InspectInfile Class Reference

Inspect input file adapter. More...

#include <OpenMS/FORMAT/InspectInfile.h>

Collaboration diagram for InspectInfile:

Public Member Functions
	InspectInfile ()
	default constructor
	InspectInfile (const InspectInfile &inspect_infile)
	copy constructor
virtual	~InspectInfile ()
	destructor
InspectInfile &	operator= (const InspectInfile &inspect_infile)
	assignment operator
bool	operator== (const InspectInfile &inspect_infile) const
	equality operator
void	store (const std::string &filename)
void	handlePTMs (const std::string &modification_line, const std::string &modifications_filename, const bool monoisotopic)
const std::string &	getSpectra () const
	Specifies a spectrum file to search.
void	setSpectra (const std::string &spectra)
const std::string &	getDb () const
	Specifies the name of a database (.trie file) to search.
void	setDb (const std::string &db)
const std::string &	getEnzyme () const
	Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values.
void	setEnzyme (const std::string &enzyme)
Int	getModificationsPerPeptide () const
	Number of PTMs permitted in a single peptide.
void	setModificationsPerPeptide (Int modifications_per_peptide)
UInt	getBlind () const
	run Inspect in a blind mode
void	setBlind (UInt blind)
float	getMaxPTMsize () const
	the maximum modification size (in Da) to consider in a blind search
void	setMaxPTMsize (float maxptmsize)
float	getPrecursorMassTolerance () const
	Specifies the parent mass tolerance, in Daltons.
void	setPrecursorMassTolerance (float precursor_mass_tolerance)
float	getPeakMassTolerance () const
	How far b and y peaks can be shifted from their expected masses.
void	setPeakMassTolerance (float peak_mass_tolerance)
UInt	getMulticharge () const
	If set to true, attempt to guess the precursor charge and mass, and consider multiple charge states if feasible.
void	setMulticharge (UInt multicharge)
const std::string &	getInstrument () const
	If set to QTOF, uses a QTOF-derived fragmentation model, and does not attempt to correct the parent mass.
void	setInstrument (const std::string &instrument)
Int	getTagCount () const
	Number of tags to generate.
void	setTagCount (Int TagCount)
const std::map< std::string, std::vector< std::string > > &	getModifications () const
	return the modifications (the modification names map to the affected residues, the mass change and the type)

Private Attributes
std::string	spectra_
	Specifies a spectrum file to search.
std::string	db_
	Specifies the name of a database (.trie file) to search. The .trie file contains one or more protein sequences delimited by asterisks, with no whitespace or other data.
std::string	enzyme_
	Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values.
Int	modifications_per_peptide_
	allowed number of modifications per peptide
UInt	blind_
float	maxptmsize_
	0 - false, 1 - true, 2 - not set
float	precursor_mass_tolerance_
	Specifies the parent mass tolerance, in Daltons. A candidate's flanking mass can differ from the tag's flanking mass by no more than this amount. <0 is not set.
float	peak_mass_tolerance_
	How far b and y peaks can be shifted from their expected masses. Default is 0.5. Higher values produce a more sensitive but much slower search. <0 is not set.
UInt	multicharge_
std::string	instrument_
	0 - false, 1 - true, 2 - not set
Int	tag_count_
	Number of tags to generate. <0 is not set.
std::map< std::string, std::vector< std::string > >	PTMname_residues_mass_type_
	the modification names map to the affected residues, the mass change and the type

Detailed Description

Inspect input file adapter.

Creates a file that can be used for Inspect search from a peak list.

Constructor & Destructor Documentation

InspectInfile() [1/2]

InspectInfile

(

)

default constructor

InspectInfile() [2/2]

InspectInfile

(

const InspectInfile &

inspect_infile

)

copy constructor

~InspectInfile()

virtual ~InspectInfile ( )

virtual

destructor

Member Function Documentation

getBlind()

UInt getBlind

(

)

const

run Inspect in a blind mode

If true, use the MS-Alignment algorithm to perform a blind search (allowing arbitrary modification masses). Running a blind search with one mod per peptide is slower than the normal (tag-based) search; running time is approximately 1 second per spectra per megabyte of database. Running a blind search with two mods is significantly slower. We recommend performing "blind" searches against a small database, containing proteins output by an earlier search.

getDb()

const std::string & getDb

(

)

const

Specifies the name of a database (.trie file) to search.

The .trie file contains one or more protein sequences delimited by asterisks, with no whitespace or other data. Use PrepDB.py (see above) to prepare a .trie file. Most .trie files have a corresponding .index file giving the names of the proteins. You can specify at most one database.

getEnzyme()

const std::string & getEnzyme

(

)

const

Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values.

getInstrument()

const std::string & getInstrument

(

)

const

If set to QTOF, uses a QTOF-derived fragmentation model, and does not attempt to correct the parent mass.

getMaxPTMsize()

float getMaxPTMsize

(

)

const

the maximum modification size (in Da) to consider in a blind search

Defaults to 200. Larger values require more time to search.

getModifications()

const std::map< std::string, std::vector< std::string > > & getModifications

(

)

const

return the modifications (the modification names map to the affected residues, the mass change and the type)

getModificationsPerPeptide()

Int getModificationsPerPeptide

(

)

const

Number of PTMs permitted in a single peptide.

getMulticharge()

UInt getMulticharge

(

)

const

If set to true, attempt to guess the precursor charge and mass, and consider multiple charge states if feasible.

getPeakMassTolerance()

float getPeakMassTolerance

(

)

const

How far b and y peaks can be shifted from their expected masses.

Default is 0.5. Higher values produce a more sensitive but much slower search.

getPrecursorMassTolerance()

float getPrecursorMassTolerance

(

)

const

Specifies the parent mass tolerance, in Daltons.

A candidate's flanking mass can differ from the tag's flanking mass by no more than this amount.

getSpectra()

const std::string & getSpectra

(

)

const

Specifies a spectrum file to search.

You can specify the name of a directory to search every file in that directory (non-recursively). Supported spectra file formats are .mzXML, .mzData, .ms2, dta, and .pkl. Multiple spectra in one .dta file are not supported.

getTagCount()

Int getTagCount

(

)

const

Number of tags to generate.

handlePTMs()

void handlePTMs	(	const std::string &	modification_line,
		const std::string &	modifications_filename,
		const bool	monoisotopic
	)

retrieves the name, mass change, affected residues, type and position for all modifications from a string

Parameters

[in]	modification_line
[in]	modifications_filename
[in]	monoisotopic	if true, masses are considered to be monoisotopic

Exceptions

FileNotReadable	if the modifications_filename could not be read
FileNotFound	if modifications_filename could not be found
ParseError	if modifications_filename could not be parsed

operator=()

InspectInfile & operator=

(

const InspectInfile &

inspect_infile

)

assignment operator

operator==()

bool operator==

(

const InspectInfile &

inspect_infile

)

const

equality operator

setBlind()

void setBlind

(

UInt

blind

)

setDb()

void setDb

(

const std::string &

db

)

setEnzyme()

void setEnzyme

(

const std::string &

enzyme

)

setInstrument()

void setInstrument

(

const std::string &

instrument

)

setMaxPTMsize()

void setMaxPTMsize

(

float

maxptmsize

)

setModificationsPerPeptide()

void setModificationsPerPeptide

(

Int

modifications_per_peptide

)

setMulticharge()

void setMulticharge

(

UInt

multicharge

)

setPeakMassTolerance()

void setPeakMassTolerance

(

float

peak_mass_tolerance

)

setPrecursorMassTolerance()

void setPrecursorMassTolerance

(

float

precursor_mass_tolerance

)

setSpectra()

void setSpectra

(

const std::string &

spectra

)

setTagCount()

void setTagCount

(

Int

TagCount

)

store()

void store

(

const std::string &

filename

)

stores the experiment data in an Inspect input file that can be used as input for Inspect shell execution

Parameters

[in]

filename

set the given filename

Exceptions

UnableToCreateFile

is thrown if the file could not be created

Member Data Documentation

blind_

UInt blind_

private

If true, use the MS-Alignment algorithm to perform a blind search (allowing arbitrary modification masses). Running a blind search with one mod per peptide is slower than the normal (tag-based) search; running time is approximately 1 second per spectra per megabyte of database. Running a blind search with two mods is significantly slower. We recommend performing "blind" searches against a small database, containing proteins output by an earlier search. (The "Summary.py" script can be used to generate a second-pass database from initial search results)

db_

std::string db_

private

Specifies the name of a database (.trie file) to search. The .trie file contains one or more protein sequences delimited by asterisks, with no whitespace or other data.

enzyme_

std::string enzyme_

private

Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values.

instrument_

std::string instrument_

private

0 - false, 1 - true, 2 - not set

If set to QTOF, uses a QTOF-derived fragmentation model, and does not attempt to correct the parent mass.

maxptmsize_

float maxptmsize_

private

0 - false, 1 - true, 2 - not set

For blind search, specifies the maximum modification size (in Da) to consider. Defaults to 200. Larger values require more time to search. <0 is not set

modifications_per_peptide_

Int modifications_per_peptide_

private

allowed number of modifications per peptide

multicharge_

UInt multicharge_

private

If set to true, attempt to guess the precursor charge and mass, and consider multiple charge states if feasible.

peak_mass_tolerance_

float peak_mass_tolerance_

private

How far b and y peaks can be shifted from their expected masses. Default is 0.5. Higher values produce a more sensitive but much slower search. <0 is not set.

precursor_mass_tolerance_

float precursor_mass_tolerance_

private

Specifies the parent mass tolerance, in Daltons. A candidate's flanking mass can differ from the tag's flanking mass by no more than this amount. <0 is not set.

PTMname_residues_mass_type_

std::map<std::string, std::vector<std::string> > PTMname_residues_mass_type_

private

the modification names map to the affected residues, the mass change and the type

spectra_

std::string spectra_

private

Specifies a spectrum file to search.

tag_count_

Int tag_count_

private

Number of tags to generate. <0 is not set.