OPENMS(7)

📦 version 2.6.0+cleaned1, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 openms — the manual page, but make it a group chat 💖

okay bestie, you found the manual page for openms — that's the OPENMS(7) page from the Miscellaneous Information Manual (section 7, iykyk). sit down, grab a strawberry 🍓, and let me tell you about the cutest little metapackage in mass spectrometry.

✨ NAME ✨

openms — library for LC/MS data management and analysis — metapackage. that's it. that's the name. 💅

🌸 DESCRIPTION 🌸

so this page documents, briefly, the openms metapackage — and here's the tea: it depends on all the components of the OpenMS software framework… except the openms-doc documentation package. yes, all of them. she's a package of packages. meta. main character energy fr fr 👑

OpenMS offers an infrastructure for the development of mass spectrometry-related software, plus powerful 2D and 3D visualization solutions. like, it's giving lab girlie with a rendering pipeline. ✨

and the analyses?? oh we eat every time 🍽️ — OpenMS offers analyses for various quantitation protocols, including:

  • label-free quantitation
  • SILAC
  • iTRAQ
  • SRM
  • SWATH…

(that trailing … is doing so much work, she's mysterious like that 🦋)

it also provides build-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like:

  • X!Tandem
  • Mascot
  • OMSSA…

and if that wasn't enough: OpenMS supports the Proteomics Standard Initiative (PSI) formats for MS data, and supports easy integration of tools into workflow engines like Knime, Galaxy, WS-Pgrade, and TOPPAS — via the TOPPtools concept and a unified parameter handling. unified params?? no chaos?? we love to see it 🙌

📚 BIBLIOGRAPHICAL REFERENCE TO BE CITED 📚

if you're gonna cite her (and you SHOULD, she's iconic), cite this exactly:

Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher (2008) OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics, 9:163. doi:10.1186/1471-2105-9-163.

that's a whole friend group of authors and honestly, respect. 🫶

👀 SEE ALSO 👀

go read these next, bestie, the lore is deep:

also: the program is documented fully in the Tutorials, which are packaged in openms-doc. so if this page left you wanting more (same), that's where you go. 🧚

💜 AUTHOR 💜

This manual page was written by Filippo Rusconi <lopippo@debian.org>. 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.

(no cap, go read the license, it's the law and also lowkey a vibe 🎀)

and that's the whole page!! this one's from way back in November 2012, and yeah, it's OPENMS(7) — Miscellaneous Information Manual, forever and always. mwah 💋✨

📦 where this page comes from