# param-medic

## Usage:

crux param-medic [options] <spectrum-file>+

## Description:

Examine the spectra in a file to estimate the best precursor and fragment error tolerances for database search.

## Input:

• spectrum-file+ – File from which to parse fragmentation spectra.

## Output:

The program writes files to the folder crux-output by default. The name of the output folder can be set by the user using the --output-dir option. The following files will be created:

• stdout – 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:

• ### param-medic options

• --pm-min-precursor-mz <float> – Minimum precursor m/z value to use in measurement error estimation. Default = 400.
• --pm-max-precursor-mz <float> – Minimum precursor m/z value to use in measurement error estimation. Default = 1800.
• --pm-min-frag-mz <float> – Minimum fragment m/z value to use in measurement error estimation. Default = 150.
• --pm-max-frag-mz <float> – Maximum fragment m/z value to use in measurement error estimation. Default = 1800.
• --pm-min-scan-frag-peaks <integer> – Minimum fragment peaks an MS/MS scan must contain to be used in measurement error estimation. Default = 40.
• --pm-max-precursor-delta-ppm <float> – Maximum ppm distance between precursor m/z values to consider two scans potentially generated by the same peptide for measurement error estimation. Default = 50.
• --pm-charges <string> – Precursor charge states to consider MS/MS spectra from, in measurement error estimation, provided as comma-separated values. Default = 0,2,3,4.
• --pm-top-n-frag-peaks <integer> – Number of most-intense fragment peaks to consider for measurement error estimation, per MS/MS spectrum. Default = 30.
• --pm-pair-top-n-frag-peaks <integer> – Number of fragment peaks per spectrum pair to be used in fragment error estimation. Default = 5.
• --pm-min-common-frag-peaks <integer> – Number of the most-intense peaks that two spectra must share in order to potentially be generated by the same peptide, for measurement error estimation. Default = 20.
• --pm-max-scan-separation <integer> – Maximum number of scans two spectra can be separated by in order to be considered potentially generated by the same peptide, for measurement error estimation. Default = 1000.
• --pm-min-peak-pairs <integer> – Minimum number of peak pairs (for precursor or fragment) that must be successfully paired in order to attempt to estimate measurement error distribution. Default = 200.
• ### Input and output

• --verbosity <integer> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = 30.
• --spectrum-parser pwiz|mstoolkit – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed here. The alternative is MSToolkit parser. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = pwiz.