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MRMaid paper in MCP

Posted on Monday 17 November 2008

On 15th November 2008, the MRMaid paper was published online in the ‘papers in press’ section of MCP Journal’s website see:

http://www.mcponline.org/papbyrecent.shtml.

It is free to download now, and is scheduled to appear in the February 2009 edition of MCP. A big thank you goes to my supervisor, Conrad Bessant, and the paper co-authors Luca Bianco, Vanessa Ottone, Kathryn Lilley, Nick Bond, Rich Kay and Chris Barton. Good job guys, thank you so much!

We hope you enjoy using our MRMaid, to see another famous Mermaid click here

Jennifer @ 8:41 pm Edit This

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MRMaid goes hollywood!

Posted on Wednesday 12 November 2008

MRMaid videos are now online, check out the first two videos at www.mrmaid.info (in the Help Area), with two more to follow very soon.

Jennifer @ 7:11 pm Edit This

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MRMaid for Quantitative Proteomics

Posted on Thursday 6 November 2008

MRMaid is a new tool that I have developed as part of my EngD project. It is a web-based program that can be used to design transitions for quantitative proteomics experiments, and it can be found at www.mrmaid.info. These type of quantitative experiments are referred to as single and multiple reaction monitoring (S/MRM) experiments.

For fast and reliable MRM transition design

For fast and reliable MRM transition design

MRMaid makes reliable transition selection fast and easy by automating prediction of candidates. A ‘transition’ is a pair of m/z values: 1) a peptide ion m/z and 2) a corresponding product ion m/z. This pair uniquely maps to a protein sequence, therefore, when the precursor and product m/z signals are observed in MS and MS/MS, respectively, you can assume that your protein of interest is present. To monitor a protein, however, you must know in advance which transitions perform well for your protein. Only when you have this information can a quantitative monitoring experiment take place. To perform quantitation using this targeted approach, you can spike a known quantity of a heavy isotope-labeled version of the peptide into your sample. This surrogate peptide can be a synthetic peptide or one expressed using a bespoke gene construct. In any case, it allows you to determine the quantity of your protein by reference to the heavy ion(s). In MRM experiments, multiple surrogates may be introduced to monitor multiple targets simultaneously.

Determining which transitions are suitable for a protein of interest can be very challenging – since each protein has many possible peptides, and each peptide many possible fragment ions. This is where MRMaid comes in handy. MRMaid speeds up the process of transition selection by predicting a shortlist of candidates by mining a database of protein identifications and spectra (GAPP database www.gapp.info) – and filtering the results by expert knowledge from MRM practitioners. Check out this brand new program, and watch out for the publication in MCP Journal, coming soon!

Jennifer @ 1:14 pm Edit This

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GAPP dev.

Posted on Wednesday 12 March 2008

Want to identify splice variants, PTMs and novel sequence in you proteomic MS experiments? Check out www.gapp.info – the new release is coming soon… so watch this space! Brand new interfaces for differential views, protein sequence graphics and spectra are also available now – so check it out…

Jennifer @ 1:35 pm Edit This

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GAPP Master

Posted on Friday 31 August 2007

Well, what’s going on with the gapp.info team at the moment?- I hear you ask. Well, glad you asked! We’re currently optimising the GAPP pipeline, so we can all be even more confident of integrity of the protein identifications it produces.

The GAPP system runs on a computational cluster of 17 computers sitting in Cranfield University, so we can perform the optimisation pretty quickly – each run usually taking only a few minutes. Jobs are submitted (in the website’s case automatically) to the master node, the ‘GAPP Master’, and then the job is split 16 ways and processed in parallel.

The GAPP Cluster

The GAPP Cluster

Hope to see you register with GAPP soon!

J

Jennifer @ 9:07 am Edit This

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Summer time

Posted on Monday 16 July 2007

I’m off to the ECCB/ISMB conference in Vienna this week – so hope to see you there!

Jennifer @ 2:43 pm Edit This

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Welcome!

Posted on Wednesday 31 January 2007

Congratulations, you’ve arrived at my webpage!

Here you’ll find details of my career so far and projects I’m working on as part of the bioinformatics research group at Cranfield University, Silsoe.

Happy surfing!

J

Jennifer @ 11:12 am Edit This

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