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Bruker, SISCAPA Assay Tech Study Suggests MALDI-MS Suitable for Clinical Protein Quantitation

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By Adam Bonislawski

Bruker and SISCAPA Assay Technologies have collaborated on a paper published in the online edition of the Journal of Proteome Research on using MALDI-TOF mass spec for peptide quantitation.

The paper is another indication of MALDI-TOF mass spec's resurgence as a possible clinical platform, a development driven by the technology's potential to deliver lower costs and higher throughput compared to other clinical proteomics approaches like triple quad-based MRM-MS assays (PM 12/20/2012).

In the past MALDI has been dismissed as a clinical platform for protein quantitation largely due to concerns about its reproducibility. In the JPR paper, however, the researchers used a Bruker autoflex speed MALDI-TOF to perform relative quantitation of peptides with coefficients of variation of between 1 and 2 percent. Unpublished results indicate that similar precision in quantifying medium- and high-abundance proteins is also possible on Bruker's less expensive microflex MALDI-TOF machine, the researchers said in a statement.

The effort was led by SAT CEO and founder Leigh Anderson and Bruker director of proteomics Detlev Suckau. The two firms have been collaborating on MALDI-based assays using the SISCAPA technology, with much of the work taking place in the lab of University of Victoria professor and SAT co-founder Terry Pearson, where PhD candidate Morteza Razavi has investigated combining the techniques to quantify protein biomarkers linked to prostate cancer (PM 12/2/2011). Pearson and Razavi were also authors on the paper.

MALDI’s reputation for high variability stems from relative quantitation experiments people have done that produced CVs of 30 percent or 40 percent, Anderson told ProteoMonitor in an interview last month discussing the work. “But it turned out that people had not really systematically investigated how good quantitation would be if you have stable isotope-labeled internal standards [as in SISCAPA],” he said.

MALDI-TOF platforms have smaller dynamic ranges than triple quads, and typically don’t offer the high level of sensitivity and specificity that MRM assays provide, but, Anderson said, Razavi’s work suggests that in many cases SISCAPA’s antibody capture step effectively generates a pure peptide analyte, enabling more effective use of MALDI-MS.

In particular, using MALDI-MS could allow researchers to cut out time-consuming chromatography steps, upping assay throughput – a key requirement for moving mass spec-based proteomics into the clinic.

SAT and Bruker are not the only people working on applying MALDI to the SISCAPA workflow. Mark Stolowitz, director of the Proteomic Core Facility at Stanford’s Canary Center for Cancer Early Detection, has developed a MALDI-based SISCAPA workflow using acoustic liquid handling technology from sample prep firm Labcyte. Stolowitz told ProteoMonitor in a December interview that the workflow offers sensitivity on par with SRM assays on a triple quad.

In the JPR paper, the Bruker and SAT researchers found that the autoflex speed MALDI-TOF provided "precise quantitation of high-to-medium abundance peptide biomarkers over a 100-fold dynamic range," they wrote.

"The results of the joint work prove that MALDI-TOF is very suitable for peptide and protein quantification in the 1-5 [percent] CV range, if done properly," Suckau said in a statement.

"The results in this publication suggest that the use of the 'LC-free' SISCAPA-MALDI-TOF workflow in pre-clinical research is quite attractive," he added. "This is an emerging market for Bruker that will further increase the visibility of our very successful MALDI-TOF product line in biomedical research."


Have topics you'd like to see covered in ProteoMonitor? Contact the editor at abonislawski [at] genomeweb [.] com.

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