Question: a good pipline for proteomics
gravatar for Nemo
3.2 years ago by
Nemo80 wrote:


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?




ADD COMMENTlink modified 3.2 years ago by Laurent Gatto1.0k • written 3.2 years ago by Nemo80
gravatar for Laurent Gatto
3.2 years ago by
Laurent Gatto1.0k
United Kingdom
Laurent Gatto1.0k wrote:

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?

ADD COMMENTlink written 3.2 years ago by Laurent Gatto1.0k

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 ? 

ADD REPLYlink written 3.2 years ago by Nemo80

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.

ADD REPLYlink written 3.2 years ago by Laurent Gatto1.0k
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