Presenter:  Robert Hammond

Discussion summary:

We discussed two exciting papers published in the May 28 issue of Nature, “A draft map of the human proteome” and “Mass spectrometry-based draft of the human proteome” (Kim et al., Nature 509, 575-581, 2014 & Wilhelm et al., Nature 509, 582-587, 2014).  Pandey and colleagues provided evidence for the expression of 17,294 protein-coding genes, and showed tissue-specific expression for some.  They identified proteins expressed from sequences previously thought to be pseudogenes and noncoding RNAs.  The second paper by Kuster and colleagues shows the expression of 18,097 human genes and highlights biomarkers in cancer cell lines, and relationships between mRNA and protein expression levels in cells.

Points that were discussed:

• What comes before the MS detector?  - SDS-PAGE gel, in-gel trypsin digest
• What is MRM vs SRM method? Is it high throughput?
  

 SRM = selected reaction monitoring; MRM= multiple reaction monitoring.  Both terms are used for experiments to monitor the                 abundance of multiple peptide species in proteomics.  Reference:  Lange et al. Mol. Syst. Biol. 2008, 4, 222.

• Clarify not seeing proteins before? – A significant minority of these genes were known previously, but protein expression had not been observed; the authors observed protein expression from these genes for the first time.  This confirms these are true genes, rather than pseudogenes.
• How does one determine which cell type, tissue type to use?
  
• It is intriguing to find proteins translated from noncoding RNAs and pseudogenes.

Conclusions –  These are landmark studies showing a draft of the human proteome, 13 years after the draft human genome was published.

The Trick is Mass Spec #fivewordpapertitle