A round up of HUPO 2012, Boston

As mentioned in a previous post, we attended the HUPO 11th Annual World Congress in Boston recently. I was lucky enough to attend so I can share some of the highlights from each day with you.

The HUPO council meeting was held on Sunday. Here HUPO shared its vision for the future. One aim is to expand the involvement of researchers at all levels and across different disciplines. This was reflected in the main scientific program for the rest of the week, which included talks on metabolomics, lipidomics and analysis of non-human samples.

The New Technology and Standardisation in Proteomics workshop  was also held on Sunday, covering  varied topics, with each talk showcasing different aspects of experimental procedure: from sample preparation to data analysis.  Due to a last minute change, I was drafted in to chair the afternoon session of the workshop. As part of this, I got to introduce Roy Martin from Waters with his presentation on the TransOmics™ Informatics software for proteomics and metabolomics that we have covered in an earlier blog post.

Launching the Human Proteome Project

On Monday, a major event was the official launch of the chromosome-based Human Proteome Project (C-HPP). This 10 year multi-site research effort was celebrated with a well-attended session that introduced the potential and challenges of this project. There were informal presentations from the major groups involved, including the leadership team, principal investigators from the labs doing the wet work, funding organisations such as the NIH, journals and the HUPO Industrial Advisory Board, of which Nonlinear are members.  It was good to be there to hear what was expected and celebrate with the cutting of the HUPO cHPP cake!

HUPO-CHPP-LAUNCHPrinciple investigators, leadership group and other organisations involved cut the cake to launch the C-HPP

The goal of the C-HPP is to produce what’s been called a “parts list”.  Each lab in the project has taken on the task of characterising the proteins that map to the genes from a specific chromosome within the human body. Supporting this are technology pillars that add context to these discoveries. There were words of praise and encouragement, but also a reality check on how industry needs to help drive this forward, much like the efforts of the Human Genome Project, and how the C-HPP must not suffer the same pitfalls as other big projects. The meeting ended on a positive note – everyone should have access to the data and it can be used by and built upon by the next generation of proteomics researchers.

Posters and Progenesis interest

HUPO-POSTEROn Tuesday I presented a poster (#108) showing how you can use gas-phase fractionation to increase proteome coverage and how Progenesis LC-MS supports that. If you’re interested to learn more about this too, then a good start is this blog post.

There were over 600 other posters shown at the meeting, with an equal number of label-free quantification compared to labelled approaches for LC-MS.  2D gels were also represented, mainly as a way of separating out proteins prior to complementary analysis by MS technologies.

Progenesis LC-MS and Progenesis SameSpots were specifically mentioned on 9 and 2 posters respectively but we also had interest in our newest product, Progenesis CoMet, for metabolomics. If you would like to try this new product to see how it can help complement your research, then please get in touch and we’ll be happy to help.


Find out more about Progenesis LC-MS

As you can see in the photo above, the exhibit hall was busy each day, especially on Tuesday and Wednesday evenings. By the final day we had answered a lot of questions from our customers about exporting and reimporting results to and from other bioinformatics packages. This is an area I feel we are quite good at, so it was good to share what we knew and if you have any questions, please get in touch and our support team can help you.

We also had quite a few enquiries from people working on quantifying proteins with post-translational modifications and separately analysis of native peptides. Progenesis LC-MS is being used for both of these applications by our current customers. If you would like details, then contact us for a demo on your data.


Next year the meeting will in Yokohama, Japan, with the tentative theme so far of “The Evolution of Technology in Proteomics”, which sounds like an interesting meeting for us. We hope to see you there to share our latest technologies for ‘omics data analysis.


View from the 50th Floor of the Prudential Building, looking over Boston at the HUPO 2012 evening social


Nonlinear team take on the Great North Run

Four of our employees – Duncan Barrie (not pictured), Ian Hargreaves, Martin Wells,  and John Renney (pictured left to right below) are taking part in this year’s Great North Run on Sunday September 16th which starts here in Newcastle upon Tyne, crosses the iconic Tyne bridge and finishes in the coastal town of South Shields.

GNR 2012 Nonlinear Team

It is a tough half-marathon course, which is world famous and attracts over 54,000 entrants each year. The route will be lined by thousands of spectators and there is live entertainment which really helps the participants complete the last few gruelling miles.

The Nonlinear team are raising money for the Tony Blair Sports Foundation (TBSF) which invests in local people by recruiting and training volunteers to increase the number of sports coaches and officials in the North East of England. Every £200 raised covers the cost for a new coach to work in sports clubs and schools, helping more young people play sport.

John Renney, our web developer, says, “I’m an Athletics Coach who is partly funded by The Tony Blair Sports Foundation as they helped me gain my qualifications. The Foundation’s support and their interest in what I do makes them an excellent team to work with.”

“Duncan Barrie, our Finance Director at Nonlinear Dynamics, approached me asking if I would like to get a team together to participate in the Great North Run to raise some money for the TBSF. Nonlinear Dynamics are very supportive of the voluntary athletics coaching I do in local first schools so it was easy for me to say yes. Here we are, training hard for the event and hoping to raise in excess of £2,000. This money will help the TBSF support another 10 sports coaches, like me, who will help to get more young people in the North East playing sport.”

After an amazing Olympic Games, if you have been inspired to take up sport either as a participant or as a helper, then further information can be found here:

We wish our 4 runners good luck, and hope there aren’t too many aches and pains in the office next Monday Smile

Solutions for your proteomics and metabolomics data analysis–come and see us at HUPO, Boston

We have made our final preparations for the HUPO 11th Annual World Congress which starts in Boston, Massachusetts on Sunday 9th Sept and we are really looking forward to what promises to be a great meeting.

We will be based in the exhibit hall, at booth #404, and our data analysis specialists will be on hand to help with all of your proteomics and metabolomics data queries.

Get a demonstration of any of the products in the Progenesis range, which  is platform independent and will integrate seamlessly into your workflow, irrespective of the instrument you are using.

Progenesis LC-MS –  allows you to visualise your complex data and minimise data loss in your experiments through the quantify-then-identify approach.

BRAND NEW! – Progenesis LC-MS now allows you to analyse SILAC data or other mass shift peptides when used alongside the Progenesis Post Processor (PPP) application.


Progenesis SameSpots – for fast 2D gel analysis which is reproducible across labs. No missing values in your results means you can confidently perform multivariate statistical analysis. There is also an integrated SpotCheck workflow so you can measure each gel to ensure it meets your lab’s quality requirements. It is a fully comprehensive, easy to use software for all your 2D needs.

2D montage large

Progenesis CoMet – reliably quantify-then-identify relative differences in compound abundance for discovery-based metabolomics. Promotes an objective approach to analysis with automatic deconvolution of ions to generate a final list of compounds which can be easily shared or validated.


In addition to our activities at the booth, my colleague, Paddy Lavery, will be presenting a poster at the meeting. It is number 108, “Proteomic Analysis of Cellvibrio japonicus UEDA 107 using Gas Phase Fractionation and 2D Gel Electrophoresis”

If you’d like to stop by, he will be presenting his poster on Tues 11th & Thurs 13th Sept – 10:30-12:00, and would be very happy to talk you through the application of Progenesis in the study.

Here’s to a successful meeting in Boston, we hope to see you there!

London 2012 – experiencing the Olympics first hand

Having only recently just made it back down to earth after my time as a volunteer Games Maker at the 2012 Olympic Games, as mentioned in an earlier blog post, I can honestly say that spending 2 weeks in London at the Olympic Park has totally inspired me in many different ways.

They tell you that an Olympic Games is a very emotional and unusual experience. Well I can confirm that it certainly is. Smile

Even when people saw me outside of the Olympic Park in my uniform, they thanked me, shook my hand, and took my picture – it was amazing!


My Games Maker role was based at the Water Polo Arena. I worked with the public, checking tickets, providing information and showing them to their seats. Occasionally I worked backstage with the athletes, their families and VIPs.

During my 10 volunteer shifts at the arena, which holds 5,000 spectators, I got to see a number of matches of this fantastic sport, which I have to admit I hadn’t seen before.

I’ll never forget the Hungarian supporters. They were passionate and always full of voice. They didn’t like to sit in their allocated seat either, which made my day interesting. Smile

The winners of the women’s competition were the USA and Croatia deservedly won the men’s.

The Olympic Stadium hosted the Athletics and I was fortunate enough to have a ticket for the men’s 100 metre final and the final of my preferred event, the steeplechase. The atmosphere on that night was electric, it was a real privilege to be there.


Being a Games Maker allowed me to enter the Olympic Park outside of my volunteer working hours. Some of us were lucky enough to get a free pass into some of the venues and I saw a great men’s hockey match.


Finally, back at the Water Polo, after the men’s gold medal match, we all had an opportunity to jump into the pool. So I took it!


Looking ahead, I’m fully committed to inspiring young people to get involved in my sport, which is athletics. I’ll be continuing to coach children at athletics clubs and in schools around the North East from September. I’ve also registered my interest in helping out at the 2014 Commonwealth Games in Glasgow. Oh, and I’m taking part in the Great North Run half marathon with some work colleagues from Nonlinear Dynamics. For more information, please visit our Just Giving page.

Now you can analyse labelled samples and perform absolute quantification with Progenesis LC-MS

A new publication and software toolkit from the Protein Function Group at the University of Liverpool has just made Progenesis LC-MS even more attractive for quantitative proteomics. The toolkit, free to download and use, allows you to:

  • Analyse SILAC data or other mass-shift labelled peptides measured at the MS1 level
  • Perform absolute quantification using Top3, or Top‘X’, peptides
  • Export peptide or protein level results in the mzQuantML PSI standard

logo-with-textThe Progenesis Post-Processor (PPP) provides a simple piece of software to use alongside your copy of Progenesis LC-MS. TIP: To run the PPP you need to make sure you have installed Java.

All that the group who developed the toolkit ask is, if you use it, cite the following reference.  D. Qi, P. Brownridge, D. Xia, K. Mackay, F. F. Gonzalez-Galarza, J. Kenyani, V. Harman, R. J. Beynon and A. R. Jones. A software toolkit and interface for performing stable isotope and top3 quantification using Progenesis LC-MS. OMICS: A Journal of Integrative Biology, 16(10), 2012(in press).



How the Progenesis Post-Processor looks for analysing results of labelled experiments

How do I use it?

The publication gives examples of analysis including an S. cerevisiae SILAC test sample, absolute quantification using Sigma48 UPS proteins of varying concentrations 0.25-20 fmol/uL  spiked into a yeast culture and exporting data as standardised mzQuantML output.

I have gone through the process of downloading and trying the Progenesis Post-Processor and even as a non-bioinformatician I found it is easy with Java already installed and Progenesis LC-MS downloaded. Just save the PPP to a suitable location, double-click the icon and it opens ready to use in the following way:

  1. Use the guided workflow of Progenesis LC-MS to generate results and in the Review Proteins view export the peptide measurements as a .csv file. The mzQuantML conversion can use an exported .csv file of peptide or protein measurements.
  2. Open the Progenesis Post-Processor and select the data processing you want from one of the three separate task tabs, applying any parameters you need.
  3. You are promoted to save the processed results as a .csv for review or to easily incorporate them into any downstream bioinformatics workflow.

The PPP, as of 15th August, is a v1.0 Beta. So if you come across any issues or have any feature requests you can post them here to help in developing future versions.

Try it yourself

Over the last year the message at meetings we have attended has been that label-free quantitation is rapidly growing in its use for proteomics research. We chose to support solving the challenges of label-free relative quantitation from the start with Progenesis LC-MS. This meant, until now, anyone using labelling approaches could not benefit from our software. With the availability of the toolkit you can see the benefits it offers whatever approach you use, including:

  • Platform independent analysis of data from a range of sources Label-free
  • Labelled and absolute quantification from one easy to use workflow
  • Support for standard proteomics data formats, including export of the new mzQuantML

Get in touch or download a free trial copy of Progenesis LC-MS to start using the workflow and see the results from your own data.

Waters and Nonlinear co-develop analysis solutions for large-scale, complex data sets

Following our earlier blog post announcing that we had embarked on a major project with Waters Corporation to supply software as part of their new ‘Omics Research Platform Solution we can bring you a progress update. The formal agreement has been signed and a press release made by Waters Corporation, which was reported the same day by GenomeWeb News.

TransOmics™ Informatics software is exclusive to Waters and separate to our own Progenesis LC-MS and Progenesis CoMet software but combines core features of the Progenesis approach with ProteinLynx™ Global SERVER 3.0 and MarkerLynx™ XS for HDMS data analysis.

Representatives from both Waters and Nonlinear have shared what they think this solution will provide.

“The complexity of biological samples is so great that the sensitivity and specificity of analytical techniques required for biological discovery presents scientists with significant challenges when it comes to managing experimental data,” said James Langridge, Ph.D., Director of Pharmaceutical & Life Sciences Discovery, Waters Division. “We believe that through our partnership with Nonlinear Dynamics we can address this situation and advance the pace of discovery.”

“I’m delighted to see this exciting partnership bring together the latest MS technology with world-renowned data analysis software,” said Will Dracup, Executive Chairman, Nonlinear Dynamics. “Researchers today are faced with large, complex data sets and they need to be able to visualize this and extract reliable results. The software Nonlinear has developed specifically addresses these issues, unlocking the potential of the valuable, content-rich, omics data that Waters’ ion mobility technology generates.” 

Our team of software developers, application scientists and product specialists have been involved in helping to demo the software at recent events including ASMS 2012 held in Vancouver Canada, May 2012 and the EuPA/BSPR meeting held in the UK, July 2012. Our team have reported back on the high number of visitors with keen interest at both the Waters demonstration sessions and both the companies stands.


Waters Omics Research Platform Solutions with TransOmics Informatics provide analysis of complex data sets generated by large-scale proteomics and metabolomics experiments.

If you want to learn more you can read a copy of the press release or visit the Waters website for more technical information about the ‘Omics Research Platform Solution.

The Olympics have come to town!

At Nonlinear Dynamics we are all very excited as the Olympics have come to town! Our headquarters are in the city of Newcastle-upon-Tyne, in the north-east of England, which has a famous football stadium called St James’ Park.  This magnificent venue has been selected to hold 9 Olympic football matches, including a men’s and women’s quarter final.

As we are part of London 2012, there are some Olympic decorations in Newcastle to welcome visitors to the matches. The iconic Tyne Bridge, which we have a great view of from our offices,  is now sporting Olympic rings which are the largest in the UK measuring 25m wide by 12m high.

Olympic Rings on Tyne Bridge

Of course most of the action will be based in and around London, with the addition of many new venues including the Olympic Stadium itself,  the Aquatics Centre and the Velopark to name just a few, but it is to the Water Polo Arena, where my colleague John Renney is heading.

John is passionate about sport, and as a former Junior GB steeplechase athlete, he knows a thing or two about competing at the very top. When it was announced that the Olympics were coming to London, John knew he wanted to be involved in some way.

Back in 2011, he completed an application form to work as a volunteer at the Olympics in London and has since been offered a role working as  Games Maker at the Water Polo Arena in the Olympic Park. A couple of trips from Newcastle to London followed, so John could collect his uniform and receive full training, and now he is all set to go.

We are all very proud to have someone from Nonlinear in the thick of it at the Olympics, and John kindly brought his uniform into the office so we could take some pictures. He was a reluctant model, but we got there in the end. Smile


John’s trip won’t all be work as he has managed to secure some tickets for the Athletics and will get to see the coveted men’s 100m final. We all hope he has a great time!

The opening ceremony  opens the games tonight. I will certainly be glued to my TV to see what surprises the organisers have in store for us.

We wish all the competitors at London 2012 the best of luck, and here’s hoping that it is a memorable Olympics.

A water-filled week at EuPA / BSPR 2012

Last week I attended 2 very watery Scottish-related events.  The first was the Wimbledon Men’s final, starring Andy Murray, which was a wet affair until the impressive centre court roof was closed.  The second was the EuPA/BSPR 2012 meeting in rain-soaked Glasgow.  Luckily I had my wellies for both!


I attended the meeting with my colleagues, Leo Pollack and Martin Wells and our booth was incredibly busy throughout the conference.

Progenesis LC-MS is used in many of the major proteomics groups in Europe.  At this meeting we were able to gather feedback and discuss future development with users from:

  • Institute of Molecular Systems Biology, ETH, Zurich
  • University of Southern Denmark
  • Universiteit Utrecht
  • EMBL, Heidelberg
  • Technische Universität München
  • Katholieke Universiteit Leuven
  • Lund University
  • Université de la Mediterranee
  • The Beatson Institute for Cancer Research
  • FingerPrints Proteomics Facility, University of Dundee
  • Institute of Integrative Biology, University of Liverpool
  • King’s College London

Here’s a recent quote from one of our core lab users:

“We have recently introduced Progenesis LC-MS in our lab and it has soon become the software of choice for the analysis of large cohorts of label-free datasets. The tool has major strengths in its intuitive GUI for data analysis and statistical interpretation. Its algorithms are very much appreciated, especially for the accuracy of alignment and peak detection. Customization of the normalization strategy and importing of identification results in standard formats make the software appealing also to the more picky scientists.”

Bas van Breukelen and Salvatore Cappadona
Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University (a.k.a as hecklab www.hecklab.com), The Netherlands

We also had plenty of interest from scientists starting label-free research.  Label-free is undoubtedly on the rise.

Are you an existing Progenesis user wanting to give us feedback? Are you new to Progenesis and wanting to know more?  Please contact us, we’ll be happy to help you.

The water-theme continued within the walls of the Concert Hall with the very well attended Waters lunchtime seminar. During the session, Robert Tonge gave a presentation titled, “Towards a common workflow for metabolite and protein profiling in unbiased discovery” which included a live demonstration of Waters’ new TransOmics™ Informatics software.

The feedback from this was hugely positive and well received by both Waters and Nonlinear Dynamics users.

Finally, there was more water at the conference dinner – tears of laughter as too many scientists attempted a Ceilidh in too small a space dodging around pillars, it was ceilidh carnage!


In all, this meeting was well organised and extremely useful for Nonlinear Dynamics – role on EuPA 2013 which is being held in St Malo, hopefully that will be more swimming than welly weather. Smile

Proof-of-principle translating discovery proteomics experiments to pre-clinical biomarker verification

A report from the Institute of Medicine has highlighted the on-going challenge of translational proteomics with this line, “transforming the great promise of these new [‘omics] technologies into clinical laboratory tests that can help patients directly has happened more slowly than anticipated.”

So, it’s good to be able to share a publication by one of our customers addressing this challenge. This paper provides a roadmap for how to go from generating a set of potential biomarkers by label-free, MS1 intensity-based, proteomics to a reliable pre-clinical toxicology screen based on SRM.

The work involved re-analysis of archived rat liver samples from the PredTox collaborative project. You can see the sample sources below and more background to the project, along with early discovery research data, is available in a previous blog post and a poster presented at ASMS 2011.

imageThe InnoMed PredTox Consortium is a partnership between pharmaceutical companies, small-medium enterprises, and academic institutions in Europe. It’s aim is to take a combined ‘omics approach to study animal models of pharmaceutical toxicity in an effort to improve pre-clinical safety evaluation.

The final publication is open access, so I don’t need to summarise the whole paper. Instead I’m going to pick out some specific aspects that may be useful to anyone considering the same approach.

The discovery phase

In re-analysing the rat liver samples the group took a number of steps to maximise quantitative and qualitative information and generate reliable results from label-free LC-MS, including:

  • Optimising run alignment by injecting a pool of all samples, which provides a reference run containing all features
  • Duty cycles of the MS instrument were optimised to maximise quality of MS1 scan data for reliable quantitation
  • Pooled samples were analysed with duty cycles optimised to generate MS/MS data for maximum peptide/protein coverage, which are merged with the existing quantitative data
  • Targeted inclusion lists were run to further increase proteome coverage by selecting MS/MS for significantly changing features not identified by pooled sample analysis
  • Filtering selected charge states and retention time sections of the LC-gradient to improve data analysis by removing less reliable features from the analysis
  • Combining data from individual peptides into a final list of quantitated and identified proteins determined as significantly changing based on fold change >1.5 and ANOVA p-value <0.05
  • Benchmarking technical variance of the analysis method using six repeat injections of a pooled sample, which showed CVs <20% for all quantified MS1 features.

These steps are supported, directly or in-directly, by Progenesis LC-MS and its approach to data analysis. To see a full set of features and how they help analyse quantitative label-free LC-MS proteomics experiments, you can download Progenesis LC-MS and try it with your own data or the tutorial data set included.

The validation phase

The list of significantly changing proteins from label-free LC-MS analysis, along with data from a previous transcriptomics study and literature searches, provided a panel of potential biomarkers for hepatoxicity. These were used to create a reliable SRM assay, helped in a large part by Skyline.

This section of the paper highlights some of the technical challenges you face moving from an untargeted, label-free proteomics approach to a targeted, multiplexed assay measuring 10’s-100’s of proteins. These include:

  • Having appropriate MS/MS data for the proteins you want to include in your panel, in this case the library of MS/MS spectra was build up using the label-free analysis approach above
  • Selecting peptides of appropriate length, amino acid composition and suitability for SRM
  • Only modest correlation between proteins showing significant changes in response to treatment by proteomics compared to transcriptomics studies

This shows why starting with an untargeted discovery approach using proteomics is necessary, since only a small percentage of potential biomarkers will be suitable for the final targeted analysis approach. In this case 717 proteins identified by label-free LC-MS, plus others included form other studies, translated into a final set of 48 proteins (<10%)  in the validated SRM approach.

Want to know more?

This publication shows what can be achieved by applying the right technologies in the right way to translate proteomics from biomarker discovery into a robust assay for pre-clinical or clinical application. It’s especially pleasing for us to see Progenesis LC-MS playing a key part. If you would like to speak to one of our product specialists about how we can help with ‘omics data analysis for your research, please contact us.

News from the ItPA 2012 Congress in Viterbo

I was lucky enough to attend the ItPA 2012 Congress in beautiful, jasmine-scented, medieval Viterbo, Italy. The meeting was held at the Tuscia Rectorate, which was very calm and cooling in the high temperatures we experienced.

We started with a very interesting opening lecture by Prof. Pierre Legrain entitled “Latest advances of the Human Proteome Project (HPP)”.   We were given an overview of how the project will be organised, with the 2 main approaches being chromosome – based and biology/disease – based.

HPP Overview

Having a background in cytogenetics, I was interested to learn that specific countries are working on specific chromosomes.  Then Prof. Legrain gave his personal view that we need to revisit the conceptual scientific thinking that preceded the recent huge advances in molecular biology.  He gave full credit to the painstakingly detailed work that is done at lab benches worldwide. He suggested that this work would benefit from being viewed alongside other disciplines, for example, the clinical picture, epi-genetics etc.  Prof. Legrain also spoke about the importance of reproducibility, an issue we take very seriously at Nonlinear Dynamics; we can uniquely prove inter-lab reproducibility and are co-founders of the Fixing Proteomics campaign.  The take-home message that I got from this refreshing lecture was that, “We need to start seeing the wood as well as looking at the trees”.  It will be very interesting to see the progress of this ambitious project in several years’ time.

The meeting got into full swing and it was lovely to meet our happy Italian customers.

Dr Brioschi has this to say about Progenesis SameSpots:

“Since we have SameSpots, our proteomics studies have really improved. It is easy to use and allows you to quickly obtain good results with a high level of confidence.”

Maura Brioschi
Monzino Cardiologic Center, Milan, Italy

Many Progenesis SameSpots users came to say hello and there were discussions about upgrades to the latest version v4.5 which includes SpotCheck.  This is our QC workflow which ensures that consistent standards are met, hence improving reproducibility.  This means that scientists can focus on running more biological replicates, producing meaningful data and having confidence in their results.

There was also a lot of interest in Progenesis LC-MS and it is clear that more and more scientists are moving to label free LC-MS.  Scientists recognise the real benefits and the posters showed it is becoming the technique of choice.  There was fresh interest in our new Progenesis CoMet metabolomics analysis technology too, so lots to follow up on.  It was a very busy meeting for Nonlinear Dynamics and a very enjoyable one.


Even my journey back to Rome was interesting; I had a long discussion with Dr Ganesh Kumar Agrawal, founder of INPPO, about the particular challenges faced by those working in plant proteomics – both biological and political.  The meeting itself was extremely well organised and I don’t think I’ve ever had an exhibition stand in such a beautiful location – a lovely cloistered quadrangle.   I just wish I could hit ‘rewind’ and do it all again. Smile

If you would like to learn more about the proven reproducible Progenesis technology, please contact us and we shall be happy to help you.