topfd(1)

💖 topfd — Top-down mass spectral Feature Detection 💖

okay bestie, sit DOWN, because topfd from the TopPIC suite is about to become your new hyperfixation. it's a command-line tool, it does top-down spectral deconvolution, and it's genuinely iconic. let's get into it 🧚✨

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✨ SYNOPSIS ✨

topfd [options] spectrum-file-names

that's it. that's the whole vibe. options first, then the file names. slay.

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🌸 DESCRIPTION 🌸

okay so TopFD (short for Top-down mass spectral Feature Detection) is a software tool for top-down spectral deconvolution. and what does that actually mean, bestie? it groups top-down mass spectral peaks into isotopomer envelopes and then converts isotopomer envelopes to monoisotopic neutral masses. so it's basically matchmaking for peaks. 💅

and that's not even all — it also extracts proteoform features from MS1 spectra. multitasking queen. 👑

🦋 1. Input

the input of TopFD is mass spectrometry data files in the mzXML or mzML format. and ngl, if you've got raw mass spectral data from whatever mass spectrometer you're using, you can convert it to mzML or mzXML files using msconvert. easy. no cap.

🎀 2. Output

TopFD outputs two LC/MS feature text files with a file extension feature, one LC/MS feature file with a file extension xml, and a deconvoluted mass spectral data file for MS/MS spectra in the msalign format with a file extension msalign — which is lowkey similar to the MGF file format, iykyk.

in addition (yes there's more, she's generous), TopFD creates two folders containing java scripts files of spectral data for spectral visualization and other files generated in spectral deconvolution.

so like, for example, when the input file name is spectra.mzML, the output includes:

• spectra_ms1.feature: a feature file containing LC/MS features.
• spectra_ms2.feature: a feature file containing MS/MS scan IDs and their corresponding LC/MS feature IDs.
• spectra_feature.xml: a feature file containing LC/MS features in the xml format.
• spectra_ms2.msalign: a list of deconvoluted MS/MS spectra.
• spectra_file: a folder containing deconvoluted MS1 spectra and annotations of LC/MS data.
• spectra_html: a folder containing java script files of MS1 and MS/MS data for spectral visualization.

six things. six!! we love a thorough girlie 🫶

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👑 OPTIONS 👑

here's the part where you take notes, bestie. every single one, no skipping, that's the rule 📝

• -h [ --help ] — Print the help message. your bestie when you're lost.
• -c [ --max-charge ] <a positive integer> — Set the maximum charge state of precursor and fragment ions. The default value is 30.
• -m [ --max-mass ] <a positive number> — Set the maximum monoisotopic mass of precursor and fragment ions. The default value is 100,000 Dalton.
• -e [ --mz-error ] <a positive number> — Set the error tolerance of m/z values of spectral peaks. The default value is 0.02 m/z.
• -r [ --ms-one-sn-ratio ] <a positive number> — Set the signal/noise ratio for MS1 spectra. The default value is 3.
• -t [ --ms-two-sn-ratio ] <a positive number> — Set the signal/noise ratio for MS/MS spectra. The default value is 1.
• -w [ --precursor-window ] <a positive number> — Set the precursor isolation window size. The default value is 3.0 m/z.
• -o [ --missing-level-one ] — Specify that the input file does not contain MS1 spectra. use this when your data is missing its level-one era 😭

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🌈 EXAMPLES 🌈

real scenarios, real commands, we're doing this together 💜

• Deconvolute a centroid data file spectra.mzML and output four files: spectra_ms2.msalign, spectra_ms1.feature, spectra_ms2.feature, spectra_feature.xml.

topfd spectra.mzML

• Deconvolute two centroid data files spectra1.mzML and spectra2.mzML and output three files for each input data file.

topfd spectra1.mzML spectra2.mzML

• Deconvolute all centroid data files in the current folder. (wildcard moment, we love her 🌟)

topfd *.mzML

• Deconvolute a centroid data file spectra.mzML that does not contain MS1 spectra.

topfd -o spectra.mzML

• Deconvolute a centroid data file spectra.mzML with a precursor isolation window size 2 m/z.

topfd -w 2 spectra.mzML

• Deconvolute a centroid data file spectra.mzML with a signal/noise ratio 2 for MS1 spectra.

topfd -r 2 spectra.mzML

• Deconvolute a centroid data file spectra.mzML with the following settings: the maximum charge state: 50, the maximum mass: 30,000 Dalton, and the signal/noise ratio for MS/MS spectra: 2. stacking flags, main character energy fr fr

topfd -c 50 -m 30000 -t 2 spectra.mzML

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🍓 SEE ALSO 🍓

the whole friend group, go say hi:

• toppic (1)
• topmg (1)
• topdiff (1)

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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.

(credit where credit is due, always 💖)

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🎀 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 bestie that's the whole page, you're officially a top-down mass spec girly now. go deconvolute something gorgeous. ✨🦋💖

and that's a wrap on version 1, dated 20200521, straight outta the TopPIC suite. mwah, periodt. 💅🌸