Author Archives: Paddy Lavery

3 ways to routinely QC your 2D analysis

If you visit our blog regularly, you will have noticed a recent theme around quality control (QC) for proteomics data and how our analysis solutions can support this. It’s one we have chosen to highlight for many reasons. Fundamentally, as my colleague Beth pointed out in this recent post, “…it’s a case of garbage in, […]

Progenesis SameSpots and 2DE: Developing assays to QC biologic production

Earlier this year, I wrote a blog post about how 2D gel analysis with Progenesis SameSpots can be used to develop reliable ELISA assays for monitoring host-cell protein (HCP) contamination during production of biologics. An example has been published by Edward Savino and others at Centocor Research and Development Inc. (known as Janssen Biotch Inc. […]

Analysing a fractionated mouse serum peptidome using Progenesis LC-MS

As a follow up to my last blog post on analysis of fractionated samples using Progenesis LC-MS, here is a published example. Geun-Cheol Gil, Jim Brennan, Dan Throckmorton, Steven Branda and Gabriela Chirica from the Systems Biology department at Sandia National Laboratories (CA, USA) studied the mouse serum proteome using a fractionation approach1. The study […]

A round up of HUPO 2011 10th Annual World Congress

We attended HUPO 2011 last week so here are the highlights of what HUPO and its members, including us, were up to during a very busy four days in Geneva. The past ten years of HUPO and the future HUPO celebrate its 10th Anniversary and the theme of the meeting was Translational Proteomics, or moving […]

Fractionate your samples and get back a protein level analysis using Progenesis LC-MS

Fractionation offers an attractive solution to capture reliable data on low molecular weight (MW), low abundant proteins or peptides, and push deeper into the proteome of highly complex samples. It is a solution that is easy to integrate into most labs and existing set-ups, for example off-line fractionation by 1D gel electrophoresis or in-line fraction […]

How to choose the best reference run for data analysis with Progenesis LC-MS

Update: Since this blog post was first published, a new version of Progenesis LC-MS  has been released with an option to automatically select an alignment reference. The run chosen will be the one that gives the best results from automatic alignment, thereby taking a lot of the subjectivity and hard work out of the equation. […]

Co-detection: The secret to reliably quantifying & identifying the same peptides on all your LC-MS runs

A question that we get asked by people new to Progenesis LC-MS is “why is the final list of proteins in my experiment exactly the same in every group?” The simple answer, and part of the power of Progenesis LC-MS, is co-detection. Co-detection is what we call our approach to peak picking based on an […]

Proteomics Methods Forum 2011 – a first report

The two-day Proteomics Method Forum (PMF), which we mentioned taking place at St. James’ Park in Newcastle, ended on Friday last week. As well as spending the breaks talking with people at our booth, we also enjoyed the program of interesting talks, with 7 out of 17 presentations citing our Progenesis LC-MS software.   Achim […]

The rate of Progenesis SameSpots publications continues to rise

Last November I blogged about the rapid rise in the number of publications citing Progenesis SameSpots and predicted a total of 96 by the end of that year, based on an average 8 publications per month achieved over the previous 10 months. It turned out to be a good estimate, our final tally was 90 […]

A new approach for metabolomics data analysis

This is an exciting post to write. It’s not often you get to announce a new product, especially one addressing a new application; the relative quantification of compounds and metabolites. This takes the Progenesis range beyond proteomics and into the complimentary area of metabolomics, or metabonomics depending on the term you prefer! Progenesis CoMet analyses […]