I get this question a lot: How much power do I need to build a PC for proteomics processing? And what components would I need?
In order to help answer this I'm going to give the configuration that I would build for processing proteomics software on a budget. The picture above is my all-time favorite PC case/test kirunch, the Antec skeleton. It is a steel frame wrapped in plastic with easy accessibility to all the components and open air processing. That big circle at the top where it says Antec? That's a great big fan. (6 inch or something close). More about the case below, but here is my shopping list..
Processor: AMD FX-8350 ($190)
I'll start here because this is going to determine what motherboard I use. For me, I just have to go with an AMD 8 core system. These come in several varieties now. The AMD 8150 runs about $150, but the newer (and 18% faster) AMD FX-8350 runs $190. When can you get 18% faster for $40? Compare this to the (SLOWER!!!) Intel I7-3920XM at $1100, and you realize what a bargain you are getting for the 8350. Is it the fastest processor in the world? No. But is it fast (4GHz) , easily modified, and <$200? Yes.
Motherboard: Asus Sabertooth 990FX ($200)
This gets significantly easier now that I've chosen a processor. My requirements: able to use the fastest RAM chips. Able to handle at least 20GB of RAM, and multiple USB 3.0 ports for fast and easy data processing. My choice is the Asus Sabertooth 990FX. It can take up to 32 GB of 1866 MHz DDR3 RAM and has 4 separate ports for USB 3.0. It runs ~$200.
RAM: Patriot Viper 1866 Mhz 16GB (8GBx2) ($115)
There are cheaper options for RAM. But I'm building a dream machine here. I like this setup because I would only be using 2 of my memory slots and the Asus motherboard has 4. If I found I needed more RAM I could just buy 2 more of these down the road (when they are much cheaper!) and slap them in.
Hard drive 1: Any 7200 RPM 1TB or bigger hard drive ($70)
Put in a bigger hard drive or two for data storage.
Hard drive 2: OCZ 120GB Agility 3 Series SSD drive ($90)
The requirement here is a 6GB/s data transfer rate and a SATA III connection (rocket fast). Use this for the samples you are analyzing at present. When you're done transfer them to Hard drive 1 for storage.
OR
High Point Rocket Cache ($155)
I wrote about this earlier. It uses the SSD as a cache to accelerate the slow drive to SSD speeds.
Boring stuff, i.e. case, power supply connections (<$200)
This is my wishlist, so I get the Antec mini skeleton in the picture above for (110 and a standard power supply wiring kit with some nice shrink wrap cable covers so it looks nice.
Windows 7 64-bit Enterprise or Pro ($150)
Total for a fast proteomics processing PC on the cheap? ~$1000 throw in the rocket cache and you're still under $1200.
For a little extra oomph, particularly if you are going to run the processor at a higher level (cause 4.0GHz isn't enough?) , you could investigate things like a water chiller for the processor. RAM can also be water cooled if you are pushing it that hard, particularly in a less well-ventilated enclosure, but this would be enough for me even when running big Q Exactive phospho files.
Now, would a 12 core Xeon processor smoke this set up? Absolutely, but you'd pay more for that processor than you would for this whole PC even if you threw in a nice monitor. Again, power for those of us without a ton of money.
It is worth noting that a lot of PC places, like TigerDirect, New Egg and Amazon bundle components. It may be possible to get the case, power supply RAM, motherboard and CPU listed above at a significant discount if you bought them together. It's worth shopping around for!
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