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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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Substitute PeptideShaker processing by MSnbase functions? #19

Closed veitveit closed 6 years ago

veitveit commented 6 years ago

I get constantly errors, e.g. when

As far as I am aware, we only need to read the mzid files from MS-GF+ and then carry out an adecuate FDR-filtering. This anyways will be done by the suggested #15

jgriss commented 6 years ago

Fine with me!

We have three: options to process the mzIdentML files

The advantage of the first two options would be, that it would be quite easy to adapt the workflow to a different search engine.

veitveit commented 6 years ago

Reading mzIdent seems to be quite straightforward with MSnbase but I never tried it out. What would we need to do?

The last one could become tricky when thinking about parsimony principle, ...

I suggest to give it further tests and see how bad things can get. Maybe very much comes down to deleting the right files (#20) before running searchgui and peptideshaker again.

2018-05-11 19:19 GMT+02:00 Johannes Griss notifications@github.com:

Fine with me!

We have three: options to process the mzIdentML files

  • Using MSnbase. Although I'm not quite sure how flexible this option is.
  • Using Python. There's a very good library to parse mzIdentML files in python and I'm using it quite regularly. So I would already have python code ready to process MSGF+ mzIdentML files.
  • Using MSGF+'s conversion function. You can directly convert the mzIdentML output files to TSV files using MSGF+.

The advantage of the first two options would be, that it would be quite easy to adapt the workflow to a different search engine.

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jgriss commented 6 years ago

OK. In that case, I'll try to fix #20 In case that doesn't work at all, we can still replace PeptideShaker at a later stage.

jgriss commented 6 years ago

I'll now close this issue since we will not do this at the time anyway.