Saturday, May 20, 2017
How to view or open Proteome Discoverer results or files
The common scenario:
Your core lab or collaborator ran some samples for you on that mass spec thing and provided you with a spreadsheet of results. After evaluating this you find some really interesting results and you need to explore this protein or pathway further. Your pathway of interest is upregulated. Is the key post translational modification present? Is the shortened proteoform there as well? General proteomics relies on upfront information. Searching every post-translation mod or sequence variation can explode the computational time and that data might very well be there, but more focused searching or filtering will probably be necessary to find it.
You can communicate all this back to the lab and get back in the data processing queue OR you can do it yourself. If they processed the data in Proteome Discoverer you can hike over with a thumb drive, get the file and look more into the data yourself with the free Proteome Discoverer Viewer.
You can get the Proteome Discoverer Viewer from two different places.
1) The Thermo-Omics Portal (https://portal.thermo-brims.com/)
2) The Thermo Flex Net (https://thermo.flexnetoperations.com/control/thmo/login)
You'll need to register at one of these, wait for your approval and then download Proteome Discoverer (PD)
Once inside you have some choices. You can follow 2 different strategies:
1) Get the version that the mass spec nerds processed your data in.
2) Get the newest version -- because new PD will always open old PD results.
My suggestion is #2. As of the writing of this post, this will be PD 2.1. PD 2.2 should be out in the middle of 2017
The newer versions of PD provide a lot more power to you, the operator of the viewer. There are specific PD viewer keys, but the best thing to do is to just go ahead and install the 60 day demo key. For 60 days you have pure, unstoppable power and can do anything with your data that you want. At the end of the 60 days most of the searching features will expire, leaving you with the Viewer functions -- basically the "Consensus" workflow nodes and the ability to open files and search through them.
I recommend the demo key version for another important reason. During these 60 days you can add free nodes to PD created by amazing external groups like OpenMS and IMP. IMP has a whole suite of nodes that will continue to function after the demo key expires. It provides a ton of capabilities to the software -- the ability to search with MSAmanda, label free quan with PeakJuggler, differential statistics and a really advanced node for reporter ion (TMT/iTRAQ) experiments.
The IMP PD-nodes (I sometimes call this the PD free version) is really incredible and these can be found and installed at pd-nodes.org (It is under IMP nodes collection)
The free OpenMS community nodes are also fantastic and can be found at http://www.openms.de/. While this software is often associated with label free quan only, this is not the case. There are some functions here that are truly unique, including a node for Protein-RNA crosslink detection. Go around any big genomics department and I bet at least someone there is looking at this problem using DNA based tools. With the right sample prep and this software you can approach this from an alternative and complementary direction.
If you think you might ever want to search proteomics data on your own -- I highly recommend you take the ten minutes to install at least the IMP PD nodes and it won't hurt to add OpenMS to your free user interface!
Other software exists as well -- and more is coming -- I don't mean to slight anyone I didn't mention here. The point of this post is for people outside of proteomics --If you paid for proteomics samples or are collaborating with a mass spectrometrist there are sometimes communication gaps. This isn't due to any shortcomings on either side. It is just that 14 years of training in analytical chemistry for the mass spectrometrist didn't leave time to become a specialist in your biological field -- and you probably don't realize what level of expertise and jargon complexity you are using. If this gap is hindering your progress you have very nice free tools to open, view, filter and even re-interrogate those beautiful, dense, and probably foreign (and crazy looking) data files yourself.
If you did download the newest PD and your data was originally processed in PD 1.4, I made a short walkthrough here that shows you how to open these results.
To you computational nerds, I would also like to mention that PD result files are simple SQLite files with a swapped suffix. You can open them with any database tools you are comfortable with that support this file type.