Question: PRIDE Mass-Spec Published data analysis?
0
gravatar for daniel.soronellas
5.3 years ago by
Spain
daniel.soronellas330 wrote:

Dear Community,

I would like to know what are your recommendations in order to re-analyze (learn) the following already published MS data, from the paper: "Endogenous Purification Reveals GREB1 as a Key Estrogen Receptor Regulatory Factor", in PRIDE database. In order to learn how to process this kind of data I would like to reproduce the figure 1 from the paper.

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?

Thanks!

mass-spect • 1.7k views
ADD COMMENTlink modified 5.3 years ago by Laurent1.6k • written 5.3 years ago by daniel.soronellas330
0
gravatar for paulamic
5.3 years ago by
paulamic20
India
paulamic20 wrote:

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

ADD COMMENTlink written 5.3 years ago by paulamic20

Didn't found anything about this topic yet, sorry!

ADD REPLYlink written 5.3 years ago by daniel.soronellas330
0
gravatar for Laurent
5.3 years ago by
Laurent1.6k
Cambridge, UK
Laurent1.6k wrote:

Dear Daniel,

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 [1] 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 [2], which should get you started to use MSstats [3]. 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).

Hope this helps.

Laurent

[1] http://bioconductor.org/packages/release/bioc/html/rpx.html

[2] http://www.bioconductor.org/packages/release/bioc/html/MSnbase.html

[3] http://www.bioconductor.org/packages/release/bioc/html/MSstats.html

ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by Laurent1.6k

Hello,

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.

Shanzida.

ADD REPLYlink written 6 months ago by jahanshanzida0
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