Do you mess around with all sorts of different search engines?
Would it be awesome if someone spent a ton of time making sure that you could look at all your data in the same downstream interface?
Paper link here.
Are there other ways to visualize data from a bunch of different engines and tools? Sure. But PDV is probably the easiest and most widely compatible — and has some features that are ridiculously handy.
This little Java file does the perfect job of looking simple but pulling off crazy powerful.
You can get it at this Github where you'll see the ridiculous number of tools it supports. I can't take a screenshot that is big enough to capture them all. Basically if you can think of a search engine, PDV can upload the results and it all comes out looking like this!
Did you, for example, reprocess a bunch of MaxQuant files from PRIDE with MetaMorpheus and MSFragger to see if the original analysis missed anything? Have 4 little Java windows open at once and look at the evidence in the same format! How valuable is that? (Can't seem to clip the other monitor simultaneously — but here is two! MaxQuant on right, MM on left.) MaxQuant has SO MANY ROWS (columns? it's early here. whatever the vertical ones are) that it can be a little tough to visualize. And that ends my complaints about this great tool I somehow missed.
There is more here. The PROTEOGENOMICS button lets you upload a gosh darned proBED or proBAM file and look at it directly in this as well. Another button lets you look for individual peptides inside a file (just type the peptide sequence in the box!) and plot it if it sees it. I put in a bunch of fake peptide sequences and the visualization was a little odd. I haven't checked it with anything real. I've got a bunch of cooking to do.
Great tool. Solidly supported with tutorials AND example files. Recently updated. Unifies a lot of our tools, which we really need to do more of so we can keep them around. 100% recommended!
Hey you! Are you looking for a tool to help you select viral peptides for targeted assays? Unrelated --- what is the best color of dinosaur? I got you, yo. Check this out. Before you panic, when they wrote the paper "Purple" was just a Python script that you can get here. I assure you this is no longer the case. There is a very straight-forward (to install) executable that will set you up with a GUI that looks just like this -- -- that you can get here. What does it do? Well, it helps you select peptides that are ideal for targeted assays from the databases you feed it. Imagine Picky, but you can load stuff that isn't human into it. (If you are doing human proteomics -- you should be using Picky, btw. It's amazing). Purple: Feed it your peptide sequences you're interested in: Feed it your contaminating background. Choose your rules. Get your peptides!