

 Protein sequencing gone awry: 1 sample, 27 labs, 20 results - jgamman
http://arstechnica.com/science/news/2009/05/protein-sequencing-gone-awry-1-sample-27-labs-20-results.ars

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biohacker42
_The proteins are chopped into smaller fragments using an enzyme called
trypsin..._

That's known as bottom up analysis. It is currently the most popular way to do
it, and IMHO it's crap.

You can do intact whole protein analysis and that's much better. More higher
end instruments will do both, starting with the intact protein, measuring its
mass, and then breaking it down and measuring the mass of the peptides.

The breaking down part is not deterministic but with the mass of the whole
protein and the genetic sequence and a few runs you can figure out exactly
what's what.

None of that will tell you what the 3D shape of the protein is. That's a whole
other ball of wax.

\--EDIT--

 _the initially deposited data had several problems, including incomplete
files, proprietary software formats, and screenshots of data displays in
software rather than actual data files_

Yep, there's companies that can help you with that:
<http://www.bioanalyte.com/>

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bbgm
I like how Ars is able to make a complex topic more accessible. MS-based
proteomics is still young, and it will take a few years for things to
stabilize. RNA expression arrays were in much the same state several years
ago. The key is to make sure that the variation comes from the biological
samples, and perhaps the instrumentation, with the methods not being a source
for those differences. Two things that the field needs to do is (a) make raw
data available so that experiments can be reproduced and (b) uses consistent
data formats. Standards can/will follow.

One experiment I would like to see is the same lab doing the same experiment
multiple times on the same sample on different instruments (of the same make
and model). Results should be interesting.

~~~
mbreese
The advantage that RNA expression arrays has over mass-spec is that the
techniques used are just a highly scaled up version of the northern and/or
southern (depending on the method) hybridization blots that have been in use
forever. The corresponding protein technique (western blots) requires
individual anti-bodies, and as such is just not scalable to the same degree.

So, instead we are left with mass-spec solutions that miss a ton of data. Not
all peptides can be read on a mass-spec, and if you do get a peptide, it's up
to the software to figure out what it was.

Also, the data analysis in proteomics has been a known issue for many years.
There are little to no standards since it takes so long to run samples. At the
same point in the microarray field, the statistical and data analysis
techniques were largely worked out. But again, this is due to the 'simplicity'
of the measurements. It is just plain easier to measure known RNA or DNA
sequences.

That's not to say mass-spec isn't useful, because it is. But I highly doubt it
will be able to ever give us a complete picture of the proteome.

It's kinda funny, because we are seeing a shift in the transcriptome world
that is now moving toward rapid sequencing approaches that mirror mass-spec a
great deal.

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xayide
Could anyone please tell me the names of some companies/non-profits
researching proteomic sequencing? Preferably ones trying to work out the kinks
that the article references? I live in the Boston area and used to analyze
genomic data for accuracy and consistency and would love to help with this
problem.

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biohacker42
Seattle Proteome Center (SPC) <http://www.proteomecenter.org/>

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xayide
Thank you! Their site gives a better idea about what's actually going on in
the world about proteomics, and is a great start about finding affiliate
companies.

