So where do I start in order to download RAW data from PRIDE database and analyze it to find significant hits. Do you recommend MS-stats R package for the analysis? Any tutorial that you are aware?
Have you found the answer? Because I have a similar question. If you do have any tutorial on Mass spec data analysis (obtained from PRIDE) please suggest. Thanks in advance.
I have not read the paper you reference, so I can't comment on reproducing exactly what they have done. But if you want to get started with PRIDE data in R, you could get a go with the rpx Bioconductor package that will allow you to query the files for a given ProteomeXchange project (in your case PXD000047). The authors have used Proteome Discoverer (PD), a commercial software. There are ways to process the data in R and/or other alternatives. If you have access to PD, you will be able to import that data into R with MSbase's readMSnSet2 function, which should get you started to use MSstats. The authors have also deposited the mzTab files (processed quantitation data), which you should be able to import into R with MSnbase::readMzTabData (please get in touch if you have issues with the latter).
I have peptide 30,000 peptide sequences from human brain sample. I want to compare these peptides with the PRIDE database peptide sequence to see whether my peptide sequence is novel or not. I am facing two problems.
Firstly, I have to download the pride dataset in Linux server because my computer doesn't support to download these huge datasets. secondly, how I can compare these in R. Please give me some suggestions.
Daniel
Have you found the answer? Because I have a similar question. If you do have any tutorial on Mass spec data analysis (obtained from PRIDE) please suggest. Thanks in advance.
Paulami
Didn't found anything about this topic yet, sorry!