param-medic 0.2
Param-Medic optimizes MS/MS search parameter settings.
License: Apache
Keywords: proteomics LC-MS/MS MS/MS spectrometry

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.