptide or beta peptide.

Returns: The relative mass.

Examples: resfile_summary.cpp.

◆ getMrExperimental()

double getMrExperimental ( ) const

Returns the observed mz value as a relative mass.

This is equal to getMrCalc() + getDelta(), so note that this will be zero if there was no match because there is no calculated value and no delta. It is generally recommended that you call ms_mascotresfilebase::getObservedMrValue() since it will always return the relative mass, even for no match.

Returns: The observed mz value as a relative mass.

Examples: resfile_summary.cpp.

◆ getNum13C()

int getNum13C	(	const double	tol,
		const std::string	tolu,
		const std::string	mass_type
	)		const

Returns the number of 13C peaks offset required to get a match with the supplied tolerance.

Sometimes, peak detection chooses the 13C peak rather than the 12C. In extreme cases, it may pick the 13C2 peak. The normal test for a precursor match is

tol > absolute(exp - calc)

Assuming the mass values and tolerance are in Da, and the PEP_ISOTOPE_ERROR field is set to 1, the test will also succeed for

tol > absolute(exp - calc - 1)

If the PEP_ISOTOPE_ERROR field is set to 2, the test will succeed for the above two conditions, plus

tol > absolute(exp - calc - 2)

This means that you can use a tight mass tolerance and still get a match to a 13C peak. If you are using a very high accuracy instrument, note that the precise shifts are the carbon isotope spacings of 1.0033548 and 2.0067096, rather than 1 and 2. However, if average rather than isotopic masses are specified in the search, the values will be 0.9926548 and 1.9853096

Parameters

tol	Is the tolerance for the search. The return value from matrix_science::ms_searchparams::getTOL() may be used.
tolu	Is the units of the tolerance supplied when performing the search. The return value from matrix_science::ms_searchparams::getTOLU() may be used.
mass_type	will either be Monoisotopic or Average. The return value from matrix_science::ms_searchparams::getMASS() may be used.

Returns

0 if the delta is within the applied tolerance;
1 if the delta minus 1.0033548is within the tolerance;
2 if the delta minus 2.0067096 is within the tolerance;
-1 if there was no match (i.e. getAnyMatch() returns 0) or if invalid tolerance units are supplied or if the delta is outside any of the above ranges.

◆ getNumberOfLinkedPeptides()

int getNumberOfLinkedPeptides ( ) const

Returns the number of peptides in this peptide-spectrum match.

In Mascot 2.7, there are two possible return values:

0 (no crosslinking)
2 (crosslinked alpha and beta peptide)

Returns: The number of peptides in this peptide-spectrum match.

◆ getNumIonsMatched()

int getNumIonsMatched ( ) const

Returns the number of ions matched.

Mascot begins by selecting a small number of experimental peaks on the basis of normalised intensity. It calculates a probability based score according to the number of matches. It then increases the number of selected peaks and recalculates the score. It continues to iterate until it is clear that the score can only get worse. It then reports the best score it found, which should correspond to an optimum selection, taking mostly real peaks and leaving behind mostly noise.

Mascot is not trying to find all possible matches in the spectrum. Many spectra have "peak at every mass" noise, and can match any ion series from any sequence if there is no intensity discrimination. So, you may look at a peptide view report and see obvious matches that are unlabelled. However, if the peak selection was to be extended to include these additional matches, it would also have to include a number of additional noise peaks, and the score would decrease.

Returns: The number of ions matched in order to get the highest score.

Examples: resfile_summary.cpp.

◆ getNumProteins()

int getNumProteins ( ) const

Returns the number of proteins that contains this peptide.

See also: getProtein(), ms_mascotresults::getAllProteinsWithThisPepMatch()

Returns: The number of proteins in the current results set that contained this peptide.

◆ getObserved()

double getObserved ( ) const

Returns the observed mass / charge value.

Returns: The observed mass / charge value.

Examples: resfile_summary.cpp.

◆ getPeaksUsedFromIons1()

int getPeaksUsedFromIons1 ( ) const

Returns number of peaks used from ions1.

It is possible, but unusual, to specify which ions series particular ions come from: https://www.matrixscience.com/help/sq_help.html#IONS

If a search specifies that some ions are from the b series, some are from the y series and that some are from any series then these will be stored separately in Ions1, Ions2 and Ions3. The number of matches to each set of ions is avaible using getPeaksUsedFromIons1(), getPeaksUsedFromIons2() and getPeaksUsedFromIons3().

For most searches, getPeaksUsedFromIons1() is the only function that needs to be used.

See also: getNumIonsMatched()

Returns: The number of peaks used from ions1.

Examples: resfile_summary.cpp.

◆ getPeaksUsedFromIons2()

int getPeaksUsedFromIons2 ( ) const

Returns number of peaks used from ions2.

It is possible, but unusual, to specify which ions series particular ions come from: https://www.matrixscience.com/help/sq_help.html#IONS

If a search specifies that some ions are from the b series, some are from the y series and that some are from any series then these will be stored separately in Ions1, Ions2 and Ions3. The number of matches to each set of ions is avaible using getPeaksUsedFromIons1(), getPeaksUsedFromIons2() and getPeaksUsedFromIons3().

For most searches, getPeaksUsedFromIons1() is the only function that needs to be used.

See also: getNumIonsMatched()

Returns: The number of peaks used from ions2.

Examples: resfile_summary.cpp.

◆ getPeaksUsedFromIons3()

int getPeaksUsedFromIons3 ( ) const

Returns number of peaks used from ions3.

It is possible, but unusual, to specify which ions series particular ions come from: https://www.matrixscience.com/help/sq_help.html#IONS

If a search specifies that some ions are from the b series, some are from the y series and that some are from any series then these will be stored separately in Ions1, Ions2 and Ions3. The number of matches to each set of ions is avaible using getPeaksUsedFromIons1(), getPeaksUsedFromIons2() and getPeaksUsedFromIons3().

For most searches, getPeaksUsedFromIons1() is the only function that needs to be used.

See also: getNumIonsMatched()

Returns: The number of peaks used from ions3.

Examples: resfile_summary.cpp.

◆ getPeptideLength()

int getPeptideLength ( const PSM psmComponent = PSM_COMPLETE ) const

Returns the length in residues of the sequence found for the peptide.

This should be faster than calling getPeptideStr() and determining the length of the returned string.

Parameters

psmComponent Type of data to return: complete molecule, alpha peptide or beta peptide.

Returns: Returns the length in residues of the sequence found for the peptide.

◆ getPeptideStr()

std::string getPeptideStr	(	bool	substituteAmbiguous = `true`,
		const PSM	psmComponent = `PSM_COMPLETE`
	)		const

Returns the sequence found for the peptide.

In a crosslinked search, the peptide-spectrum match may contain one linear peptide or the complete crosslinked peptide (alpha and beta). The psmComponent argument chooses the type of data to return. If you pass PSM_COMPLETE, the method returns a concatenated sequence: alpha sequence + "][" + beta sequence. The characters "][" represent the alpha C-terminus and beta N-terminus.

The psmComponent argument is optional in a non-crosslinked search.

See Crosslinked search results.

Parameters

substituteAmbiguous	If true, and if there were any ambiguous residues, then the returned result will have the substituted residues rather than an 'X', 'B' or 'Z'.
psmComponent	Type of data to return: complete molecule, alpha peptide or beta peptide.

Returns: The peptide sequence – will be the empty string if there was no match.

Examples: peptide_list.cpp, resfile_summary.cpp, and tools_aahelper.cpp.

◆ getPercolatorScores()

void getPercolatorScores	(	double *	posteriorErrorProbability,
		double *	qValue,
		double *	internalPercolatorScore,
		double *	mascotIonsScore
	)		const

Returns the percolator scores and original Mascot ions score.

See Using Percolator scores for further information and Multiple return values in Perl, Java, Python and C#.

Parameters

[out]	posteriorErrorProbability	is the probability that individual match with this Percolator score is random match.
[out]	qValue	is equivalent to the FDR if all matches with this Percolator score or higher were accepted
[out]	internalPercolatorScore	is not used in Mascot Parser. See Percolator documentation.
[out]	mascotIonsScore	is the ions score that Mascot originally assigned.

◆ getPrettyRank()

int getPrettyRank ( ) const

Similar to getRank() except that equivalent scores get the same rank.

For a peptide summary, the top 10 peptide matches for each query are saved. These are scored with rank 1 to 10, and the rank can be obtained using the getRank() function. However, if say, the top three matches are the same, it is generally better to say (in a report) that these are all rank 1. The following table shows an example:

Rank	Pretty Rank	Score	Peptide	Protein
1	1	78	`ABCDEFG`
2	1	78	`ABCDEGF`	gi\|123456
3	1	78	`BACDEFG`
4	4	65	`ASDADSD`
5	4	65	`SDFSGSD`
6	6	12	`DFGHDFG`
7	7	8	`SSDFDFD`
8	8	7	`RTYRYRY`
9	9	4	`RTYRYRY`
10	10	2	`TYUTUTU`

For a protein summary, getPrettyRank() will always return the same as getRank().

Returns: The 'pretty rank'.

Examples: resfile_summary.cpp.

◆ getPrimaryNlStr()

std::string getPrimaryNlStr ( const PSM psmComponent = PSM_COMPLETE ) const

Returns neutral loss information associated with any modification for the peptide.

Neutral loss information is encoded in a similar way to variable modifications. Use the relevant number from this function as an offset into the array returned from ms_searchparams::getVarModsNeutralLosses() to determine the neutral loss used for scoring.

The neutral loss string is a string of digits, one digit for the N terminus, one for each residue and one for the C terminus. Each digit specifies the modification used to obtain the match: 0 indicates no modification, 1 indicates NeutralLoss1, 2 indicates NeutralLoss2 etc., in the masses section.

Parameters

psmComponent Type of data to return: complete molecule, alpha peptide or beta peptide.

Returns: A string with neutral loss information, or an empty string.

◆ getProtein()

const ms_protein * getProtein ( int num ) const

Returns a pointer to a protein that contains this peptide.

It is normally better to use ms_mascotresults::getAllProteinsWithThisPepMatch() than this function.

This function returns all the proteins that are seen in the top level report that contain this peptide. If grouping is enabled, it will only return proteins that are returned from ms_mascotresults::getHit – it will not return proteins that would be returned from ms_mascotresults::getNextSimilarProtein().

The function will only return proteins up to the number of hits that were requested when creating the ms_mascotresults object.

See Maintaining object references: two rules of thumb.

Parameters

num	should be in the range 1.. getNumProteins() or this function will return a null value.

Returns: A pointer to protein if found, or a null value if not found.

◆ getProteins()

const std::vector< int > getProteins ( ) const

Return a list of hit numbers for the proteins that contain this peptide.

See also: getProtein()

Returns: a vector of protein hit numbers. See Using STL vector classes vectori, vectord and VectorString in Perl, Java, Python and C#.

◆ getQuery()

int getQuery ( ) const

Each peptide is associate with a query.

Thread safe: This method is safe to use from multiple threads. See also Using Parser in multithreaded applications.

Returns: The query number in the range 1..ms_mascotresfilebase::getNumQueries().

Examples: resfile_summary.cpp.

◆ getRank()

int getRank ( ) const

Return the 'rank' of the peptide match.

Each spectrum will match to a number of different peptides. The best (highest scoring) match will have a rank value of 1.

In a peptide summary, this will be in the range 1..10.

In a protein summary, this will be the hit number (1..50).

See also: ms_mascotresults::getMaxRankValue()

Returns: The rank.

Examples: resfile_summary.cpp.

◆ getSeriesUsedStr()

std::string getSeriesUsedStr ( ) const

Returns the series used as a string.

The string is a set of 0s and 1s and 2s.

0 - no significant match
1 - significant match, but not used in score
2 - significant match, used for scoring

The 'position' in the string is used to indicate which series:

01 - A series
02 - placeholder (was A - NH3 series in older versions of Mascot)
03 - A++ series
04 - B series
05 - placeholder (was B - NH3 series in older versions of Mascot)
06 - B++ series
07 - Y series
08 - placeholder (was Y - NH3 series in older versions of Mascot)
09 - Y++ series
10 - C series
11 - C++ series
12 - X series
13 - X++ series
14 - Z series
15 - Z++ series
16 - Z+H series
17 - Z+H++ series
18 - Z+2H series
19 - Z+2H++ series

For example, 00020010000000000 would indicate b series used for scoring, and y series significant, but not used for scoring. Note that earlier versions of Mascot did not look for all these ions series, so the string will not necessarily be 17 characters long.

Returns: series used

Examples: resfile_summary.cpp.

◆ getSummedModsNlStr()

std::string getSummedModsNlStr ( const PSM psmComponent = PSM_COMPLETE ) const

Returns neutral loss information associated with any summed modification for the peptide.

Neutral loss information is encoded in a similar way to summed modifications. Use the relevant number from this function as an offset into the array returned from ms_searchparams::getVarModsNeutralLosses() to determine the neutral loss used for scoring.

The neutral loss string is a string of digits, one digit for the N terminus, one for each residue and one for the C terminus. Each digit specifies the modification used to obtain the match: 0 indicates no modification, 1 indicates NeutralLoss1, 2 indicates NeutralLoss2 etc., in the masses section.

See also: getSummedModsStr()

Parameters

psmComponent Type of data to return: complete molecule, alpha peptide or beta peptide.

Returns: A string with neutral loss information, or an empty string.

◆ getSummedModsStr()

std::string getSummedModsStr ( const PSM psmComponent = PSM_COMPLETE ) const

Summed variable modifications as a string of digits.

When two modifications occur at the same site, the extra modification is stored in the q1_p1_summed_mods= string in the results file. Summed mods are only supported when using quantitation methods with exclusive modifications. The exclusive modification will always be returned by getVarModsStr(), while getSummedModsStr() is used for post translational modifications to the same site.

One digit is used for the N terminus, one for each residue and one for the C terminus. Each digit specifies the modification used to obtain the match: 0 indicates no modification, 1 indicates delta1, 2 indicates delta2 etc., in the masses section. An 'X' is used to indicate an error tolerant modification that can be retrieved using matrix_science::ms_peptidesummary::getErrTolModName().

To support numbers greater than 9, the letters A..W are permitted, with A being 10 and W being 32.

See also: Multiple modifications for the same site; ms_peptide::getVarModsStr(); ms_mascotresults::getReadableVarMods(); ms_searchparams::getMULTI_SITE_MODS; Increase in the number of variable modifications.

In a crosslinked search, the peptide-spectrum match may contain one linear peptide or the complete crosslinked peptide (alpha and beta). The psmComponent argument chooses the type of data to return.

The psmComponent argument is optional in a non-crosslinked search.

See Crosslinked search results.

Parameters

psmComponent Type of data to return: complete molecule, alpha peptide or beta peptide.

Returns: Summed variable modifications as a string of digits.

◆ getVarModsStr()

std::string getVarModsStr ( const PSM psmComponent = PSM_COMPLETE ) const

Variable modifications as a string of digits.

One digit is used for the N terminus, one for each residue and one for the C terminus. Each digit specifies the modification used to obtain the match: 0 indicates no modification, 1 indicates delta1, 2 indicates delta2 etc., in the masses section. An 'X' is used to indicate an error tolerant modification that can be retrieved using matrix_science::ms_peptidesummary::getErrTolModName().

To support numbers greater than 9, the letters A..W are permitted, with A being 10 and W being 32.

See also: ms_mascotresults::getReadableVarMods()

In a crosslinked search, the peptide-spectrum match may contain one linear peptide or the complete crosslinked peptide (alpha and beta). The psmComponent argument chooses the type of data to return.

The psmComponent argument is optional in a non-crosslinked search.

See Crosslinked search results.

Parameters

psmComponent Type of data to return: complete molecule, alpha peptide or beta peptide.

Returns: Variable modifications as a string of digits.

Examples: resfile_summary.cpp.

◆ isSamePeptideStr()

bool isSamePeptideStr	(	ms_peptide *	peptide,
		bool	substituteAmbiguous = `true`
	)		const

Returns true if the two peptides are identical.

Calling this function may be faster than calling getPeptideStr() twice and doing the compare on the returned peptide.

Parameters

peptide	is a pointer to the peptide object with the sequence to compare.
substituteAmbiguous	should be set to true to compare sequences after substituting any X for the residue used to get a match.

Returns: true if the peptides are the same.

◆ isSameSummedModsStr()

bool isSameSummedModsStr ( ms_peptide * peptide ) const

Returns true if the two summed variable modifications are identical.

Calling this function may be faster than calling getSummedModsStr() twice and doing the compare on the returned peptide.

Parameters

peptide is a pointer to the peptide object with the summed mods string to compare.

Returns: True if the summed variable modifications for the two peptides are the same.

◆ isSameVarModsStr()

bool isSameVarModsStr ( ms_peptide * peptide ) const

Returns true if the two variable modifications are identical.

Calling this function may be faster than calling getVarModsStr() twice and doing the compare on the returned peptide.

Parameters

peptide is a pointer to the peptide object with the mods string to compare.

Returns: True if the variable modifications for the two peptides are the same.

◆ setLocalModsStr()

void setLocalModsStr	(	const std::string	str,
		const PSM	psmComponent = `PSM_COMPLETE`
	)

Query-level variable modifications as a string of digits.

One digit is used for the N terminus, one for each residue and one for the C terminus. Each digit specifies the modification used to obtain the match: 0 indicates no modification, while digits and letters 1..9 and A..W indicate the corresponding modification in the IT_MODS array of the input query.

Note that query-level modifications can never include error tolerant modifications, so the string never contains an 'X'.

See also: ms_mascotresults::getReadableVarMods()

Setting the string does not cause a re-calculation of the peptide mass – this needs to be done manually.

In a crosslinked search, the peptide-spectrum match may contain one linear peptide or the complete crosslinked peptide (alpha and beta). The psmComponent argument chooses the type of data to set. The caller is responsible for data consistency between PSM_COMPLETE, PSM_CROSSLINK_ALPHA and PSM_CROSSLINK_BETA.

The psmComponent argument is optional in a non-crosslinked search.

See Crosslinked search results.

Parameters

str	is the new query-level variable modifications as a string of digits.
psmComponent	Type of data to set: complete molecule, alpha peptide or beta peptide.

◆ setSummedModsStr()

void setSummedModsStr	(	const std::string	str,
		const PSM	psmComponent = `PSM_COMPLETE`
	)

Summed variable modifications as a string of digits.

When two modifications occur at the same site, the extra modification is stored in the q1_p1_summed_mods= string in the results file. Summed mods are only supported when using quantitation methods with exclusive modifications. The exclusive modification will always be returned by getVarModsStr(), while getSummedModsStr() is used for post translational modifications to the same site.

One digit is used for the N terminus, one for each residue and one for the C terminus. Each digit specifies the modification used to obtain the match: 0 indicates no modification, 1 indicates delta1, 2 indicates delta2 etc., in the masses section. An 'X' is used to indicate an error tolerant modification that can be retrieved using matrix_science::ms_peptidesummary::getErrTolModName().

To support numbers greater than 9, the letters A..W are permitted, with A being 10 and W being 32.

See also: ms_mascotresults::getReadableVarMods()

Setting the string does not cause a re-calculation of the peptide mass – this needs to be done manually.

In a crosslinked search, the peptide-spectrum match may contain one linear peptide or the complete crosslinked peptide (alpha and beta). The psmComponent argument chooses the type of data to set. The caller is responsible for data consistency between PSM_COMPLETE, PSM_CROSSLINK_ALPHA and PSM_CROSSLINK_BETA.

The psmComponent argument is optional in a non-crosslinked search.

See Crosslinked search results.

Parameters

str	is the new variable modifications as a string of digits.
psmComponent	Type of data to set: complete molecule, alpha peptide or beta peptide.

◆ setVarModsStr()

void setVarModsStr	(	const std::string	str,
		const PSM	psmComponent = `PSM_COMPLETE`
	)

Variable modifications as a string of digits.

One digit is used for the N terminus, one for each residue and one for the C terminus. Each digit specifies the modification used to obtain the match: 0 indicates no modification, 1 indicates delta1, 2 indicates delta2 etc., in the masses section. An 'X' is used to indicate an error tolerant modification that can be retrieved using matrix_science::ms_peptidesummary::getErrTolModName().

To support numbers greater than 9, the letters A..W are permitted, with A being 10 and W being 32.

See also: ms_mascotresults::getReadableVarMods()

Setting the string does not cause a re-calculation of the peptide mass – this needs to be done manually.

In a crosslinked search, the peptide-spectrum match may contain one linear peptide or the complete crosslinked peptide (alpha and beta). The psmComponent argument chooses the type of data to set. The caller is responsible for data consistency between PSM_COMPLETE, PSM_CROSSLINK_ALPHA and PSM_CROSSLINK_BETA.

The psmComponent argument is optional in a non-crosslinked search.

See Crosslinked search results.

Parameters

str	is the new variable modifications as a string of digits.
psmComponent	Type of data to set: complete molecule, alpha peptide or beta peptide.

The documentation for this class was generated from the following files:

ms_peptide.hpp
ms_peptide.cpp

Public Types

Public Member Functions

Detailed Description

Member Enumeration Documentation

◆ PSM

◆ PSM_TYPE

Constructor & Destructor Documentation

◆ ms_peptide() [1/2]

◆ ms_peptide() [2/2]

Member Function Documentation

◆ anyPercolatorResults()

◆ getAmbiguityString()

◆ getAnyMatch()

◆ getAnyProteinTermination()

◆ getCharge()

◆ getComponentStr()

◆ getDelta()

◆ getExpectationValue()

◆ getFirstProtAppearedIn()

◆ getIntactLinks() [1/2]

◆ getIntactLinks() [2/2]

◆ getIonsIntensity()

◆ getIonsScore()

◆ getIsFromErrorTolerant()

◆ getIsFromLibrary()

◆ getLessThanMinPepLen()

◆ getLocalModsNlStr()

◆ getLocalModsStr()

◆ getLoopLinks() [1/2]

◆ getLoopLinks() [2/2]

◆ getMissedCleavages()

◆ getMonoLinkStr()

◆ getMrCalc()

◆ getMrExperimental()

◆ getNum13C()

◆ getNumberOfLinkedPeptides()

◆ getNumIonsMatched()

◆ getNumProteins()

◆ getObserved()

◆ getPeaksUsedFromIons1()

◆ getPeaksUsedFromIons2()

◆ getPeaksUsedFromIons3()

◆ getPeptideLength()

◆ getPeptideStr()

◆ getPercolatorScores()

◆ getPrettyRank()

◆ getPrimaryNlStr()

◆ getProtein()

◆ getProteins()

◆ getQuery()

◆ getRank()

◆ getSeriesUsedStr()

◆ getSummedModsNlStr()

◆ getSummedModsStr()

◆ getVarModsStr()

◆ isSamePeptideStr()

◆ isSameSummedModsStr()

◆ isSameVarModsStr()

◆ setLocalModsStr()

◆ setSummedModsStr()

◆ setVarModsStr()