LUTEFISK(1)

💖 LUTEFISK(1) — the manual page, bestie edition 💖

okay so this is the section 1 manual page for lutefisk, and honestly? it's giving peptide whisperer. let's get into it. 🧚✨

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✨ NAME ✨

lutefisk — software for the de novo interpretation of peptide CID spectra

like. it reads your spectra and figures out the peptide sequences. no cap. 🎀

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🌸 SYNOPSIS 🌸

lutefisk [-q ] [ -m ] [ -d] [ -p ] [ -r ] [ -s ] [ -v] [ -h]  [-o ]
<infile>

(yes bestie, the spacing is exactly like that, I don't make the rules 💅)

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🦋 DESCRIPTION 🦋

okay so lutefisk is a software for the de novo interpretation of peptide CID spectra. it's literally that girl. ✨

what it does: it takes peptide CID data plus some ancillary data files (and you tell it where those live on the command line, okay? on the command line) and then it outputs a results file containing all the sequences hypothetically matching the CID data. all of them. it's not gatekeeping. 🫶

and when you invoke lutefisk with the -h option, the program lists to the command line all the options that are available. it's basically the program saying "here's the menu, bestie." 🎀

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👑 OPTIONS 👑

• -h — Print a list of options. the little "what can I even do" moment.
• -q — Run in quiet mode. shhh. 🤫
• -m — Precursor ion mass.
• -d — Pathname to the details file.
• -p — Pathname to the params file.
• -r — Pathname to the residues file.
• -s — Pathname to the file with database sequences to score.
• -v — Run in verbose mode. the opposite of -q, she's talking. 💬
• -o — Output file.
• <infile> — CID data file. the main character, honestly. 🌟

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🍓 PROGRAM DATA 🍓

The data required to run the program are located in /usr/share/lutefisk.

that's the spot. remember the spot. 📍

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🌈 EXAMPLE DATA 🌈

Example data are located in /usr/share/doc/lutefisk/examples.

go play with it, bestie, that's what it's there for 💜

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📚 BIBLIOGRAPHICAL REFERENCES TO BE CITED 📚

these are the ones you gotta cite, no skipping, periodt:

• R. S. Johnson and J. A. Taylor (2002) "Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry", Mol. Biotechnology Vol. 22, No. 3. (November 2002), pp. 301-315.
• J. A. Taylor and R. S. Johnson (2000) "Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry". Anal. Chem. 73:2594-2604.
• R. S. Johnson and J. A. Taylor (2000) "Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry", "Protein and Peptide Analysis: Advances in the Use of Mass Spectrometry", 146:41-61 (Methods in Molecular Biology series, Humana Press).
• J. A. Taylor and R. S. Johnson (1997) "Sequence database searches via de novo peptide sequencing by tandem mass spectrometry". Rapid Comm. Mass Spec. 11:1067-1075.

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🔥 SEE ALSO 🔥

lutefisk-doc(7).

that's it. that's the whole list. go read it if you want more lore 📖

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💅 AUTHORS 💅

• Richard S. Johnson <jsrichar@alum.mit.edu>.
  • Program author. the actual icon behind the whole thing 👑
• Filippo Rusconi <rusconi-debian@laposte.net>.
  • Man-page author for the Debian distribution. thank you for your service 🫡

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⭐ COPYRIGHT ⭐

Copyright © 1995-1999 Richard S. Johnson

Copyright © 2009 Filippo Rusconi

This manual page was written for the Debian system (but may be used by others).

Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 3 or (at your option) any later version 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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okay and that's the whole thing, bestie 🎀 this page is from 2009/04/29, and the source/version situation is the LUTEFISK(1) manual page itself — so go forth, interpret some peptides, and slay 💖✨🦋