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Hello,
I am searching for a good pipeline to use R for proteomics.
Actually my main idea is protein identifications so how can i do it ? is there any example or something like this?
Thanks
0
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I would suggest you look into the RforProteomics package vignette, which provides an overview of some of the tools that are available in R/Bioc. In particular for peptide identification, have a look at MSGFplus. See MSnID for filtering of your PSMs. Are you looking for anything specific for protein inference?
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thanks for your comment. I have studied your package as well as the paper you wrote both for visualization and data analysis.
the problem is that you don't use simple way to show what one can understand from a data with an example (at least I thought so). Anyway, what i want is to identify as many proteins as possible from an untargeted sample.
do you have any suggestion ?
My suggestions above still hold. Note that you can also use any third party search engine and import the identification results (as an mzIdentML) file and/or add these ids to the raw or quantified results.
May be the data analyses and results are not easy. As many proteins as possible is not, IMHO, a reasonable goal. I would personally aim for confidence in identification, or strike a reasonable balance between number and confidence. Look also at the MSGFgui package, which will provide a graphical interface to navigate your identification results.