InspectInfile Class Reference

Inspect input file adapter. More...

#include <OpenMS/FORMAT/InspectInfile.h>

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

Private Attributes
String	spectra_
	Specifies a spectrum file to search. More...
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. More...
String	enzyme_
	Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values. More...
Int	modifications_per_peptide_
	allowed number of modifications per peptide More...
UInt	blind_
float	maxptmsize_
	0 - false, 1 - true, 2 - not set More...
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. More...
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. More...
UInt	multicharge_
String	instrument_
	0 - false, 1 - true, 2 - not set More...
Int	tag_count_
	Number of tags to generate. <0 is not set. More...
std::map< String, std::vector< String > >	PTMname_residues_mass_type_
	the modification names map to the affected residues, the mass change and the type More...

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 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 String& getEnzyme

(

)

const

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

getInstrument()

const 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<String, std::vector<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 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 String &	modification_line,
		const String &	modifications_filename,
		const bool	monoisotopic
	)

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

Parameters

modification_line
modifications_filename
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 String &

db

)

setEnzyme()

void setEnzyme

(

const String &

enzyme

)

setInstrument()

void setInstrument

(

const 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 String &

spectra

)

setTagCount()

void setTagCount

(

Int

TagCount

)

store()

void store

(

const String &

filename

)

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

Parameters

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_

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_

String enzyme_

private

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

instrument_

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<String, std::vector<String> > PTMname_residues_mass_type_

private

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

spectra_

String spectra_

private

Specifies a spectrum file to search.

tag_count_

Int tag_count_

private

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