| OpenMS 2.5.0

Public Member Functions | Private Attributes | List of all members
InspectInfile Class Reference
Format » File IO

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.