Proteome Cluster from Bioproximity, a fee-for-service on-line protein database MS search engine

A brief and by no means comprehensive look at Proteome Cluster


Demo on 5/10/2011 update 11/6/2012
(Historical note, this was probably the first MS demo tweeted in progress on twitter. Follow @ionsource)

This is meant to be a brief look at Proteome Cluster.  We just wanted to see how easy it was to get started and use.  If you would like to do a similar demo you can request a temporary password from Bioproximity

We went into this demo naive just to see what we would run into. We feel that naive tests are the best tests.  The first thing we found out was that the program is not compatible with Microsoft's Internet Explorer. (Since we wrote that last sentence PC has fixed this problem and it has been tested on IE9.  They are responsive, hmm we are not used to that.) Previously, we switched over to the most current version of FireFox and everything worked. Other compatible browsers and file formats are listed on their website.

If you would like to repeat the demo for yourself go to the bottom of this page and download the data files that we used, or use your own data file.


This is what the log in page looks like. It is very simple, see Figure 1 below.


Figure 1.

Log In Page


As shown in Figure 2 below there are really only four pages to explore: Upload, Runs, Searches and Search Parameters.


Figure 2.


The upload page as shown in Figure 2, above, is where you upload your files to be searched. Just press on the "Upload a file" button and browse to a file on your hard drive. The compatible file formats are MGF, mzML or mzXML.   We will be uploading our data in MGF format, "Mascot Generic Format".  The MGF format was developed by Matrix-Science,  At first we tried to upload concatenated DTA files (an old Thermo data format), but that is not an acceptable file format for Proteome Cluster, as of yet.  If you have individual DTA's concatenate them into MGF format with the tools provided by Matrix-Science, . Once these tools are downloaded and unzipped use the tool to make your MGF file. Many MS manufacturers will allow you to export your proteomics data in the allowable formats without the need for conversion.

As usual before you can start a search you must decide on your search parameters.  We decided to do an OMSSA search. Here is what the search parameters page looks like, see Figure 3 below. We will talk more about OMSSA later. For the most part the default parameters will work, but you may want to change the mass tolerances depending on the capability of your instrument and you will want to choose a species database that is appropriate for your sample.  Proteome Cluster currently supports four search algorithms: OMSSA, X!Tandem, X!Tandem using k-score (also called Comet), and X!Hunter.


Figure 3

Search Parameters Page



The "Runs Page" below lets you select which file should be searched and also allows you to start the search. Just check the box next to your uploaded data file and click "Launch!"  It will ask you to confirm the search, this is a safety feature since outside of the demo the search time will cost you money.


Figure 4.

Runs Page



Go to the Searches page, see Figure 5 below, to see if your search is done.  Once it says "complete" you can download your OMSSA results.  Just click on the link to download.


Figure 5.


Searches Page


To view your OMSSA proteomic result you will need to download OMSSA and choose to open the results file that you just downloaded.  You can download the OMSSA browser free at You can also do searches on your local computer using OMSSA.  To learn more about OMSSA we have a review here,  We did not review the X!Tandem search.


Figures 6 and 7 below shows you some of the things that you can see with your OMSSA browser.  In Figure 6 you can see the protein coverage of one of the hits, and in Figure 7 you can see one of the MS/MS matches of one of the peptides.


Figure 6.

OMSSA Protein Coverage Details



Figure 7.

 OMSSA MS/MS spectral match


Conclusion:  Proteome Cluster was easy to use and the web interface was intuitive.  We did not go into an exhaustive review of the product, and only wanted to take a look, and see what it was, and how easy it was to use. Proteome Cluster was simple, and we know that simple and intuitive isn't always so simple to produce, so good job Proteome Cluster, and Bioproximity.  We did run into a few problems but that is because we did not read the instructions right in front of us. We think that this is a real fine place for Proteome Cluster and Bioproximity to start.  We will be checking back soon.


1.) Bioproximity
2.) Proteome Cluster
3.) Watch a YouTube video of Proteome Cluster
4.) Request a Proteome Cluster demo


1.) Download the Xcalibur (ThermoFisher) raw data file that we used in this tutorial. (zipped 9.5 MB)

2.) Download the zipped dta files associated with the above data file (zipped 3.3 MB)

3.) Visit to get a temp demo password.

4.) Download the concatenation tools from Matrix-Science if you need them.

You can use these files courtesy of IonSource for your own fun or comparisons, but not for profit.  Feel free to to use them in any non-profit publication or presentation you wish as long as you cite as the source of the data.  We paid about $350 for that data file.




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