ProMex Usage

ProMex is an LC-MS feature extraction tool that detects isotopomer envelopes of intact protein ions and determines their monoisotopic masses and abundances. The detected features are output to a .ms1ft file containing information including monoisotopic mass, range of charge states, elution-time span (consecutive spectra) and abundance.

Inputs

1. An instrument file or previously created .pbf file
2. Command line options

Outputs

• A *.ms1ft file
• A *_ms1ft.png image of features
• A *.pbf file (if a .pbf file was not provided)

ProMex Syntax

ProMex version 1.0.7569 (September 21, 2020)

Usage: ProMex.exe

  -?, -help            Show this help screen

  -i, arg#1            Required. Input file or input folder; supports .pbf,
                       .mzML, and several vendor formats (see documentation)

  -o                   Output directory. (Default: directory containing input
                       file)

  -minCharge           Minimum charge state (Default: 1, Min: 1, Max: 60)

  -maxCharge           Maximum charge state (Default: 60, Min: 1, Max: 60)

  -minMass             Minimum mass in Da (Default: 2000, Min: 600, Max: 100000)

  -maxMass             Maximum mass in Da (Default: 50000, Min: 600,
                       Max: 100000)

  -featureMap          Output the feature heatmap (Default: True)

  -score               Output extended scoring information (Default: False)

  -maxThreads          Max number of threads to use (Default: 0 (automatically
                       determine the number of threads to use))

  -csv                 Also write feature data to a CSV file (Default: False)

  -scoreTh             Likelihood score threshold (Default: -10)

  -ms1ft               ms1ft format feature file path (use '.' to infer the name
                       from the pbf file)

  -ParamFile           Path to a file containing program parameters. Additional
                       arguments on the command line can supplement or override
                       the arguments in the param file. Lines starting with '#'
                       or ';' will be treated as comments; blank lines are
                       ignored. Lines that start with text that does not match a
                       parameter will also be ignored.

  -CreateParamFile     Create an example parameter file. Can supply a path; if
                       path is not supplied, the example parameter file content
                       will output to the console.

  NOTE:                arg#1, arg#2, etc. refer to positional arguments, used
                       like "AppName.exe [arg#1] [arg#2] [other args]".

Examples

With a previously created .pbf file:

ProMex.exe -i MyDataset.pbf -minCharge 2 -maxCharge 60 -minMass 3000 -maxMass 50000 -score n -csv n -maxThreads 0

With a instrument/spectra file:

ProMex.exe -i MyDataset.raw -minCharge 2 -maxCharge 60 -minMass 3000 -maxMass 50000 -score n -csv n -maxThreads 0
ProMex.exe -i MyDataset.mzML -minCharge 2 -maxCharge 60 -minMass 3000 -maxMass 50000 -score n -csv n -maxThreads 0

To create a PNG of the features in an existing ms1ft file (requires both a .pbf file and a .ms1ft file):

ProMex.exe -i dataset.pbf -ms1ft dataset.ms1ft -featureMap

System Requirements and Recommendations

Minimum required:

• .NET 4.7.2

Minimum recommended:

• 2.4 GHz, quad-core CPU
• 16 GB RAM
• Windows 7 or newer
• 250 GB hard drive