Using PXD015169 data from PRIDE

[MonnieMcGee]

Dear rpx,

I am new to MS/MS data analysis. I am trying to load a data set from the PRIDE data base into R using rpx. The accession number for PRIDE is in the subject line, and here is the paper reference: https://www.nature.com/articles/s41597-022-01871-9. According to the paper, the MS data was obtained from MaxQuant.

I am trying to follow the rpx vignette (actually, the book "R for Mass Spectrometry"), but I'm having a little trouble.

My problem is that the files from PRIDE have .raw, .mzid, and .MGF extensions. Those file extensions do not match the extensions that are used in the rpx vignette. How can I import PXD015169 data into R? I don't really care what package I use - I just want to get the data into R. Here's what I have thus far:

library(rpx)

Need to create a cache

my_cache <- BiocFileCache::BiocFileCache(tempfile())
my_cache
px <- PXDataset2("PXD015169", cache = my_cache)
pxfiles(px, 61)

Output at the end of this email due to its length.

This is as far as I got because I am not sure which files need to be imported into R for analysis.

All I have access to are the files in PRIDE. I don't have any text files from MaxQuant.

Thanks,
MMc

Project PXD015169 files (61):
[remote] GM22647_fraction1_replicate1.raw
[remote] GM22647_fraction1_replicate2.raw
[remote] GM22647_fraction2_replicate1.raw
[remote] GM22647_fraction2_replicate2.raw
[remote] GM22647_fraction3_replicate1.raw
[remote] GM22647_fraction3_replicate2.raw
[remote] GM22647_fraction4_replicate1.raw
[remote] GM22647_fraction4_replicate2.raw
[remote] GM22647_replicate1.mzid.gz
[remote] GM22647_replicate2.mzid.gz
[remote] GM22648_fraction1_replicate1.raw
[remote] GM22648_fraction1_replicate2.raw
[remote] GM22648_fraction2_replicate1.raw
[remote] GM22648_fraction2_replicate2.raw
[remote] GM22648_fraction3_replicate1.raw
[remote] GM22648_fraction3_replicate2.raw
[remote] GM22648_fraction4_replicate1.raw
[remote] GM22648_fraction4_replicate2.raw
[remote] GM22648_replicate1.mzid.gz
[remote] GM22648_replicate2.mzid.gz
[remote] GM22649_fraction1_replicate1.raw
[remote] GM22649_fraction1_replicate2.raw
[remote] GM22649_fraction2_replicate1.raw
[remote] GM22649_fraction2_replicate2.raw
[remote] GM22649_fraction3_replicate1.raw
[remote] GM22649_fraction3_replicate2.raw
[remote] GM22649_fraction4_replicate1.raw
[remote] GM22649_fraction4_replicate2.raw
[remote] GM22649_replicate1.mzid.gz
[remote] GM22649_replicate2.mzid.gz
[remote] GM22650_fraction1_replicate1.raw
[remote] GM22650_fraction1_replicate2.raw
[remote] GM22650_fraction2_replicate1.raw
[remote] GM22650_fraction2_replicate2.raw
[remote] GM22650_fraction3_replicate1.raw
[remote] GM22650_fraction3_replicate2.raw
[remote] GM22650_fraction4_replicate1.raw
[remote] GM22650_fraction4_replicate2.raw
[remote] GM22650_replicate1.mzid.gz
[remote] GM22650_replicate2.mzid.gz
[remote] GM22651_fraction1_replicate1.raw
[remote] GM22651_fraction1_replicate2.raw
[remote] GM22651_fraction2_replicate1.raw
[remote] GM22651_fraction2_replicate2.raw
[remote] GM22651_fraction3_replicate1.raw
[remote] GM22651_fraction3_replicate2.raw
[remote] GM22651_fraction4_replicate1.raw
[remote] GM22651_fraction4_replicate2.raw
[remote] GM22651_replicate1.mzid.gz
[remote] GM22651_replicate2.mzid.gz
[remote] Mudpit_Experiment project64_01a_OL_1_2 from 20190401a_OL_1_2_2.mzid_Mudpit_Experiment_project64_01a_OL_1_2_from_20190401a_OL_1_2_2.MGF
[remote] Mudpit_Experiment project64_01a_OL_2_2 from 20190401a_OL_2_2_2.mzid_Mudpit_Experiment_project64_01a_OL_2_2_from_20190401a_OL_2_2_2.MGF
[remote] Mudpit_Experiment project64_01a_OL_3_2 from 20190401a_OL_3_2_2.mzid_Mudpit_Experiment_project64_01a_OL_3_2_from_20190401a_OL_3_2_2.MGF
[remote] Mudpit_Experiment project64_01a_OL_4_2 from 20190401a_OL_4_2_2.mzid_Mudpit_Experiment_project64_01a_OL_4_2_from_20190401a_OL_4_2_2.MGF
[remote] Mudpit_Experiment project64_01a_OL_5_2 from 20190401a_OL_5_2_2.mzid_Mudpit_Experiment_project64_01a_OL_5_2_from_20190401a_OL_5_2_2.MGF
[remote] Mudpit_Experiment project64_228a_OL_1_2 from 20190228a_OL_1_2.mzid_Mudpit_Experiment_project64_228a_OL_1_2_from_20190228a_OL_1_2.MGF
[remote] Mudpit_Experiment project64_228a_OL_2_2 from 20190228a_OL_2_2.mzid_Mudpit_Experiment_project64_228a_OL_2_2_from_20190228a_OL_2_2.MGF
[remote] Mudpit_Experiment project64_228a_OL_3_2 from 20190228a_OL_3_2.mzid_Mudpit_Experiment_project64_228a_OL_3_2_from_20190228a_OL_3_2.MGF
[remote] Mudpit_Experiment project64_228a_OL_4_2 from 20190228a_OL_4_2.mzid_Mudpit_Experiment_project64_228a_OL_4_2_from_20190228a_OL_4_2.MGF
[remote] Mudpit_OL5_1_ 20190328a_OL_5_1.mzid_Mudpit_OL5_1__20190328a_OL_5_1.MGF
[remote] README.txt

[lgatto]

• raw: binary raw file (Thermo propitiatory format).
• MGF: peaks like, probably only contain MS2 data, used to run the identification search, produced from the raw files (with msconvert or ThermoRawFileParser), can be imported into R with Spectra and MsBackendMgf; I would advice conerting the raw files to mzML and use these.
• mzid: identification results, can be imported into R with the PSMatch package.

rpx isn't going to help reading the files into R, only downloading them locally.

[MonnieMcGee]

Laurent, Thank you for the prompt response. I figured out the raw file and the mzid around the time you were sending this email. Nevertheless, having corroboration from an expert that I am correct is encouraging. And the additional information on the MGF is helpful. Best, Monnie

…

________________________________ From: Laurent Gatto ***@***.***> Sent: Monday, April 3, 2023 2:07 PM To: lgatto/rpx ***@***.***> Cc: McGee, Monnie ***@***.***>; Author ***@***.***> Subject: Re: [lgatto/rpx] Using PXD015169 data from PRIDE (Issue #23) [EXTERNAL SENDER] * raw: binary raw file (Thermo propitiatory format). * MGF: peaks like, probably only contain MS2 data, used to run the identification search, produced from the raw files (with msconvert or ThermoRawFileParser), can be imported into R with Spectra<http://rformassspectrometry.github.io/Spectra> and MsBackendMgf<https://rformassspectrometry.github.io/MsBackendMgf/>; I would advice conerting the raw files to mzML and use these. * mzid: identification results, can be imported into R with the PSMatch<https://rformassspectrometry.github.io/PSMatch/> package. rpx isn't going to help reading the files into R, only downloading them locally. — Reply to this email directly, view it on GitHub<#23 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADK2IRACZWMT2SSTAV5K6D3W7MNWDANCNFSM6AAAAAAWRWNKHA>. You are receiving this because you authored the thread.Message ID: ***@***.***>