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FeatureFinderIdentification

Detects features in MS1 data based on peptide identifications.

pot. predecessor tools $ \longrightarrow $ FeatureFinderIdentification $ \longrightarrow $ pot. successor tools
PeakPickerHiRes ProteinQuantifier
IDFilter

This tool detects quantitative features in MS1 data based on information from peptide identifications (derived from MS2 spectra). It uses algorithms for targeted data analysis from the OpenSWATH pipeline.

Note
It is important that only high-confidence peptide identifications and centroided (peak-picked) LC-MS data are used as inputs!

For every distinct peptide ion (defined by sequence and charge) in the input (parameter id), an assay is generated, incorporating the retention time (RT), mass-to-charge ratio (m/z), and isotopic distribution of the peptide. The parameter reference_rt controls how the RT of the assay is determined if the peptide has been observed multiple times. The relative intensities of the isotopes together with their m/z values are calculated from the sequence and charge.

The assays are used to perform targeted data analysis on the MS1 level using OpenSWATH algorithms, in several steps:

1. Ion chromatogram extraction

First ion chromatograms (XICs) are extracted from the data (parameter in). For every assay, the RT range of the XICs is given by extract:rt_window (around the reference RT of the assay) and the m/z ranges by extract:mz_window (around the m/z values of all included isotopes). As an exception to this, if extract:reference_rt is adapt, a more complex procedure is used to find the RT range: A range of size rt_window around every relevant peptide ID is considered, overlapping ranges are joined, and the largest resulting range is used for the extraction. In that case, the reference RT for the assay is the median RT of the peptide IDs within the range.

See Also
OpenSwathChromatogramExtractor

2. Feature detection

Next feature candidates are detected in the XICs and scored. The best candidate per assay according to the OpenSWATH scoring is turned into a feature.

See Also
OpenSwathAnalyzer

3. Elution model fitting

Elution models can be fitted to every feature to improve the quantification. For robustness, one model is fitted to all isotopic mass traces of a feature in parallel. A symmetric (Gaussian) and an asymmetric (exponential-Gaussian hybrid) model type are available. The fitted models are checked for plausibility before they are accepted.

Finally the results (feature maps, parameter out) are returned.

Note
This tool aims to report a feature for every distinct peptide ion given in the id input. Currently no attempt is made to filter out false-positives (although this may be possible in post-processing based on the OpenSWATH scores). If only high-confidence peptide IDs are used, that come from the same LC-MS/MS run that is being quantified, this should not be a problem. However, if e.g. inferred IDs from different runs (see MapAlignerIdentification) are included, false-positive features with arbitrary intensities may result for peptides that cannot be detected in the present data.
Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

FeatureFinderIdentification -- Detects features in MS1 data based on peptide identifications.
Version: 2.0.0 Mar 30 2016, 12:52:33, Revision: GIT-NOTFOUND

Usage:
  FeatureFinderIdentification <options>

Options (mandatory options marked with '*'):
  -in <file>*                     Input file (LC-MS raw data) (valid formats: 'mzML')
  -id <file>*                     Input file (peptide identifications) (valid formats: 'idXML')
  -out <file>*                    Output file (features) (valid formats: 'featureXML')
  -lib_out <file>                 Output file (assay library) (valid formats: 'traML')
  -chrom_out <file>               Output file (chromatograms) (valid formats: 'mzML')
  -trafo_out <file>               Output file (RT transformation) (valid formats: 'trafoXML')

Parameters for ion chromatogram extraction:
  -extract:reference_rt <choice>  Method for selecting the reference RT, if there are multiple IDs for a pept
                                  ide and charge. 'adapt': adapt (extend) RT windows based on IDs; 'score':
                                  RT of the best-scoring ID; 'intensity': RT of the ID with the most intense
                                  precursor; 'median': median RT of all IDs; 'all': no single reference, use
                                  RTs of all IDs (requires further processing of results). (default: 'adapt'
                                  valid: 'adapt', 'score', 'intensity', 'median', 'all')
  -extract:rt_window <value>      RT window size (in sec.) for chromatogram extraction. (default: '60' min: 
                                  '0')
  -extract:mz_window <value>      M/z window size for chromatogram extraction (unit: ppm if 1 or greater, 
                                  else Da/Th) (default: '10' min: '0')
  -extract:isotope_pmin <value>   Minimum probability for an isotope to be included in the assay for a peptid
                                  e. (default: '0.03' min: '0' max: '1')

Parameters for detecting features in extracted ion chromatograms:
  -detect:peak_width <value>      Elution peak width in seconds for smoothing (Gauss filter) (default: '30' 
                                  min: '0')

Parameters for fitting elution models to features:
  -model:type <choice>            Type of elution model to fit to features (default: 'symmetric' valid: 'symm
                                  etric', 'asymmetric', 'none')

                                  
Common TOPP options:
  -ini <file>                     Use the given TOPP INI file
  -threads <n>                    Sets the number of threads allowed to be used by the TOPP tool (default: 
                                  '1')
  -write_ini <file>               Writes the default configuration file
  --help                          Shows options
  --helphelp                      Shows all options (including advanced)

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+FeatureFinderIdentificationDetects features in MS1 data based on peptide identifications.
version2.0.0 Version of the tool that generated this parameters file.
++1Instance '1' section for 'FeatureFinderIdentification'
in Input file (LC-MS raw data)input file*.mzML
id Input file (peptide identifications)input file*.idXML
out Output file (features)output file*.featureXML
lib_out Output file (assay library)output file*.traML
chrom_out Output file (chromatograms)output file*.mzML
trafo_out Output file (RT transformation)output file*.trafoXML
log Name of log file (created only when specified)
debug0 Sets the debug level
threads1 Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse Disables progress logging to command linetrue,false
forcefalse Overwrite tool specific checks.true,false
testfalse Enables the test mode (needed for internal use only)true,false
+++extractParameters for ion chromatogram extraction
reference_rtadapt Method for selecting the reference RT, if there are multiple IDs for a peptide and charge. 'adapt': adapt (extend) RT windows based on IDs; 'score': RT of the best-scoring ID; 'intensity': RT of the ID with the most intense precursor; 'median': median RT of all IDs; 'all': no single reference, use RTs of all IDs (requires further processing of results).adapt,score,intensity,median,all
rt_window60 RT window size (in sec.) for chromatogram extraction.0:∞
mz_window10 m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)0:∞
isotope_pmin0.03 Minimum probability for an isotope to be included in the assay for a peptide.0:1
+++detectParameters for detecting features in extracted ion chromatograms
peak_width30 Elution peak width in seconds for smoothing (Gauss filter)0:∞
all_featuresfalse Return all features detected by OpenSWATH for an assay, instead of only the best one. (This requires further processing of the results.)true,false
+++modelParameters for fitting elution models to features
typesymmetric Type of elution model to fit to featuressymmetric,asymmetric,none
add_zeros0.2 Add zero-intensity points outside the feature range to constrain the model fit. This parameter sets the weight given to these points during model fitting; '0' to disable.0:∞
unweighted_fitfalse Suppress weighting of mass traces according to theoretical intensities when fitting elution modelstrue,false
no_imputationfalse If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimatetrue,false
++++checkParameters for checking the validity of elution models (and rejecting them if necessary)
boundaries0.5 Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting0:1
width10 Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores; '0' to disable0:∞
asymmetry10 Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable0:∞

OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 16:18:43 using doxygen 1.8.5