Ever since Bio-Rad's acquisition of Ciphergen's SELDI MS (surface enhanced laser desorption/ionisation mass spectrometry) technology late last year, it has been fighting against the spectre of "controversial" research results obtained using the technology.
The acquisition of the technology in November last year cost Bio-Rad $20m (€14.5m) and since then Ciphergen's successful defence of the SELDI patents has triggered a clause for a further payment of $2m.
SELDI allows researchers to capture proteins of interest on a chip and then analyse them by MS in a similar way to MALDI (matrix assisted laser desorption/ionisation) MS.
In MALDI, a biological sample is mixed with a matrix and deposited on a surface before allowing to dry, whereas in SELDI the sample is spotted on a surface that is modified to bind certain proteins while the rest of the sample is washed away.
This leads to simpler mass spectra with fewer background peaks to confuse the identification of low abundance species.
The 'controversy' surrounding the use of the technology originated with work published in the journal The Lancet that described the use of SELDI TOF (time-of-flight) MS techniques to detect the early stages of ovarian cancer.
In the article, Petricoin and Liotta described the use of the technology combined with a cluster analysis algorithm to determine identify the presence of early stage ovarian cancer. The findings were remarkable and the authors claimed a 94 per cent positive predictive value.
However, research published in the journal Bioinformatics that re-examined the earlier work by Petricoin and Liotta suggested that there were inconsistencies in the experimental procedure.
Indeed the authors wrote: "these concerns suggest that much of the structure uncovered in these experiments could be due to artefacts of sample processing, not the underlying biology of cancer."
According to Dr Nelson Cooke, marketing manager for Protein Detection at Bio-Rad: "the controversy has been whether or not you can really use the pattern based method that Petricoin published to distinguish between diseased and non-diseased states and thatissue has generated a negative image for the entire SELDI platform."
This is perhaps surprising as the issue with the techniques used has never been with the specific MS approach but rather with the sample preparation and data analysis steps.
Nevertheless, the controversy led to Ciphergen selling the instrument part of its business to Bio-Rad with the company announcing a name change to Vermillion as it refocuses on developing diagnostic tests using the technology.
Meanwhile, Bio-Rad is focussing the technology at applications in biomarker discovery, immunoaffinity and protein interaction analyses, SELDI assisted purification and process proteomics.
"The beauty about the SELDI technique is that the SELDI chip itself allows on-chip retentate chromatography, where the analytes of interest stick to the chip for analysis," said Dr Cooke.
This approach can be used to retain various different proteins much like affinity chromatography and the company is working on various applications that could allow users to adhere specific antigens or antibodies to the chip to give the system as much flexibility as possible.
Dr Cooke continued by explaining that because the dynamic range of proteins in proteomics is so complex the ability to adhere specific types of proteins to the chip and wash away all the other parts of the sample simplifies the spectra by removing compounds that cause background noise.
In addition, the enrichment allows the proteins of interest to be studied with increased sensitivity because the salts and detergents that cause ion suppression in the MS have been washed away.
"We believe it is the best tool available for biomarker discovery," said Dr Cooke.
The chip-based design of the system allows high throughput experimentation which is very important in proteomics experiments where large numbers of samples are needed for valid correlations to be made between a potential disease state and the expression levels of certain proteins.
"One of the problems in proteomics is that people have been using sample sets that are too small to give statistically meaningful results," said Dr Cooke.
"With the SELDI technology you can process hundreds of samples a day whereas with HPLC MS based approaches that would take much longer and be prohibitively expensive."
The MS instrument is a linear TOF-MS, which has been designed to have a very high sensitivity, which Cooke believes is essential for proteomics experiments.
"The instrument itself is very sensitive and that's very important for detecting low abundant proteins," said Dr Cooke.
The platform also comes with its own data analysis software to avoid the problems encountered by Petricoin and Liotta and make researchers lives easier.
"We are trying to help our customers conduct these difficult proteomic experiments by optimising the entire workflow," said Dr Cooke.
The company believes that its approach of looking at every step of the process and ensuring it is conducted in a very reproducible manner will avoid researchers having to waste time developing their own procedures and worrying about whether the results they generate will be valid.