Metrics of one run, including its isolation windows. More...

#include <DIAuditor/include/DIAQCMetrics.h>

Public Member Functions
	RunMetrics ()

Public Attributes
std::string	source_file
	file name without directory and extension

std::string	input_path
	path of the input file or directory (for mzQC)

FileTypes::Type	input_type = FileTypes::MZML
	format of the input (for mzQC): mzML, Thermo RAW or Bruker TDF

std::string	file_sha1
	SHA-1 of the input file (for mzQC); may be empty.

std::string	instrument
	instrument model name

std::string	serial_number
	instrument serial number

std::string	start_time_stamp
	start of the acquisition as written in the file

double	rt_min
	seconds, over all spectra

double	rt_max
	seconds, over all spectra

Size	ms1_count = 0

Size	msn_count = 0
	spectra of MS level 2 and higher

Size	ms2_count = 0
	spectra of MS level 2

Size	spectra_without_rt = 0
	spectra without retention time (not used for other metrics)

Size	ms2_multiple_precursors = 0

Size	ms2_scan_ion_mobility = 0
	MS2 spectra that look like single ion mobility scans (no range or IM array)

Size	ms2_im_array_without_range = 0

double	precursor_mz_min
	lowest precursor m/z of the MSn spectra (selected ion, or isolation target)

double	precursor_mz_max
	highest precursor m/z of the MSn spectra

double	ms1_mass_resolving_power
	median over MS1 spectra

TICQuantileRTs	ms1_tic_quantile_rt

double	ms1_total_tic = 0.0

double	ms1_cycle_time_median

PeakCountSummary	ms1_peak_count

TICQuantileRTs	ms2_tic_quantile_rt

double	ms2_total_tic = 0.0

PeakCountSummary	ms2_peak_count

Size	window_count = 0
	DIA isolation windows (not counting without_isolation_window)

Size	windows_measured_once = 0
	windows with a single MS2 spectrum

double	window_spectra_min
	fewest spectra of any window

double	window_spectra_max
	most spectra of any window

double	window_mz_min
	lowest lower m/z of any window

double	window_mz_max
	highest upper m/z of any window

double	window_width_min

double	window_width_max

double	window_cycle_time_mean
	mean of the windows' median cycle times (DIAuditor's AverageMedianCycleTime)

double	window_cycle_time_median
	median of all times between consecutive spectra of the same window

double	window_half_tic_rt_min
	earliest of the windows' 50% TIC retention times

double	window_half_tic_rt_max
	latest of the windows' 50% TIC retention times

double	window_total_tic_min

double	window_total_tic_max

double	window_peak_count_median_min

double	window_peak_count_median_max

std::vector< WindowMetrics >	windows
	the DIA isolation windows

WindowMetrics	without_isolation_window

Detailed Description

Metrics of one run, including its isolation windows.

Constructor & Destructor Documentation

◆ RunMetrics()

RunMetrics ( )

Member Data Documentation

◆ file_sha1

std::string file_sha1

SHA-1 of the input file (for mzQC); may be empty.

◆ input_path

std::string input_path

path of the input file or directory (for mzQC)

◆ input_type

FileTypes::Type input_type = FileTypes::MZML

format of the input (for mzQC): mzML, Thermo RAW or Bruker TDF

◆ instrument

std::string instrument

instrument model name

Referenced by DIAQCMetrics::compute().

◆ ms1_count

Size ms1_count = 0

Referenced by DIAQCMetrics::compute().

◆ ms1_cycle_time_median

double ms1_cycle_time_median

Referenced by DIAQCMetrics::compute().

◆ ms1_mass_resolving_power

double ms1_mass_resolving_power

median over MS1 spectra

Referenced by DIAQCMetrics::compute().

◆ ms1_peak_count

PeakCountSummary ms1_peak_count

Referenced by DIAQCMetrics::compute().

◆ ms1_tic_quantile_rt

TICQuantileRTs ms1_tic_quantile_rt

Referenced by DIAQCMetrics::compute().

◆ ms1_total_tic

double ms1_total_tic = 0.0

Referenced by DIAQCMetrics::compute().

◆ ms2_count

Size ms2_count = 0

spectra of MS level 2

Referenced by DIAQCMetrics::compute().

◆ ms2_im_array_without_range

Size ms2_im_array_without_range = 0

MS2 spectra with an isolation window and an ion mobility array, but no ion mobility range of the window (e.g. diaPASEF from TIMSCONVERT)

Referenced by DIAQCMetrics::compute().

◆ ms2_multiple_precursors

Size ms2_multiple_precursors = 0

MS2 spectra with more than one isolation window, i.e. precursor element (e.g. multiplexed acquisition such as MSX); only the first is used

Referenced by DIAQCMetrics::compute().

◆ ms2_peak_count

PeakCountSummary ms2_peak_count

Referenced by DIAQCMetrics::compute().

◆ ms2_scan_ion_mobility

Size ms2_scan_ion_mobility = 0

MS2 spectra that look like single ion mobility scans (no range or IM array)

Referenced by DIAQCMetrics::compute().

◆ ms2_tic_quantile_rt

TICQuantileRTs ms2_tic_quantile_rt

Referenced by DIAQCMetrics::compute().

◆ ms2_total_tic

double ms2_total_tic = 0.0

Referenced by DIAQCMetrics::compute().

◆ msn_count

Size msn_count = 0

spectra of MS level 2 and higher

Referenced by DIAQCMetrics::compute().

◆ precursor_mz_max

double precursor_mz_max

highest precursor m/z of the MSn spectra

Referenced by DIAQCMetrics::compute().

◆ precursor_mz_min

double precursor_mz_min

lowest precursor m/z of the MSn spectra (selected ion, or isolation target)

Referenced by DIAQCMetrics::compute().

◆ rt_max

double rt_max

seconds, over all spectra

Referenced by DIAQCMetrics::compute().

◆ rt_min

double rt_min

seconds, over all spectra

Referenced by DIAQCMetrics::compute().

◆ serial_number

std::string serial_number

instrument serial number

Referenced by DIAQCMetrics::compute().

◆ source_file

std::string source_file

file name without directory and extension

◆ spectra_without_rt

Size spectra_without_rt = 0

spectra without retention time (not used for other metrics)

Referenced by DIAQCMetrics::compute().

◆ start_time_stamp

std::string start_time_stamp

start of the acquisition as written in the file

Referenced by DIAQCMetrics::compute().

◆ window_count

Size window_count = 0

DIA isolation windows (not counting without_isolation_window)

Referenced by DIAQCMetrics::compute().

◆ window_cycle_time_mean

double window_cycle_time_mean

mean of the windows' median cycle times (DIAuditor's AverageMedianCycleTime)

Referenced by DIAQCMetrics::compute().

◆ window_cycle_time_median

double window_cycle_time_median

median of all times between consecutive spectra of the same window

Referenced by DIAQCMetrics::compute().

◆ window_half_tic_rt_max

double window_half_tic_rt_max

latest of the windows' 50% TIC retention times

Referenced by DIAQCMetrics::compute().

◆ window_half_tic_rt_min

double window_half_tic_rt_min

earliest of the windows' 50% TIC retention times

Referenced by DIAQCMetrics::compute().

◆ window_mz_max

double window_mz_max

highest upper m/z of any window

Referenced by DIAQCMetrics::compute().

◆ window_mz_min

double window_mz_min

lowest lower m/z of any window

Referenced by DIAQCMetrics::compute().

◆ window_peak_count_median_max

double window_peak_count_median_max

Referenced by DIAQCMetrics::compute().

◆ window_peak_count_median_min

double window_peak_count_median_min

Referenced by DIAQCMetrics::compute().

◆ window_spectra_max

double window_spectra_max

most spectra of any window

Referenced by DIAQCMetrics::compute().

◆ window_spectra_min

double window_spectra_min

fewest spectra of any window

Referenced by DIAQCMetrics::compute().

◆ window_total_tic_max

double window_total_tic_max

Referenced by DIAQCMetrics::compute().

◆ window_total_tic_min

double window_total_tic_min

Referenced by DIAQCMetrics::compute().

◆ window_width_max

double window_width_max

Referenced by DIAQCMetrics::compute().

◆ window_width_min

double window_width_min

Referenced by DIAQCMetrics::compute().

◆ windows

std::vector<WindowMetrics> windows

the DIA isolation windows

Referenced by DIAQCMetrics::compute().

◆ windows_measured_once

Size windows_measured_once = 0

windows with a single MS2 spectrum

Referenced by DIAQCMetrics::compute().

◆ without_isolation_window

WindowMetrics without_isolation_window

MS2 spectra without an isolation window, as one group (spectrum_count 0 if there are none). This is not a DIA isolation window: it is neither in windows nor in the window statistics above.

Referenced by DIAQCMetrics::compute().

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ RunMetrics()

Member Data Documentation

◆ file_sha1

◆ input_path

◆ input_type

◆ instrument

◆ ms1_count

◆ ms1_cycle_time_median

◆ ms1_mass_resolving_power

◆ ms1_peak_count

◆ ms1_tic_quantile_rt

◆ ms1_total_tic

◆ ms2_count

◆ ms2_im_array_without_range

◆ ms2_multiple_precursors

◆ ms2_peak_count

◆ ms2_scan_ion_mobility

◆ ms2_tic_quantile_rt

◆ ms2_total_tic

◆ msn_count

◆ precursor_mz_max

◆ precursor_mz_min

◆ rt_max

◆ rt_min

◆ serial_number

◆ source_file

◆ spectra_without_rt

◆ start_time_stamp

◆ window_count

◆ window_cycle_time_mean

◆ window_cycle_time_median

◆ window_half_tic_rt_max

◆ window_half_tic_rt_min

◆ window_mz_max

◆ window_mz_min

◆ window_peak_count_median_max

◆ window_peak_count_median_min

◆ window_spectra_max

◆ window_spectra_min

◆ window_total_tic_max

◆ window_total_tic_min

◆ window_width_max

◆ window_width_min

◆ windows

◆ windows_measured_once

◆ without_isolation_window