TANDEM(1)

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✨ TANDEM — bestie's guide to peptide sequencing ✨

okay so this is tandem, from the tandem-mass package — a mass spectrometry software moment for peptide sequencing and protein identification, and honestly? it's giving icon status. this is the General Commands Manual page, and i'm gonna walk you through it like we're texting. no cap. 💅

🌸 NAME 🌸

tandem — X!Tandem mass spectrometry software for peptide sequencing 🦋

✨ SYNOPSIS ✨

tandem <input.xml> <output.xml>

💖 DESCRIPTION 💖

so like, this manual page is here to briefly document the tandem-mass package, which brings you a mass spectrometric software software for peptide sequencing and protein identification. (yes bestie, "software software", that's what it says, i'm not touching it, it's canon now 😭)

this software has a very simple, unsophisticated application programming interface (API). like, it's not doing the most. it just takes an XML file full of instructions on its command line, and it outputs the results into an XML file, which has been specified in the input XML file. that's it. that's the whole vibe. the output file format is described at http://www.thegpm.org/docs/X_series_output_form.pdf. 🎀

now here's the part where it's lowkey better than some earlier generation search engines: all of the X! Series search engines calculate statistical confidence (expectation values) for all of the individual spectrum-to-sequence assignments. all of them. every single one. 👑

they also reassemble all of the peptide assignments in a data set onto the known protein sequences, and assign the statistical confidence that this assembly and alignment is non-random. the formula for which can be found here. so basically — separate assembly and statistical analysis software, e.g. PeptideProphet and ProteinProphet, do not need to be used. they're just not required. the engine ate and left no crumbs. ⭐

📚 BIBLIOGRAPHICAL REFERENCE TO BE CITED 📚

you GOTTA cite this, bestie, it's the rules:

Robertson Craig and Ronald C. Beavis. (2004) TANDEM: matching proteins with mass spectra. Bioinformatics, 20, 1466-1467.

see more references pertaining to this software at http://www.thegpm.org/GPM/references.html. 💜

🫶 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. periodt. ✨

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. 🌈

aaaand that's the whole page bestie 🎀 that was the tandem-mass General Commands Manual situation, dated November 2012 — mwah, iconic, no notes. 💖🦋✨

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