Have you ever searched a proteomics data file in under 1 minute?

Before every PC leaves our little lab, we put it through a series of high pressure benchmarks and closely monitor the processor temperatures as a metric of how our PCs will handle your normal working environment. We can use the freeware of your choice or software that you send us. Our goal is for this PC to be the perfect tool for processing your data.

We recently obtained generous permission from some organizations to benchmark our PCs with various popular software packages and to make this data public.

Our local Thermo Applications scientist provided us with a couple of files to help us out.

We will eventually benchmark all of our PCs the same way and make that information available here. For now, we have fully benchmarked the Proteome Destroyer 12 Core system with 64 GB of DDR4 RAM.

In three separate search engines and three replicates, this system reliably obtained over 2,000 protein IDs from a whole cell digest in around 1 minute

The best runs were

Mascot:  42 seconds

Morpheus: 79 seconds.  This search can be completed in 64 seconds on the Maximum Destroyer

Proteome Discoverer: 139 seconds


Further experimental details

A Thermo Raw Data file that contains a 2 hour run from a 1ug HeLa digest containing approximately 26,000 MS/MS spectra. MS1 spectra was acquired at 60,000 resolution and MS2 spectra were obtained at 15,000 resolution.

The data was searched against the Human Uniprot database with 10ppm MS1 tolerance and 0.02 Da MS/MS fragment tolerance.

False discovery rate was used with a 1% target.  

For Mascot analysis, the file was converted to MGF with Proteome Discoverer 1.4

We searched this file with 3 search engines, Mascot, SequestHT in Proteome DIscoverer and the Morpheus program developed at the University of Wisconsin.

Static modification of cysteine alkylation and dynamic modification of methionine oxidation