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Downloading human proteome?

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Downloading human proteome? ayacoob  2024-10-17 08:54
 

Hi!

I was asked to download the human, mouse, and bovine proteome (reviewed) to load into Skyline. I've used programs with spectral libraries before, like Bruker's XRD spectral libraries, Thermo's FT-IR databases, etc... Usually they're pre-loaded or my lab purchased them for a few years, but I'm still new to Skyline and haven't really done this before.

My instrument is a Thermo Scientific TSQ Altis (QQQ), and I just needed some help on trying to understand where I go to find these databases/libraries so that I could download it and upload to Skyline and presumably use the library to extract/detect as many proteins as I can in a sample.

The best I've done is using the PRIDE Peptidome website and trying to download their spectrum libraries, but I'm not able to open or import the .msp.gz files into any program. I'd be grateful for any help!

Thanks!
 
 
Brian Pratt responded:  2024-10-17 09:24

In this case I think all you need is the FASTA file from UniProt. Skyline will handle calculating peptides and peptide fragments - a spectral library isn't strictly required. You can just use File > Import > FASTA to get started.

I would recommend working through the introductory tutorials to get a better idea of how that works, if you haven't already.

Thanks for using the Skyline support board,

Brian Pratt
 
ayacoob responded:  2024-10-17 11:05

Thanks for the quick reply, Brian! This was really helpful in finding the FASTA file from UniProt. I don't think I know how to import the document into Skyline to make it usable though. When I downloaded the file, it is downloaded as ".fasta.gz" and when I go to File > Import, I see only these options: Results, Peak Boundaries, Assay Library, Transition List, Document, and Annotations. I tried each of them, and none of them were able to open the file.

Are the introductory tutorials on UniProt or are you referring to Skyline tutorials? Do you think you could hyperlink me to where that is?
 
Brian Pratt responded:  2024-10-17 11:40

You will need to uncompress the FASTA file (.gz is kind of like .zip, it's more commonly used in linux than windows) using a tool like 7Zip. https://www.7-zip.org/download.html

It sounds like you might have Skyline's user interface in small molecule mode - see the attached picture.

I was referring to the Skyline tutorials at https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorials