# `mzdeisotope` - Tools for deisotoping and charge deconvolution for mass spectra
## Components
- `mzdeisotope` - A Rust library with tools for deconvolution of peak lists
- `mzdeisotoper` - An executable tool for applying the deconvolution process whole mass spectrometry data files
## Library Usage
**TODO**
## Tool Usage
```
$ mzdeisotoper --help
Deisotoping and charge state deconvolution of mass spectrometry files.
Read a file or stream, transform the spectra, and write out a processed mzML file or stream.
Usage: mzdeisotoper [OPTIONS] <INPUT_FILE>
Arguments:
<INPUT_FILE>
The path to read the input spectra from, or if '-' is passed, read from STDIN
Options:
-o, --output-file <OUTPUT_FILE>
The path to write the output file to, or if '-' is passed, write to STDOUT
[default: -]
-t, --threads <THREADS>
The number of threads to use, passing a value < 1 to use all available threads
[default: -1]
-r, --time-range <BEGIN-END>
The time range to process, denoted [start?]-[stop?]
If a start is not specified, processing begins from the start of the run.
If a stop is not specified, processing stops at the end of the run.
-g, --ms1-averaging-range <MS1_AVERAGING_RANGE>
The number of MS1 spectra before and after to average with prior to peak picking
[default: 0]
-b, --ms1-background-reduction <MS1_DENOISING>
The magnitude of background noise reduction to use on MS1 spectra prior to peak picking
[default: 0]
-a, --ms1-isotopic-model <MS1_ISOTOPIC_MODEL>
The isotopic model to use for MS1 spectra
[default: peptide]
[possible values: peptide, glycan, glycopeptide, permethylated-glycan, heparin, heparan-sulfate]
-s, --ms1-score-threshold <MS1_SCORE_THRESHOLD>
The minimum isotopic pattern fit score for MS1 spectra
[default: 20]
-A, --msn-isotopic-model <MSN_ISOTOPIC_MODEL>
The isotopic model to use for MSn spectra
[default: peptide]
[possible values: peptide, glycan, glycopeptide, permethylated-glycan, heparin, heparan-sulfate]
-S, --msn-score-threshold <MSN_SCORE_THRESHOLD>
The minimum isotopic pattern fit score for MSn spectra
[default: 10]
-v, --precursor-processing <PRECURSOR_PROCESSING>
How to treat precursor ranges
[default: selected-precursors]
Possible values:
- full: Process the entire MS1 mass range and all MSn spectra
- selected-precursors: Process only the MS1 regions that are selected for MSn and all MSn spectra
- tandem-only: Process only MSn spectra without examining MS1 spectra
- ms1-only: Process only the MS1 spectra without examining MSn spectra
-z, --charge-range <CHARGE_RANGE>
The range of charge states to consider for each peak denoted [low]-[high] or [high]
[default: 1-8]
-m, --max-missed-peaks <MS1_MISSED_PEAKS>
The maximum number of missed peaks for MS1 spectra
[default: 1]
-M, --msn-max-missed-peaks <MSN_MISSED_PEAKS>
The maximum number of missed peaks for MSn spectra
[default: 1]
-h, --help
Print help (see a summary with '-h')
-V, --version
Print version
```
`mzdeisotoper` can read mzML, MGF, and if built with the `mzmlb` feature, mzMLb from the file
system. The program can also receive mzML or MGF over STDIN, letting you pipe the output of a
tool like `msconvert` or `curl` into it.