In a rare move, I’m going to largely copy across a post from my work blog, because I hope it contains useful information. For background, I’m trying to write a simple python script that extracts particular metadata from a .RAW file, produced by a Thermo Finnigan mass spectrometer. Tools that exist for parsing these files require access to proprietary XCalibur libraries, which I do not have.
Thermo provided a link to MSFileReader, a ‘freeware’ COM object that should allow interaction with RAW files without an XCalibur installation. They also sent a PDF guide to the COM object. Although this will allow XCalibur to be avoided, the work is still Windows-bound.
Python and COM objects
Python can talk to COM objects, through the win32com.client package. As a test, I installed Python and MSFileReader and the pywin32 libs on my netbook (which is a Windows 7 machine). Can import the required Python module, but need to extent the PATH somewhat:
XRawfileCtrl is used to call the Open() method. However, this and MSFileReader as “NAME” both fail (Invalid class string).
Found ‘multiplierz‘ which seems to use MSFileReader to create mzAPI – which focusses on access to the actual data, rather than the metadata. The code gives some good clues as to how to use the COM object. [doi:10.1186/1471-2105-10-364]
MSFileReader.XRawfile is used as “NAME” in this code.
I know that the beauty industry has made a habit of twisting science somewhat for it’s own ends (see this and this for instance), but this one takes the biscuit.
The wife spotted a piece in Harper’s Bazaar while she was in the hairdressers yesterday, about an amazing new beauty treatment (the article itself is hard to link to, but it’s number 3 in the list of “9 Skin Secrets for Spring“). Injections of telomerase for $1,500 a pop. Apparently it ‘stimulates resting stem cells’. Obviously the Harper’s piece has guff about it being Nobel-prize winning technology.
Telomerase is an enzyme that amplifies DNA repeats at the ends of chromosomes, without this activity, the telomeres would get progressively shorter until the “Hayflick limit” is reached and the cell will stop dividing, or undergo programmed cell death (there’s a reasonable review of the role of telomerase here: http://www.jco.ascopubs.org/cgi/content/full/18/13/2626).
Now I’m no expert, but as far as I know, telomerase is turned off in normal somatic cells, and telomerase activity has been associated with up to 90% of cancers (even its Wikipedia entry will tell me this much, a rather old paper with some concrete figures can be found here: http://dx.doi.org/10.1016/S0959-8049(97)00062-2). I’m not suggesting for a second that injecting telomerase will give you cancer (the overwhelming probability is it will do nothing at all), but this seems to be an amazing example of abusing science in the name of ‘beauty’.
(Graphs from The Independent (London), 21 June 2008)
Today was one of those days where lots of interesting stuff turns up. On the BBC, there was 2 very good pieces about the flaws in the scientific process, specifically closed peer reviewand impact factors.
I also notice that the BBC are running a daily piece about the history of computing in the UK this week, parts one and two have already been published. Today’s article about Colossus is especially good.
Also, after last week’s excellent, and damning, judgement from the GMC -
- regarding Andrew Wakefield’s reprehensible behaviour in his research into the ‘link’ between MMR and autism, today The Lancet finally pulled the paper in which his findings were published 12 years ago. Wakefield et al (1998) (doi:10.1016/S0140-6736(97)11096-0) has now been retracted from the public record after the Lancet concluded that the claims made by the researchers were ‘false’ (http://www.thelancet.com/journals/lancet/article/PIIS0140-6736%2810%2960175-7/fulltext – apologies for paywall).
At the heart of Systems Biology is a vast hunger for measurements. mRNA abundance, metabolite concentration, reactions rates, degradation rates, protein abundance. This last measurement has long been problematic for researchers, mass spectrometers get increasingly accurate and powerful, but are still hindered by the simple fact that observed signal intensity does not necessarily correlate directly with the abundance of that peptide in the sample. Factors such as peptide ionisation efficiencies, dominant neighbour effects, and missing observations all give rise to erroneous estimates of peptide quantities. Until recently, the best way to get close to measures of protein abundance was to use a peptide tagging methodology, but these are typically expensive, and provide only relative quantification (useful for expression proteomics studies, less useful if you need to know the absolute levels of a protein for a Systems Biology study).
Recently, a three step method has been proposed for determining the absolute quantities of proteins in the cell, on a proteome scale. Step one is isoelectric focussing of tryptic digests of whole cell extracts. Step two, calculating the absolute abundance of a small group of proteins by Selective Reaction Monitoring (SRM). SRM uses spike in, isotopically labelled peptides of known concentration as references to calculate the actual abundance of peptides of interest. Finally, step three uses these abundances as reference points to calculate the abundance of all proteins in the sample, using the median intensities from the 3 most intense peptides for each protein.
Leptospira interrogans (Wikimedia Commons)
Using this methodology, the abundances of >50% of the proteome of a human parasite (Leptospira interrogans) have been determined to an accuracy of ~2-fold. These abundance measurements were confirmed by almost literally counting the number of flagellar proteins present in a cell by cryo-electron tomography.
Although current hardware probably limits this technique to a few thousand proteins, that is still a big step forward on what was previously possible. If whole proteome scale absolute abundance measurements become an achievable reality, maybe proteomics can finally take on microarrays as the dominant technique in the post genomics world.
Malmström, J., Beck, M., Schmidt, A., Lange, V., Deutsch, E., & Aebersold, R. (2009). Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans Nature, 460 (7256), 762-765 DOI: 10.1038/nature08184
I love my free Nature Methods subscription. It allows me to get my hands on a paper journal, which I rarely get to do these days, and the content is actually pretty marvellous.
You can still apply for a free subscription, and if you are eligible to do so (individuals in North America and Europe involved in research within the life sciences or chemistry), I would urge you to.
