OpenSwathTSVWriter Class Reference

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

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

Collaboration diagram for OpenSwathTSVWriter:

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