Lectures of MaxQuant Summer School

It's summertime that means it's time for MaxQuant Summer School. For the 10th time proteomics research gather to get to know the hints and tricks about dealing with proteomics software maxQuant.

Over the time span of a decade MaxQuant have become the leading software for shotgun proteomics and quantification via Lable-Free-Quantification, Tandem-Mass-Tag and SILAC.

Briefly, MaxQuant consists of a search engine Andromeda, which is similar to mascot or crux and a visualization tool, called Perseus which provides comprehensive statistical analysis, such as normalization and hypothesis testing.

https://www.youtube.com/watch?v=tAihiwLhzHc

For more detailed information about the specific feature of MaxQuant check out the great youtube channel, to which all the lecture of current and former summer schools are uploaded.

micro pillar array - the future of chromatography?!

Nowadays, high sensitivity LCMS requires nanoLC in front of a state of the art mass spec. However, these nanoLC-MS systems need to be maintained intensively to avoid downtimes (due to column clogging), especially when analyzing an high number of samples.
This means improving robustness and performance of nanoLC are a major objective in academia and industry.

While skiming to keynote lecture of the MaxQuant Summer School the invention of micro chip pillar array column as chromatographic device integrated into LCMS setup was mentioned.
In my optinion these chips offer a great opportunity to overcome the limits of traditional nanoLC since they eliminate the column specific eddy dispersion and display incrediable low backpressure at column length of up to 2m.

I took this picture from the introductional video...really impressive and worth watching https://vimeo.com/230455032
I try to find out how these chips are manufactured. Which brought me to an belgian company called pharmafluidics.

https://www.pharmafluidics.com/

By the way for the people out there seeking for a new challenge they have open job vacancies currently. But back to the micro pillar chips - They are made of silicon pillars which are the result of an etching process which removes the interstitial volume in a really reproducible and homogeneous manner. These manufacturing methods have been successfully applied in the semiconductor industry. I am really looking forward to read studies evaluting proteomics performance of these chips.

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Documentary about proteomics

I have watched this current documentary about proteomics last weekend. Some of the major players in the field contributed in this. It is made for a broader audience to gain an understanding about the proteomics and challenges scienists currently facing.

Really interesting was the inside view into the Beijing Proteome Research Center (BPRC) and its organization. "...ground floor with mass spectrometers, 2nd floor with molecular biology lab, 3rd floor accommodates the bioinformatics group and on the top floor a super computer is located. Why would one harbor a supercomputer on the top floor?

https://www.youtube.com/watch?time_continue=619&v=8m2_Rs-MaZA
Its worth watching!

Great stereochemistry tutorial

Back in the days I hated lectures about stereochemistry, but this tutorial, which I came across recently is definitly going to change this. Its well structured and I really like the 3D Jmol images.

Beautifully done Miss Burrmann.
http://www.chemeddl.org/resources/stereochem/

Breaking the 10000 Protein Group IDs for mammalian cells

This worth noticing and really a milestone in proteomics -
nanoLC-MS is complex method it combines the orthogonality of an nanoflow LC and an cuting edge MS, which either acquires and fragments bottom up peptide ions in parallel or superfast (i.e. a beam type instrument). During the years MS vendors and research groups came up with innovative acquisition modii pushing the border of the maximum protein identification.
Investigators of the MPI Munich have developed a new aquisition mode, called BoxCar Acquistion which let them identify over 10000 protein group IDs in mouse cells and 6200 protein IDs in human cell.

As far as I understood BoxCar Acquistion optimized the MS1 precursor sampling by filtering only decidated m/z ranges by the quadrupole, injecting and storing them into the C-trap. The advantage here is that ions, which wont be visible within an full scan are now observed with sufficient S/N. The S/N can be controlled by the injection time of m/z mass ranges of interest.

Since this is a beautiful new tool in the hands of mass spectrometrist therefore it is deserved to be published in Nature.
https://www.nature.com/articles/s41592-018-0003-5

It's not Einsteinian stuff - Brain Chait

OK - there we go! This is going to be my first post and I have choosen to write about an interview i recently read. Its from 2008 and illuminates the life and academic carrier of one of the other mass spec master (besides me ;) ) Professor Brain Chait.
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Apart from his scientific accomplishments he talks about this school time and the inhumane situtation in South Africa during the 1950s. A time during which rassistic apartheid laws got applied in south african soceity.
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Since he has been contributing to the mass spec community for more then 30year he also worked with radioactive ionization sources, such as Californium-252 (Cf252). These plasma desorption sources are by based on nuclear fission of Cf252, which produces fission neutrons which are being adsorbed by the analyte and knock off electrons.
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Quite encouraging was the end of the interview were Prof. Chait relativizies his appoarches, although there have been awesome, as none Einsteinian stuff.


Wish being in such state at some point.


If you'd like to find out more about Prof. Chait or the research his is currently conducting visit
Rockefeller University New York