topdiff(1)

✨ topdiff(1) — the TopPIC suite glow-up ✨

okay bestie, sit down, hydrate, and let me tell you about topdiff 💖 this is a page from the TopPIC suite manual, and honestly? it's giving "quiet little tool that does something genuinely iconic."

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🌸 NAME 🌸

topdiff — top-down mass spectrometry-based identification of differentially expressed proteoforms 🦋

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🎀 SYNOPSIS 🎀

topdiff [options] database-file-name spectrum-file-names

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💅 DESCRIPTION 💅

So. TopDiff (which stands for Top-down mass spectrometry-based identification of Differentially expressed proteoforms, no cap) compares the abundances of proteoforms and finds the ones that are differentially expressed — by using identifications of top-down mass spectrometry data from several protein samples. It's a whole comparison arc, and it ate. 🔥

1. Input 🧚

Things you gotta hand over:

• A protein database file in the FASTA format
• Several mass spectrum data files in the msalign format
• Proteoform identification files of the mass spectrum data files in the xml format, e.g. spectra_ms2_toppic_proteoform.xml

2. Output 👑

TopDiff outputs a csv file containing proteoform identifications and their abundances in the input mass spectrum data. The default output file name is sample_diff.csv. periodt 💖

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✨ OPTIONS ✨

• -h, --help — print the help message. simple. iconic. ask for help, bestie, it's free 🫶
• -f, --fixed-mod <C57|C58|a fixed modification file> — set fixed modifications. You've got three options here: C57, C58, or the name of a text file that specifies fixed modifications (go peek at the example file 👀). If you pick C57, then carbamidomethylation on cysteine is the only fixed modification. If you pick C58, then carboxymethylation on cysteine is the only fixed modification. pick your fighter 💅
• -e, --error-tolerance <a positive number> — set the error tolerance for mapping identified proteoforms across multiple samples, measured in Dalton. Default value: 1.2 Dalton. yes it wants a positive number, so pls don't be chaotic 🙈
• -t, --tool-name <toppic|topmg> — specify the name of the database search tool: toppic or topmg. Default: toppic. choose wisely, it's giving main character energy ✨
• -o, --output <a file name> — specify the output file name. Default: sample_diff.csv. name your baby 🌸

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🌈 EXAMPLES 🌈

• Compare proteoform abundances using TopPIC identifications of two spectrum files spectra1_ms2.msalign and spectra2_ms2.msalign. The protein sequence database file name is proteins.fasta.

topdiff proteins.fasta spectra1_ms2.msalign spectra2_ms2.msalign

• Compare proteoform abundances using TopPIC identifications of two spectrum files spectra1_ms2.msalign and spectra2_ms2.msalign. The protein sequence database file name is proteins.fasta and a fixed modification, carbamidomethylation on cysteine, is used in database search.

topdiff -f C57 proteins.fasta spectra1_ms2.msalign
spectra2_ms2.msalign

• Compare proteoform abundances using TopMG identifications of two spectrum files spectra1_ms2.msalign and spectra2_ms2.msalign. The protein sequence database file name is proteins.fasta and a fixed modification, carbamidomethylation on cysteine, is used in database search.

topdiff -f C57 -t topmg proteins.fasta spectra1_ms2.msalign
spectra2_ms2.msalign

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🦋 SEE ALSO 🦋

• topfd (1)
• toppic (1)
• topmg (1)

the whole squad, fr fr 💜

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🎬 MAN PAGE PRODUCTION 🎬

This man page was written by Filippo Rusconi <<lopippo@debian.org>>. Material was taken from <http://proteomics.informatics.iupui.edu/software/toppic/manual.html>.

Author 👑

Filippo Rusconi <lopippo@debian.org> and upstream authors (Dr. Xiaowen Liu's Lab at Indiana University-Purdue University Indianapolis and others)

Copyright ⭐

Filippo Rusconi and Indiana University-Purdue University Indianapolis

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okay that's the whole page, you're fully caught up 💖 this was page 1 of the manual, from 20200521 (that's the date, bestie, mark your calendar 📅), and the source is the TopPIC suite — topdiff(1), out. slay, go compare some proteoforms 🎀💅✨