Proteomics

In the June 2006 issue of BioTechniques, Thomas Conrads and colleagues wrote an article about mass spectrometry used in biomarker discovery [1]. It is part of a “Special Section” devoted to mass spectrometry for proteomics analysis that is worth reading in itself. But one figure caught my attention. In this figure (reproduced below), they plot the mass spectrometry data acquisition effort and bioinformatic effort -vs- the experimental focus. In the few past years, people relied too much on the increasing power of mass spectrometry and bioinformatic tools in their experimental design. The authors criticise the fact that people “are overly dependent on technology and suffer from lack of imaginative sample preparation”. It’s not because analysis power is available downstream that sample collection and processing could be neglected. ...

This week was quite busy … In the proteomic lab, I released the first version of IPGPhor2 Reader (see also the previous post). Of course, since we didn’t fail any recent experiment ;-) we don’t see the immediate usefullness of this software. The main purpose of this software is that it allows to see where and when an experiment failed, how the current was given during the IEF and when it was not correctly supplied. ...

IPGPhor is a device from GE Healthcare (formerly Amersham Biosciences) that performs an isoelectrofocusing of proteins. Version 2 of IPGPhor can be connected to any computer via a serial cable. GE Healthcare provides a monitoring software but no post-hoc analysis software. This gap is efficiently filled by IPGPhor 2 Reader. Today, I wrote “IPGPhor 2 Reader”. Its goal is to parse log (text) files resulting from an experiment with the IPGPhor and to plot graphs. This software (for MS-Windows, since IPGPhor logs are collected on a MS-Windows computer) is available here. ...

The Open2Dprot project is “a community effort to create an open source n-dimensional (n-D) protein expression data analysis system”. It looks very promising and has a lot of interesting thoughts about how a 2D (nD) gel analysis should be done. It has a modular approach (each step will be caried by a specific tool or “subproject”; I think this is a good thing, à-la-Unix), it’s based on an old but functional version of Gellab-II and will be using Java (for the disponibility of the proprietary-JVMs under many operating systems), R (for the stats), SVG for graphics and MySQL/PostgreSQL for storing data. They even have plans to extend the use of Open2Dprot to n dimensions, incorporating tools for microarrays, liquid chromatography, mass spectrometry. When it will be finished, it will be a cool and useful tool, from the beginning of the proteome(s) analysis to its end. And we won’t be dependent on proprietary - and costly - software from big companies anymore. ...