| OpenMS 2.5.0

Public Member Functions | Private Attributes | List of all members
OpenSwathTSVWriter Class Reference

Class to write out an OpenSwath TSV output (mProphet input). More...

`#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathTSVWriter.h>`

## Public Member Functions

| OpenSwathTSVWriter (const String &output_filename, const String &input_filename="inputfile", bool ms1_scores=false, bool sonar=false)
bool | isActive () const
void | writeHeader ()
| Initializes file by writing TSV header. More...
String | prepareLine (const OpenSwath::LightCompound &pep, const OpenSwath::LightTransition *transition, const FeatureMap &output, const String id) const
| Prepare a single line (feature) for output. More...
void | writeLines (const std::vector< String > &to_output)
| Write data to disk. More...

## Private Attributes

std::ofstream | ofs
String | input_filename_
bool | doWrite_
bool | use_ms1_traces_
bool | sonar_

## Detailed Description

Class to write out an OpenSwath TSV output (mProphet input).

The output is organized as a set of rows where each row describes a single peak in a chromatogram with a start and end retention time. Per chromatogram multiple rows can be reported if more than one potential peak was found. See also OpenSwathOSWWriter for another output format.

The class can take a FeatureMap and create a set of string from it suitable for output to tsv using the prepareLine() function. These lines can also be directly written to a file using writeLines().

The output format written by this class is a TSV file (tab-separated plain text file) with the following columns:

transition_group_id | string | designates the transition group [e.g. peptide/molecule] to which this transition belongs
peptide_group_label | string | designates to which peptide label group (as defined in MS:1000893) the peptide belongs to2
run_id | integer | LC-MS/MS run (currently always 0)
filename | string | filename of the raw LC-MS/MS file
RT | float | peak group retention time (apex)
id | string | unique peak group identifier
Sequence | string | Peptide sequence
MC | int | Number of missed cleavages
FullPeptideName | string | Full peptide sequence including modifications 1
Charge | string | Peptide (analyte) precursor charge
m/z | string | Peptide (analyte) precursor m/z
Intensity | float | Peptide (analyte) intensity (sum over all fragment ion intensities)
ProteinName | string | Protein Identifier
GeneName | string | Gene identifier
decoy | string | Whether peak group was found in a decoy chromatogram (0 = false)
assay_rt | string | The retention time at which the peptide (analyte) was expected to elute based on the retention time calibration
delta_rt | string | The difference in retention between expected retention time (assay_rt) and peak group retention time (RT)
leftWidth | float | Retention time start of the peak (left width) in seconds
main_var_xx_swath_prelim_score | float | Preliminary separation for pyProphet initialization
norm_RT | string | The position of the peak group in the normalized retention time space (e.g. fx(RT) where fx describes the transformation fx)
nr_peaks | int | The number of transitions used
peak_apices_sum | float | The sum of the peak apices intensities
potentialOutlier | string | Potential outlier transition
initialPeakQuality | float | Initial peak quality score (if computing peak quality was enabled)
rightWidth | string | Retention time end of the peak (left width) in seconds
rt_score | string | sequence
sn_ratio | float | Signal-to-Noise ratio
total_xic | float | Total XIC
var_... | float | A variable used for the post-processing and scoring
aggr_prec_Peak_Area | float-list | MS1 Precursor peak area (for each isotope)
aggr_prec_Peak_Apex | float-list | MS1 Precursor peak apex (for each isotope)
aggr_prec_Annotation | string-list | MS1 Precursor annotation (for each isotope)
aggr_Peak_Area | float-list | Fragment ion peak area (for each transition)
aggr_Peak_Apex | float-list | Fragment ion peak apex (for each transition)
aggr_Fragment_Annotation | string-list | Fragment ion annotation (for each transition)
masserror_ppm | string | Fragment-level mass error for each transition (see aggr_Fragment_Annotation for order)
rt_fwhm | string | Fragment-level FWHM (full width half maximum) for each individual transition (see aggr_Fragment_Annotation for order)

Remarks:

- 1. modifications should be supplied inside the sequence using UniMod identifiers or freetext identifiers that are understood by OpenMS. See also OpenMS::AASequence for more information. For example:
  - PEPT(Phosphorylation)IDE(UniMod:27)A )
- 2. peptide label groups designate groups of peptides that are isotopically modified forms of the same peptide species. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label. For example:
  - PEPTIDEAK -> gets label "PEPTIDEAK_gr1"
  - PEPTIDEAK[+8] -> gets label "PEPTIDEAK_gr1"
  - PEPT(Phosphorylation)IDEAK -> gets label "PEPTIDEAK_gr2"
  - PEPT(Phosphorylation)IDEAK[+8] -> gets label "PEPTIDEAK_gr2"

## Constructor & Destructor Documentation

## ◆ OpenSwathTSVWriter()

OpenSwathTSVWriter | ( | const String & | output_filename,
|  | const String & | input_filename = `"inputfile"`,
|  | bool | ms1_scores = `false`,
|  | bool | sonar = `false`
| ) |  |

## Member Function Documentation

## ◆ isActive()

bool isActive | ( |  | ) | const

## ◆ prepareLine()

String prepareLine | ( | const OpenSwath::LightCompound & | pep,
|  | const OpenSwath::LightTransition * | transition,
|  | const FeatureMap & | output,
|  | const String | id
| ) |  | const

Prepare a single line (feature) for output.

The result can be flushed to disk using writeLines (either line by line or after collecting several lines).

Parameters

  pep | The compound (peptide/metabolite) used for extraction
  transition | The transition used for extraction
  output | The feature map containing all features (each feature will generate one entry in the output)
  id | The transition group identifier (peptide/metabolite id)

Returns
  A string to be written using writeLines

## ◆ writeHeader()

void writeHeader | ( |  | ) |

Initializes file by writing TSV header.

## ◆ writeLines()

void writeLines | ( | const std::vector< String > & | to_output | ) |

Write data to disk.

Takes a set of pre-prepared data statements from prepareLine and flushes them to disk

Parameters

  to_output | Statements generated by prepareLine to be written to a file

Note
  Only call inside an OpenMP critical section

## Member Data Documentation

## ◆ doWrite_

bool doWrite_

private

## ◆ input_filename_

String input_filename_

private

## ◆ ofs

std::ofstream ofs

private

## ◆ sonar_

bool sonar_

private

## ◆ use_ms1_traces_

bool use_ms1_traces_

private