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ProtProtocols / IsoProt

Protocol of the analysis of iTRAQ/TMT proteomics data including quantification, statistical analysis and maybe clustering
https://protprotocols.github.io
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Add Protein-level FDR filter #15

Open jgriss opened 6 years ago

jgriss commented 6 years ago

Use pubs.acs.org/doi/10.1021/acs.jproteome.7b00899 as basis.

veitveit commented 6 years ago

I see mainly 2 options (papers states "inclusion" and "Fido" as good choices):

a) Use PeptideShaker protein FDRs but be aware that PTMs and others are included as configured (as described in #6 )

b) Run Percolator (includes Fido), https://github.com/percolator/, via command line from R or python to estimate protein FDR. They also provide a convertor from MS-GF+

This issue becomes a major decision when considering future use of PeptideShaker (allows using different search engines through SearchGUI) and (#19) or directly processing the database search results (direct control of peptide inference, ...).

jgriss commented 6 years ago

Hi @veitveit,

In the long run I prefer to use Percolator. As far as I know, Percolator can be used with tab-delimited files. We can extract these from PeptideShaker and thereby still use PeptideShaker's functionality to convert the different search engine results (if we want to change in the future, for example) to this tab-delimited format.

But I'd argue that this is something that should not be included for our features for version 0.1

veitveit commented 6 years ago

Agree

2018-07-12 11:11 GMT+02:00 Johannes Griss notifications@github.com:

Hi @veitveit https://github.com/veitveit,

In the long run I prefer to use Percolator. As far as I know, Percolator can be used with tab-delimited files. We can extract these from PeptideShaker and thereby still use PeptideShaker's functionality to convert the different search engine results (if we want to change in the future, for example) to this tab-delimited format.

But I'd argue that this is something that should not be included for our features for version 0.1

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