Input format template?

[heejongkim]

Hi,
I would like to give a shot pyquant with my MSGF+/Percolator coupled workflow to quantify SILAC datasets.
However, I'm having a little bit of difficulty on locating the required file format as an input for pyquant.
Can you please help me locate it?

Thanks.
heejong

[Chris7]

Hi @heejongkim,

Could you let me know how you are trying to run PyQuant? What are your input files to it? I think mzidenML files are similar to pepxml, which pyquant can parse.

Chris

[heejongkim]

Hi @Chris7

I checked the github io page about the generic format but I got confused a little bit so it would be great if you have a template for that.
I'm currently using MS-GF+/Percolator coupled very simple workflow for SILAC. (search twice for light and heavy and percolator is done separately)

Thanks.

heejong

[Chris7]

Ok, it's a bit clearer now what you are asking for, and I now realize there isn't really a reference file showing the generic format.

First, It might help to give a quick overview of how PyQuant works to understand what the generic format needs. At a very simple level, PyQuant needs to identify a point in the m/z vs. RT matrix where a signal is. It then searches around this space for what looks like a strong signal, and identifies a possible peak in there, which is then fit and the area under the curve is established. In the SILAC scenario (or any labeling), this provides a set of additional peaks that PyQuant should look for based on that initial point.

So, the generic tsv format should provide where to look for this signal (I had to name it .txt because of some nonsense with github).

generic example.txt

This file file goes with the following label state: https://github.com/Chris7/pyquant/blob/master/label_templates/maxquant_3state.tsv

Where the first column is the "label state" mapping, the second column is what amino acid can be labeled, the 3rd column the mass due to this label, and the 4th column is the human readable name in pyquant's output.

To process this file, the following pyquant parameters would be used:
--tsv generic_example.txt --peptide-col Peptide --mz "Precursor Mass" --rt "Retention Time" --charge "Charge" --source "Raw File" --scan-col "MS/MS Scan Number" --label "Labeling State" --file-dir directory_to_your_mzml_files