I realise it’s old news, seeing as the article has been available on the web since February, but I thought I should officially mention that our latest reserach is now in the Journal of Proteome Research, so please check it out. You can find the article here: Comparison of Novel Decoy Database Designs for Optimizing Protein Identification Searches Using ABRF sPRG2006 Standard MS/MS Data Sets

Registration for the 15th Annual Proteomics Symposium of the Australasian Proteomics Society is now open, click here for more info.  This conference is held at Mantra Erskine Beach Resort, Lorne, Victoria between 4th – 7th February, 2010, and  I will be giving a pre-conference workshop session and lecture on proteomic bioinformatics, for MRM transition design and other web-based services for proteomics.  I hope to see you all there!  I am really looking forward to experiencing the proteome bioinformatics scene in this part of the world.

No this is not the name of a new girl band…. Thank you to Kathryn Lilley for organising the quiz for the BSPR conference dinner.  One of the prizes was for the best team name, and guess what, our table won!!  Thanks to Aisling, Kasper, and the gang, and of course, Miss Cleavage herself, Jules.  Until next year…!

Another great conference, the British Society of Proteome Research meeting (Multiscale Proteomics: From Cells to Organisms), took place on 14th-16th July.  Although it is a British society, scientists from America (Mike MacCoss, Neil Kelleher, Gary Siuzdak & Brian Searle) took the majority of the spotlight this year.  The conference kicked off with a keynote lecture from Prof. Matthias Mann, whose lab is pioneering the high-throughput approach to proteomics, achieving virtually complete coverage of peptides in yeast. At the conference, we presented a poster of our…Continue Reading “BSPR Conference, Hinxton, UK”

It was great to see you all again. I presented a poster with the latest developments for MRMaid (our MRM transition design tool): MRMaid: automating the design of multiple reaction monitoring (MRM) experiments using expert knowledge and MS/MS data-mining Using new datasets, including MS/MS spectra for proteins in horse serum,  I showed that (in several cases) MRMaid could successfully pick the top transition, when only a single MS/MS dataset was available as evidence in GAPP database.  A video presentation, describing the information in the poster,…Continue Reading “ISMB / ECCB 2009, Stockholm, Sweden”

As well as Duncan’s point (see post below), Sherman, Molloy and co-workers, also in Proteomics (vol 9), believe that monitoring the transition of a single precursor to product ion is not specific enough to define a unique peptide anyway.  This is because several peptide precursors may have equivalent mass, or may appear to have, due to inadequate mass resolution of the MS/MS instrument. Moreover, particularly in complex samples, MS/MS level product ions derived from different precursors may fall within the same m/z window producing overlapping…Continue Reading “Can you be more specific, please?!”

I hate the word ‘should’ – it always implies that there is something you have to do but you’d rather put it off.  Well, I recently came across a viewpoint article that made me think we really ‘should’ be doing more to make SRM more reliable.  This commentary, in Proteomics (vol 9: 1124-1127), suggests that SRM is not quite fool-proof…shame. According to Duncan et al we should all realise that quantification of a target protein cannot be achieved by targeting a single peptide however straight…Continue Reading “Should we be more selective?”

According to the International Union of Pure and Applied Chemistry (IUPAC), the body that makes recommendations regarding nomenclature  used in mass spectrometry, ‘Multiple Reaction Monitoring’ (MRM) is an “incorrect term” .  They suggest instead that ‘selected reaction monitoring’ (SRM) is more appropriate. This subject came up at the ASMS conference in 2008 (Denver, CO), but I didn’t attend and can’t view the abstract.  However, Murray et al implied the term Multiple Reaction Monitoring “will soon be deprecated by IUPAC” – quoted from Sherman et al…Continue Reading “MRM is not allowed”

Do you need a little help finding out which proteomics data repository is for you?  Would you like to know what each one has to offer?  Would you like some help navigating to the right resource for your needs? Lucky for you, Conrad Bessant, Luca Bianco and myself have put together a new review article, which gives details of virtually all the useful public resources for proteomics data on the internet.  The article is now available at Proteomics Journal’s website (click here). This article is…Continue Reading “Do you find proteomics databases confusing?”