Proteomics Methods Forum
Fifth PMF Meeting: West Park Conference Centre, Dundee, 18th - 19th June 2008
Contact
Participants
Sponsors
Aim
Programme
Location
Parking
Registration
Accommodation
Word of thanks
Contact:
| Mr Dougie Lamont | Mr Kenny Beattie |
| (General and programme) | (Registration and accommodation) |
| Fingerprints Proteomics facility | Fingerprints Proteomics facility |
| College of Life Science | College of Life Science |
| MSI/WTB/JBC Complex | MSI/WTB/JBC Complex |
| University of Dundee | University of Dundee |
| Dow Street | Dow Street |
| Dundee DD1 5EH | Dundee DD1 5EH |
| Tel: 01382-38-8275/4797 | Tel: 01382-38-8275/4797 |
| Fax: 01382-385764 | Fax: 01382-385764 |
| E-mail: d.j.lamont@dundee.ac.uk | E-mail: k.a.beattie@dundee.ac.uk |
| Mrs Isabelle Nett | Dr Sarah Goodbrand |
| (Registration and Accommodation) | (Vendors) |
| Division of BCDD | Fingerprints Proteomics facility |
| College of Life Science | College of Life Science |
| MSI/WTB/JBC Complex | MSI/WTB/JBC Complex |
| University of Dundee | University of Dundee |
| Dow Street | Dow Street |
| Dundee DD1 5EH | Dundee DD1 5EH |
| Tel: 01382-38-5852 | Tel: 01382-38-8275/4797 |
| Fax: 01382-385764 | Fax: 01382-385764 |
| E-mail: i.r.e.nett@dundee.ac.uk | E-mail: sarahgoodbrand@nhs.net |
Participating Universities and Research Institutes:
Aberdeen University, Dundee University, Edinburgh University, Glasgow University, St Andrews University and a few of the main Institutes including the Beatson in Glasgow and the Moredun in Edinburgh, Oxford University, Cambridge University, York University, Cardiff University, Surrey University, Cranfield University, Liverpool University, Leicester University, Sheffield University, Manchester University (Including Paterson Institute), Sunderland University, Newcastle University, Leeds University, the John Innes Centre, Northumbria University, Sussex University and Cancer Research UK.
Participating Sponsors
Agilent, Applied Biosystems, Dionex, Perkin Elmer, CEM, Bruker Daltonics, Presearch, Matrix Science, Texol, ThermoFisher Scientific, Waters, Sigma, Proxeon, Crawford scientific, GE Healthcare, Merck, Varian, Geneva Bioinformatics, Genomic Solutions, Thames Restek, Genologics, VWR, Fermentas Life Sciences and Peak Scientific.
Aim:
To provide a national, informal forum for groups involved in protein mass spectrometry and informatics in the UK. Its focus is upon the practical methods of analysis and sharing of information between peers. "Building a community".
Programme
| Day 1 | |
| 12:00 - 12:55 | Registration, Buffet Lunch and Exhibitors |
| 12:55 - 13:00 | Welcoming Remarks |
| Session 1: Bioinformatics I (Sponsored by Genologics) | |
| 13:00 - 13:25 | Automated phosphopeptide annotation of large data sets. |
| Isabelle Nett (University of Dundee) | |
| 13:25 - 13:50 | OpenMS - An open-source framework for mass spectrometry and TOPP - The OpenMS Proteomics Pipeline. |
| Eva Lange (Beatson Institute for Cancer Research, Glasgow) | |
| 13:50 - 14:15 | Bridging the GAPP: using GAPP's new database mining tools for differential expression analysis and MRM transition design. |
| Jennifer Mead (Cranfield University) | |
| 14:15 - 14:45 | Tea/Coffee & Biscuits and Exhibitors |
| Session 2: Techniques (Sponsored by Crawford Scientific) | |
| 14:45 - 15:10 | Characterisation of protein artifacts generated in vitro during Coomassie gel staining. |
| David Sumpton (Beatson Institute for Cancer Research, Glasgow) | |
| 15:10 - 15:35 | HELPR: An alternative string to the phosphopeptide detection bow? |
| Duncan Smith (Paterson Institute for Cancer Research, University of Manchester) | |
| 15:35 - 16:00 | Solutions for membrane protein analysis. |
| Iain Fearnley (University of Cambridge) | |
| 16:00 - 16:25 | Nano-ESI and ion trap-ETD/PTR-MS/MS for the analysis of post-translational modifications. |
| Frank Sobott (University of Oxford) | |
| 16:25 - 16:50 | Tea/Coffee & Biscuits and Exhibitors |
| Session 3: Quantitative Proteomics (Sponsored By Applied Biosystems) | |
| 16:50 - 17:15 | 14N/15N Metabolic labelling: Understanding error in quantitative proteomics. |
| Matthew Russell (University of Cambridge) | |
| 17:15 - 17:40 | Quantifying SILAC datasets using both MSQuant and MaxQuant. |
| Laura Trinkle-Mulcahy (University of Dundee) | |
| 17:40 - 18:05 | A look at global quantitative proteomic analyses using iTRAQ and label-free quantifications. |
| Saw-Yen OW (University of Sheffield) | |
| 18:05 - 18:30 | Multidimensional liquid phase protein separations in conjunction with stable isotope labelling for quantitative proteomics. |
| Mark Dickman (University of Sheffield) | |
| 18:30 - 19:30 | Cheese and Wine Reception with Exhibitors (Sponsored by ThermoFisher Scientific) |
| 19:30 - 21:30 | Conference Dinner |
| 21:30 - 00:45 | Bar |
| Programme Day 2 | |
| 8:30 - 9:00 | Tea/Coffee & Biscuits with Exhibitors |
| Session 4: Bioinformatics II | |
| 9:00 - 9:20 | Validation approaches in protein identification: use cases with Phenyx. |
| Pierre-Alain Binz (Geneva Bioinformatics) | |
| 9:20 - 9:40 | A rigorous strategy for label free quantification and identification of proteins. |
| Mark McDowall (Waters Corporation) | |
| 9:40 - 10:00 | Software Solutions for Biomarker Discovery, Verification and Validation. |
| Cathy Lane (Applied Biosystems) | |
| 10:00 - 10:20 | Novel workflow concept for biomarker discovery using label free quantitation. |
| Laura Main (Bruker Daltonics) | |
| 10:20 - 10:40 | Proteome Discoverer: A Proteomics Bioinformatics Platform. |
| Martin Hornshaw (Thermo Fisher Scientific) | |
| 10:40 - 11:10 | Tea/Coffee & Biscuits with Exhibitors |
| Session 5: Post-Translational Modifications (Sponsored by Dionex) | |
| 11:10 - 11:35 | N-terminal Protein Acetylation+. |
| Willy Bienvenut (Beatson Institute for Cancer Research, Glasgow) | |
| 11:35 - 12:00 | Proteomic scale analyses of GPI membrane anchors. |
| Angela Mehlert (University of Dundee) | |
| 12:00 - 12:25 | A strategy for comprehensive phosphorylation site analysis. |
| Stacey Warwood (University of Manchester) | |
| 12:25 - 12:50 | Ubiquitination Site and Chain Architecture Analysis by Mass Spectrometry. |
| Emma Carrick (University of Dundee) | |
| 12:50 - 13:15 | Novel methods of phosphopeptide enrichment for phosphoproteome studies. |
| Franck Vandermoere (University of Dundee) | |
| 13:15 - 13:30 | Closing Remarks and Future Meetings |
Location:
The forum will be held in the West Park Conference Centre in Dundee (http://www.westpark.co.uk/) where accommodation will also be available (please see Registration/Accommodation forms). The main meeting will be held in the Sidlaw Suite with the Conference dinner in the Henderson Restaurant.
A map and directions to the West Park Conference Centre can be found here: (http://www.westpark.co.uk/page.cfm?menu_object_ID=1&page_ID=34)
Car Parking:
Car parking will be available on-site (105 spaces) and off-site (100 spaces).
Registration:
As in previous meetings, registration is free, since we have secured commercial sponsorship. However, to allow us to plan, please download and save the Registration form and email a completed version to PMF2008@dundee.ac.uk by the 12th of May 2008.
Accommodation:
West Park Conference Centre, 319 Perth Rd, Dundee, DD2 1NN - Tel: 01382 647171:
Details of the accommodation available at the West Park are provided on the Accommodation Booking Form. Please download, save the form and either email a completed version with payment (e.g. credit card) to PMF2008@dundee.ac.uk or alternatively post the completed form with payment (e.g. cheque) to:
Fingerprints Proteomics Facility,
College of Life Sciences,
MSI/WTB/JBC Complex,
University of Dundee,
Dow Street,
Dundee, DD1 5EH.
Completed accommodation forms should be with us by the 12th of May 2008. Any questions on accommodation should be referred to either Mr Kenny Beattie ( k.a.beattie@dundee.ac.uk ) or Mrs Isabelle Nett (i.r.nett@dundee.ac.uk).
Hotels:
Local Hotels/B&Bs are available in Dundee but all require car transport to the West Park Conference Centre.
| Hotel | Website | Telephone No. | Approx. Cost/Night - from |
| Swallow Hotel | www.swallow-hotels.com | 01382-631200 | £60.00 (inc breakfast) |
| Shaftesbury Hotel | www.shaftesbury-hotel.co.uk | 01382-669216 | £55.00 (inc breakfast) |
| Grampian Hotel | www.grampianhotel.com | 01382-667785 | £45.00 (inc breakfast |
| Invercarse Hotel | www.bw-invercarsehotel.co.uk | 01382-669231 | £70.00 |
| Travel Lodge (North) | www.premierinn.com | 0870 990 6420 | £55.00 |
| Travel Lodge (West) | www.premierinn.com | 08701 977 081 | £55.00 |
| Travel Lodge (Centre) | www.premierinn.com | 08701 977 079 | £68.00 |
Please book hotels directly
Word of thanks:
We would like to take this opportunity on behalf of the PMF to thank Adam Huffman at the University of Manchester for maintaining and updating the PMF website which provides a useful point of contact for the forum.