MSCONVERT(1)

💖 MSCONVERT(1) — the glow-up edition 💖

okay bestie, so we're in the General Commands Manual corner of the terminal, and today's main character is msconvert. pull up a chair, grab a strawberry 🍓, and let's get into it.

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✨ NAME ✨

msconvert — literally just converts mass spectrometry data file formats. that's the whole job. she's a converter. she converts. 💅

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🦋 SYNOPSIS 🦋

msconvert [options] [filemasks]

that's it. that's the shape of her. options go brrr, then the filemasks. slay.

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🌸 DESCRIPTION 🌸

so this manual page is here to give you the brief tea on the msconvert software that ships inside the libpwiz-tools package. 🫶

this program lets you convert mass spectrometry data files from one format to another. format glow-up, basically. ✨

but listen — important one. because this version is built on the Free Software Debian platform, only conversions involving Free Software can be performed. that means not conversions involving proprietary Microsoft Windows-based dynamic linking libraries (dlls). no dlls, no drama. periodt.

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👑 OPTIONS 👑

here come all of them, no skips, no cuts, full list, we don't gatekeep:

• -v | --verbose — spill the tea on everything. displays detailed processing progress information. 👀
• --help — shows you this message, plus extra detail on the filter options. the friend that explains things. 🎀
• -f | --filelist filename — uses the contents of filename, which is a file that lists filenames. yes, a list of files. very meta, we love her. 💜
• -o | --outdir dir — sets the output directory to dir ('-' means stdout, cute). by default the output directory is '.', aka the current working directory. home sweet home. 🏠
• -c | --config filename — sets the configuration file to filename. 🗂️
• --outfile filename — overrides the name of the output file. she said "I'll name her." 💅
• -e | --ext ext — sets the extension of the output files to ext. can be mzML or mzXML or mgf or txt. pick your fighter. ⭐
• --mzML — writes mzML format (this is the default, bestie). 👑
• --mzXML — writes mzXML format.
• --mgf — writes mgf Mascot generic format. 🧚
• --text — writes ProteoWizard internal text format.
• --ms1 — writes MS1 format.
• --cms1 — writes CMS1 format.
• --ms2 — writes MS2 format.
• --cms2 — writes CMS2 format.
• --64 — sets default binary encoding to 64-bit precision (default, iconic).
• --32 — sets default binary encoding to 32-bit precision.
• --mz64 — encodes m/z values in 64-bit precision (default).
• --mz32 — encodes m/z values in 32-bit precision.
• --inten64 — encodes intensity values in 64-bit precision.
• --inten32 — encodes intensity values in 32-bit precision (default).
• --noindex — do not write index. she's going index-free, unbothered. 🙈
• -i | --contactInfo filename — use filename for contact info. 📇
• -z | --zlib — use zlib compression for binary data. squeezed. 🫧
• -g | --gzip — gzip the entire output file (this adds .gz to the filename, heads up).
• --filter arg — add a spectrum list filter. 🧃
• --merge — creates a single output file from multiple input files by merging file-level metadata and concatenating spectrum lists. she's a uniter, not a divider. 🫶
• --simAsSpectra — writes selected ion monitoring as spectra, not chromatograms.
• --srmAsSpectra — writes selected reaction monitoring as spectra, not chromatograms.

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🌈 EXAMPLES 🌈

convert data.RAW to data.mzXML

msconvert data.RAW --mzXML

put output file in my_output_dir

msconvert data.RAW -o my_output_dir

extract scan indices 5...10 and 20...25

msconvert data.RAW --filter "index [5,10] [20,25]"

extract MS1 scans only

msconvert data.RAW --filter "msLevel 1"

extract MSn scans for n>1

msconvert data.RAW --filter "msLevel 2-"

use a configuration file

msconvert data.RAW -c config.txt

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🔥 RETURN VALUE 🔥

the number of failed files. that's the exit vibe. if it's zero, we ate. 😭

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🎀 AUTHOR 🎀

Filippo Rusconi <lopippo@debian.org> 💖

this manual page was written by Filippo Rusconi <lopippo@debian.org> (initial writing 05 december 2013). permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 3, published by the Free Software Foundation.

on a Debian system the complete text of the GNU General Public License version 3 can be found in the file /usr/share/common-licenses/GPL-3.

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and that's the whole page, bestie — it's the MSCONVERT(1) manual page, living under the General Commands Manual, with that initial writing energy from 05 december 2013. now go convert something. mwah. 💋✨