Healing the Achilles Heel of Proteomics
4 February 2010
Our own Fixing Proteomics Initiative, co-ordinated by Bio-Rad, Nonlinear Dynamics and Novartis Institutes for Biomedical, has been included in this article published on Monday 1st February in Genetic Engineering News.
The article is a great summary of the challnges facing proteomics and success stories from some of groups and companies trying to tackle them, all of whom are covered on this website.
Hope this encourages you to see what's possible and if you have a success story of your own, get in touch with details and we'll happily help you promote it to the Proteomics community, just email editor@fixingproteomics.org
Executive summary of the ESF QC in Proteomics meeting
23 December 2009
This week I saw a draft of the scientific report from the ESF QC in Proteomics meeting. It's a great reminder of the good things we achieved and that we'll capitalise on in 2010. I'll link to the final report when it's published in the new year but I can provide an executive summary early here.
Attendees of the ESF QC In Proteomics meeting, 24-27 Nov 2009, enjoying the last rays of the sun after a day of lively discussion
The workshop was well-timed, and managed to assemble a critical mass around the topic, with actions that will reach out into the community. Firstly, a whitepaper will be written to summarize the discussions that took place and provide a vision for the future with regards to quality control. There's also strong progress towards special issues on QC in Proteomics with two prominent journals. A steering committee has been set up with very broad and representative membership including liaisons to various existing initiatives, such as Fixing Proteomics, active around quality control in proteomics. Finally, a follow-up workshop is planned for next year.
With these various initiatives in place, or well advanced, the outcome of the meeting will be highly visible in the field. From the feedback of the participants, it's clear there is a strong demand for a more quality control in the field of proteomics.
This is the last post for 2009 and this decade, so best wishes to everyone and looking forward to 2010 when Fixing Proteomics can raise its profile even higher...
ESF QC in Proteomics meeting
27 November 2009
The ESF QC in Proteomics meeting here in Cambridge (organised by Prof. Lennart Martens) has officially finished today and I'm officially exhausted BUT it's been an excellent three days listening to what people are doing to QC their proteomics research now and how we can share lessons learnt and practical tools from these efforts.
There were over 40 delegates representing industry, academia, vendors, journals, funding bodies and people involved in initiatives already trying to "fix proteomics".
It was a great mix of people, who were all action orientated but with different opinions and perspectives. Best of all it was a friendly, supportive and collaborative environment. Lennart did a great job of bringing us together and getting some strong actions out of this mix.
The Fixing Proteomics Campaign got good air time and is a part of what's coming out of this gathering. I can't say be specific for now but watch this space for news when I can reveal it.
Fixing Proteomics was also representing itself over dinner with this photo!
I am off to go though my pages of notes and ideas from this meeting and share the interesting bits of scrawl that I can via the blog...
Happy 2nd Birthday to us
16 November 2009
Our website was made live two years ago, using quirky images of a cow, a child, a rabbit and a kettle to create interest and get the word spread about Fixing Proteomics and try to restore faith in a field in the doldrums.
Two years later and we've had over 7,000 new visitors and over 3,000 people who return to visit to see whats new. We've also been providing practical advice and evidence to show proteomics can deliver on its potential.
So a big THANK YOU to the Supporters and Founders, who contribute and actively support Fixing Proteomics, helping to make this community grow.
New papers and articles of interest
13 November 2009
There's been quite a few papers and articles added to this site demonstrating the need for Fixing Proteomics efforts and showing latest studies aimed at overcoming the issues facing proteomics.
For example the HUPO test sample study revealed common problems in MS-based proteomics and a commentary by Matthias Mann in the five year anniversary special edition of Nature Methods that starts with "The potential of mass spectrometry-based proteomics to advance biology is nearly unlimited, but so is its potential for generating bad data..."
On a positive note news from the latest on improving measurements in clinical proteomics from the NCI-CPTAC network. There was a paper published in June on how "existing MS technologies have been used to a multilaboratory study to assess reproducibility, recovery, linear dynamic range and limits of detection and quantification of multiplexed, MRM-based assays" (linked here). Another paper from this network, published in Mol Cell Proteomics last month, has practical advice for benchmarking LC-MS platform performance.
We're back and ready for more!
12 November 2009
Okay first an apology for lack of news and updates. I hope you're still with us because we've been doing a lot of behind the scenes to put Fixing Proteomics and the website in a position to do more. So this is the first blog of what we hope will be a more active period for Fixing Proteomics.
To kick things off and show we haven't just been taking an extended vaction there are now two Editorials from people who are active supporters and you can discuss them in our new forum due for official release in Dec - watch for the PR!)
One of the Editorial writers, Lennart Martens, is hosting a meeting called "QC in Proteomics" this month. Unfortunately registration closed last month but Fixing Proteomics will be there and giving updates from the ground.
We'll be there adding our stock of ideas to a mix of ingredients that includes a cross spectrum of people from academic and industrial organisations, different perspectives from various positions and many insights from current and past experiences. The raw ingredients will be simmered together in what Lennart called a "pressure cooker" (a hotel in Cambridge) for 3 days. We hope the final result will be a hearty stew that we can all enjoy and benefit from...
Editorial: Sample preparation - a necessary evil or the key to proteomics?
30 April 2009
Over the years, the main focus of proteomics has been on technological aspects such as capacity and dynamic range of 2D gels, masspectrometry resolution and sensitivity. Enormous amounts of money and effort have been spent on this work while the softer side of proteomics; study design, sample preparation and reproducibility have been left out in the cold. The old saying "garbage in, garbage out" holds as true for proteomics as other parts of life, no matter how many millions of Euros you spend on for instance mass spectrometers. In order to fix proteomics and release its full inherent potential these softer aspects must be allowed a place on centre stage.
Continue reading...
Maximum number of labs needed for the Phase II study has been reached
27 April 2009
We've had a great response to recruitment for the 2D-gel Reproducibility Study Phase II and have enough labs needed to produce meaningful conclusions and get the results presented in time for Sept 2009 so the study is now closed for new entries. Thanks to everyone taking part and we look forward to sharing the results with you soon.
The protocols are still available here for you to share the experimental details and we'll update all Fixing Proteomics supporters when the gold standard samples and images are available to try in your own lab.
Register for updates here
2D-Gel Reproducibility Study Phase II reported in Biotechniques
24 April 2009
News of the 2D gel reproducibility Phase II has been reported in Biotechniques, The International Journal of Life Science Methods and the story will be distributed in their weekly newsletter.
Read the story
ProteoMonitor feature about 2D-Gel Reproducibility Study Phase II
17 April 2009
ProtoeoMonitor published a favorable article covering Phase II of the 2D Gel Reproducibility Study. It gives a thorough background knowledge on the initiative and includes interviews with Hans Voshol (Novartis Institutes for BioMedical Research) who is Lead Scientist on the study as well as the two other organisers, Kumar Bala (Bio-Rad Laboratories) and Will Dracup (Nonlinear Dynamics).
Read the article
2D-Gel Reproducibility Study Phase II Update
3 March 2009
A total of 15 labs from seven different countries have now volunteered to participate in Phase II of the Reproducibility Study. Most of those labs have now run their 2D gel experiments, on their own platforms, using a common reference HeLa cell sample. Their data have been gathered and are being analysed.
The results will be presented at the Hupo Annual World Congress this September in Toronto, and will be submitted for publication thereafter.
Read the official press release
ProteoMonitor feature about Fixing Proteomics
15 October 2008
Following on from their article last year, ProteoMonitor have published a new article looking at the Fixing Proteomics Campaign
The campaign, Fixing Proteomics, debuted a year ago by a group of researchers and industry executives to recharge a field that had begun to buckle under the weight of what some consider unrealistic expectations and underwhelming results. One of its credos: If a lab's results cannot be reproduced "then they should not be published." More...
When the first article was published, the website had only been live for a month. Now, less than a year later, over 3,000 people have been exposed to the Fixing Proteomics Campaign messages. However, depending on which reports you believe as to how many proteomics researchers there are in labs around the world, this could translate to only a small amount of global audience.
The awareness is starting to build at the right time. People are talking about it on web forums and conversations at conferences show the message is reaching small labs and big names in proteomics. The need for reproducibility of proteomics experiments was a topic spoken about at HUPO 2008 directly and indirectly by the researchers and the people who fund the research. So Fixing Proteomics is helping to change attitudes and activity across the entire proteomics community, and is in a perfect position to carry on doing this.
Initial data from the HUPO Reproducibility Study
10 September 2008
Initial data from the HUPO Reproducibility Study — showing 2D PAGE expression analysis is reproducible across-labs and within-lab — was presented during the HUPO 2008 7th World Congress and as a poster at the 8th Siena meeting. The main sources of variation in the study were highlighted as user manipulation and interpretation of images, which could be eliminated using a standard protocol to make experimental procedures extremely robust.
Full details and results are being submitted for publication and will be available soon.
Proteomics Validation Workshop at HUPO 2008
14 August 2008
If you're going to the HUPO 2008 meeting in Amsterdam next week there's a workshop on Proteomics Validation on the Tuesday evening (19th August) you might be interested in.
Hans Voshol from Novartis Institutes for Biomedical Research is going to present results from the HUPO Reproducibility Study proving cross-lab reproducibility is possible for proteomics using 2D gels. It's a late start on the Tuesday night, but this is a chance to see some of the data for the first time and find out what's happening as a result. Researchers from the five labs around the world who took part in the study will be there so it's a good opportunity to talk with the people involved.
It's the Workshop on Proteomics Validation. "What Does Proteomics Validation Mean to the Users, Regulators and Public Health", Room: L, Tuesday 19th August, 8pm-10:30pm, chair: Sudhir Srivastava.
Growing support for Fixing Proteomics
22 July 2008
Support for Fixing Proteomics has been growing, we've had a huge increase in people visiting the website over the last few months. Positive feedback from visitors has been showing the value of the practical information provided as well as supporting the need for Fixing Proteomics. The protocols and 4-steps to Fixing Proteomics are proving particularly popular.
You can read the full press release for more information.
Mass Spec protocol
9 July 2008
A new Mass Spec protocol has been added to the practical advice section. This protocol is applicable to any protein complex that can be isolated to sufficient purity and quantity, its components separated by gel electrophoresis and sequence databases for the source organism are available. Using this protocol, repeated LC-MS/MS analysis of an SDS-PAGE gel band identifies 90% of proteins in all three replicate and 94% in two out of three replicate LCMS/MS experiments.
FixingProteomics on Facebook
3 July 2008
If you want to join in discussions around fixing proteomics, and talk to others facing similar problems, you can join our FixingProteomics group on Facebook
Nature editorial says reproducibility is the key issue for Proteomics
10 June 2008
In a recent editorial in Nature they point out some of the reproducibility problems Proteomics has suffered from:
...many studies involving mass-spectrometry profiling have proved difficult to reproduce. And the field has so far largely failed to deliver the disease-tracking biomarkers on which these early efforts were sold. There are few examples of clear, clinically proven benefits.
They also note that the work being done for the HUPO Reproducibility Study is a big step to improving things:
The Human Proteome Organisation (HUPO) has taken some praiseworthy steps towards resolving these issues with, for example, a project to show that different labs can now produce identical results from the same sample. With the rapid evolution of proteomic techniques, the field's reputation and utility is likely to pick up. But HUPO - and the proteomics community - still has a lot to prove and a successful Human Proteome Project is its chance to prove it.
HeLa Cell Standard Study
4 June 2008
A new study is being run with the goal of testing a HeLa cell protein standard that Novartis and CILBiotech have been developing. This new study builds on the success of the HUPO Reproducibility Study, the results of which will be published shortly. The initial study proved conclusively that quantitative proteomics can be reproduced across different labs.
If this new study is successful, the intent is this standard can be used by any lab to check the reproducibility of their set-up before working with their own samples. The Fixing Proteomics Campaign shows why this is important but the fact that major life science companies are willing to promote the same standard shows how important they also believe it is.
If you would like to take part is this study, click here to find out how.
Practical Advice: Protocols for across-lab reproducibility
11 April 2008
The sample preparation and general 2D running protocol used in the HUPO Reproducibility Study, written by Dr Hans Voshol and Dr Sjouke Hoving, are now available here.
Bad science: When the facts get in the way of a story
29 March 2008
An award winning article by Ben Goldacre in The Guardian from 2006 covering some of the statistical issues we all need to be aware of.
Practical Advice: Designing quantitative proteomics experiments
28 March 2008
Dr. Natasha Karp at the Cambridge Centre for Proteomics talks about what to consider when designing quantitative proteomics experiments.
Click here for the presentation
Fixing Proteomics Campaign gets tried on for size at ABRF 2008 in Salt Lake City, USA
9 February 2008
Fixing Proteomics Campaign presented to the HUPO Initiative Committee
8 January 2008
Including a presentation of the 4-steps to Fixing Proteomics, which lie at the core of the Fixing Proteomics Campaign.
Phase 2 of the Fixing Proteomics Campaign website is launched
14 December 2007
The Campaign is on the road again at the Swiss Proteomics Society meeting in Lausanne, Switzerland
3 December 2007
HUPO's IAB Finds 2D Gel Experiments are Reproducible
15 November 2007
"In preliminary results from its first study aimed at addressing a longstanding problem associated with 2D gels, the Industry Advisory Board of the Human Proteome Organization has determined that experiments using the technology can be reproduced."
more...
The Campaign is unveiled at the HUPO 6th Annual World Congress in Seoul Korea
6 October 2007
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