Progenesis overcomes the challenge of cross-lab reproducibility for proteomics

Progenesis SameSpots helps you overcome the biggest challenge facing everyone in quantitative proteomics today, cross-lab reproducibility of results. If you can achieve this then you can be confident in measuring real biological effects that can make a difference, not just reporting artefacts of an experimental approach. Progenesis LC-MS applies a similar unique approach so we hope it can show the same benefits and cross-lab reproducibility with your quantitative MS proteomics analysis.

The HUPO Reproducibility Study

Results from the groundbreaking HUPO Reproducibility Study, which used standard protocols and Progenesis SameSpots, prove that protein expression analysis is reproducible across-labs and highly reproducible within-lab. A publication is in-progress but some of the initial data^{1, 2} are represented below. You can read full details and see the poster of results presented at HUPO 2008 and the 8th Siena Meeting 2008.

	Unconstrained User Analysis	Automatic Analysis
Lab1	92%	98%
Lab2 UserA	84%	98%
Lab2 UserB	76%	100%
Lab2 UserC	88%	100%
Lab3	70%	88%
Lab4	88%	84%
Lab5 UserA	90%	94%
Lab5 UserB	94%	82%
Lab5 UserC	94%	94%

Fully automatic analysis of 2D PAGE images using Progenesis SameSpots produced results with better reproducibility than user-editing, even by experts. The values show the similarity (%) of the top 50 differential spots from each image set following analysis with user-editing and with fully automatic analysis compared to a constrained analysis from a professional analyst. View more results presented at HUPO 2008.

Whole image pixel-based Pearson correlation coefficients for intra-lab datasets (across all gels including the treatment differences) show very high reproducibility across the five individual labs who took part in the study.

How does Progenesis achieve this?

The unique Progenesis workflow perfectly aligns data prior to analysis allowing all detected features to be 100% matched and compared directly across every run without the need to validate or edit each individual feature. This means you can quickly see the real expression differences without laborious, subjective editing and make valid conclusions using multivariate statistics applied to a complete data set.

The algorithms and workflow have been specifically applied for 2D and LC-MS data analysis with Progenesis SameSpots and Progenesis LC-MS. So whichever proteomics technique you run the result is always rapid unbiased analysis and high quality data for publication.

¹ Oral presentation, "Reproducibility of 2D gel-based proteomics experiments" Dr. Hans Voshol, Novartis Institutes for BioMedical Research, Workshop for Proteomics Validation, HUPO 2008, 7th Annual World.

² Poster on "Reproducibility of 2D gel-based proteomics experiments", Dr. Sjouke Hoving, Novartis Institutes for BioMedical Research, 8th Siena Meeting.