This webpage came up in a conversation over the weekend. Its one of those things that has been around for so long I thought everyone used it. This site by GraphPad will do statistical calcuations (unpaired student's t test, and Welch's t...
Monday, June 25, 2012
Saturday, June 23, 2012
Pinpoint
Okay, so this is probably a weird entry. Weird because I don't want to lose credibility with my small audience because I'm writing about a product produced by my new employer. Regardless, I really wanted to write this entry because Pinpoint...
What mass range contains the most (and best) fragment ions? Part 2
This is a continuation of an entry from a couple of weeks ago. The question is this: If I'm using an LTQ Orbitrap system, should I always be scanning in MS1 (and selecting fragment ions) with an m/z from 300 to 2000, or am I wasting valuable...
Monday, June 18, 2012
Protein Identification using Top-Down
I admit it, I first downloaded this article in June's MCP because I thought that it was going to be a nice review of recent advances in top down proteomics. For anyone who hasn't done this kind of work, this is where you do not digest your proteins...
Wednesday, June 13, 2012
Systematic Comparison of Fractionation Methods for In-Depth Analysis of Plasma Proteomes
This paper from Cao, et al., came to my attention while digging through references for a paper I am constructing with my soon-to-be ex-lab. I've read this through 4 times, because I am absolutely amazed by how different the protocols described...
Tuesday, June 5, 2012
What mass ranges yield the most (and best) fragment ions?
Here is the experimental setup: normal mouse serum was taken and depleted of the 4 most common proteins, albumin, transferrin, IGg, and the fourth one (I forget).The remaining proteins were digested in trypsin overnight, using a simple FASP-like...
Sunday, June 3, 2012
Static exclusion on an Orbitrap Velos
One of the most useful, and possibly least exploited features on an Orbitrap is the Reject Mass List dialog box. This feature allows you to create a list of up to 2,000 ion masses that are ignored when ions are selected for fragmentation. For uncovering...
Saturday, June 2, 2012
Enhanced Identification of Peptides Lacking Basic Residues
The new issue of Proteomics has 2 articles in it that I find really interesting. The first is by Martin Biniossek and Oliver Schilling of the BIOSS Center. This paper begins to address one of the gaping holes in shotgun proteomics, the requirement...
Friday, June 1, 2012
New Position
Things have been happening really quickly in my life recently. First off, I am leaving the world of government contracting to begin my new career as a Field Applications Scientist for Thermo Fisher Scientific. Second, I am leaving the grinding...
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