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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

by bbgm 17y ago

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 17y ago
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.
sneakums 17y ago
I love Ars Technica for articles like this. I just wish they'd stop the front-page crapflooding they've been doing since the acquisition, since it makes the gems so much harder to pick out.

by bbgm 17y ago

mbreese 17y ago

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.

sneakums 17y ago

I love Ars Technica for articles like this. I just wish they'd stop the front-page crapflooding they've been doing since the acquisition, since it makes the gems so much harder to pick out.