Metadata-Version: 1.1
Name: param-medic
Version: 0.2
Summary: Param-Medic optimizes MS/MS search parameter settings.
Home-page: UNKNOWN
Author: Damon May
Author-email: damonmay@uw.edu
License: Apache
Description: param-medic
        ===========
        
        Param-Medic breathes new life into MS/MS database searches by optimizing
        search parameter settings for your data.
        
        Usage:
        ------
        
        param-medic [--options] <spectra file>+
        
        Description:
        ------------
        
        In shotgun proteomics analysis, search engines compare tandem mass
        spectrometry spectra with theoretical spectra to make peptide-spectrum
        matches (PSMs). Proper selection of various parameters is critical to
        achieving good search performance. In particular,
        
        -  precursor mass tolerance defines the peptide candidates considered
           for each spectrum, and
        -  fragment mass tolerance (or bin size) determines how close observed
           and theoretical fragments must be in order to be considered a match.
        
        For each of these parameters, too large a setting yields randomly
        high-scoring false PSMs, while too small excludes true PSMs.
        
        Param-Medic finds pairs of spectra that are likely to have been
        generated by the same peptide and uses these pairs to infer optimal
        parameters for search with Comet, Tide and other search engines. If
        multiple input files are provided, then they will be processed together.
        
        Param-Medic may fail if too few paired spectra are discovered, or if the
        observed precursor m/z values appear to have been artificially
        manipulated.
        
        With permission, Param-Medic makes use of code repurposed from Jacob
        Schreiber's `Pomegranate <https://github.com/jmschrei/pomegranate>`__
        mixture-modeling software.
        
        Input
        -----
        
        -  <spectra file>+: The path to one or more files from which to parse
           fragmentation spectra, in .mzML or .ms2 format.
        
        Output
        ------
        
        The program prints to standard output the estimated parameter values for
        precursor mass tolerance (in ppm) and fragment bin size (in Th), as well
        as the standard deviations of the estimated error distributions for
        precursor and fragment masses.
        
        Options
        -------
        
        -  --min-precursor-mz : Minimum precursor m/z value to consider.
        -  --max-precursor-mz : Maximum precursor m/z value to consider.
        -  --min-frag-mz : Minimum fragment m/z value to consider.
        -  --max-frag-mz : Maximum fragment m/z value to consider.
        -  --min-scan-frag-peaks : Minimum fragment peaks an MS/MS scan must
           contain to be considered.
        -  --max-precursor-delta-ppm : Maximum ppm distance between precursor
           m/z values to consider two scans potentially generated by the same
           peptide.
        -  --charge : Precursor charge state to consider MS/MS spectra from.
           Ideally, this should be the most frequently occurring charge state in
           the given data.
        -  --top-n-frag-peaks : Number of most-intense fragment peaks to
           consider, per MS/MS spectrum.
        -  --pair-top-n-frag-peaks : Number of fragment peaks per spectrum pair
           to be used in fragment error estimation.
        -  --min-common-frag-peaks : Number of the most-intense peaks that two
           spectra must share in order to be potentially generated by the same
           peptide.
        -  --max-scan-separation : Maximum number of scans two spectra can be
           separated by in order to be considered potentially generated by the
           same peptide.
        -  --min-peak-pairs : Minimum number of peak pairs (for precursor or
           fragment) that must be successfully paired in order to attempt to
           estimate error distribution.
        -  --debug : If this flag is set, verbose debug logging will be enabled.
        
Keywords: proteomics LC-MS/MS MS/MS spectrometry
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
