Tuesday, November 17, 2015

Ever wanted a great label free proteomics dataset?

"Hey guys, here's this awesome new algorithm for label free analysis!!!!"

Want a GREAT dataset to test it out on?

EDIT 8/22/16: Since I've been sending this paper link and/or the PXD number to everyone I know we found two things: 1) I miscopied the PRIDE number (fixed) and 2) I overlooked the fact that 3 author contributed equally to this.  This incredibly useful resource should correctly be called:

Claire Ramus, Agnes Hovasse, Marlene Marcellin, Anne-Marie Hesse, et al., 

{End EDIT}

Check out this cool new paper from Claire Ramus et al.,!  In this, they developed a great standard that all of us can download and use for free. They also use it to test a bunch of the current algorithms people are using.

The sample is the Sigma UPS1 48 protein mix (all equimolar proteins) spiked into a Yeast digest background at different concentrations. The spike-ins range from 50amol to 12,500 amol (yeah...there is a more efficient way of writing this, but I'm not great at metrics...thanks American public schools! I love sounding like an idiot to everyone else in the world...)

You can download the dataset...wow...my internet is slow right now...well, I guess you can download the dataset...from PRIDE. It will be PXD001819 after it is published. The authors were kind enough to provide a way to download the dataset prior to publication (wow, right!??!) that you can find in the abstract.

Got a couple files. This study was on an Orbitrap Velos running High-Low (FT for MS1 and CID ion trap MS/MS scans). It looks like 60k resolution at the MS1 (around 400m/z)

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