Single tube sample prep

[Doug]

A new paper from Mathias Mann's group published in Nature Methods describes a sample prep method that does lysis, reduction, alkylation, and digestion, and cleanup all in a single StageTip. I hope the next step is an automated liquid handling system that does it. I think I spent about 50% of my PhD doing these things.

Kulak NA, Pichler G, Paron I, Nagaraj N, Mann M. Minimal, encapsulated
proteomic-sample processing applied to copy-number estimation in eukaryotic
cells. Nat Methods. 2014 Feb 2. doi: 10.1038/nmeth.2834. [Epub ahead of print]
PubMed PMID: 24487582.

[Christopher]

When I initially read this paper I questioned the amount of 'innovation' it was really offering. At the end of the day it really is just still a StageTip protocol, and is thus limited by the same things the regular protocol is. I think in general proteomics it offers a lot of benefits, but will still be incompatible with applications where detergents or other harsh reagents are necessary or desired. It seems it also struggles a bit with low amounts of material based on the supplemental HeLa data for low cell numbers.

I think for general proteomics it is an interesting method, but for moving forward into ultra-sensitive, clinical, and high-throughput areas, I don't see its utility. Interesting paper nonetheless!

[tsbatth]

Good points. However, the thing about this stage tip protocol for me is that it's fairly easy to do for most labs without an intensive investment ($$$). Judging by some recent publications it looks like there is a push towards developments in sample prep for high throughput lossless analysis on low starting material, especially when it comes to clinical samples and cell populations. It still comes down to accessibility and cost of the product, stage-tips is a good example, they're basically common in every lab because it's simple, effective, and cheap. On that point, I saw a talk recently at a conference about another development for single tube sensitive analysis which I'm really looking forward to .

[Christopher]

I agree. The StageTip protocol is nice because it is very familiar, simple, and cheap. I also agree that there is a push currently to develop high throughput methods that are compatible with very small amounts of sample. In spite of the mentioned benefits, I am not sure the stagetip platform offers an ideal solution to these problems.

Which conference was this if you don't mind my asking?