Proteomics sample submission process
Prior to submitting samples for a new project, please arrange for a free consultation with any member of the WEHI Proteomics Lab.
Please note: Users are asked to perform their own in-gel digests before submitting samples.
We provide free aliquots of the necessary reagents (including trypsin and a BSA control) and a dedicated ‘skin-free’ workstation to help reduce sample contamination. All you need to do is follow the recommended In-gel Digestion Protocol (pdf). Any of our staff members will happily guide you through the entire process here at the facility.
When you are ready to submit your samples, download our Sample Analysis Request Form (doc), complete the submission details and hand in the form together with your sample at the WEHI Proteomics Lab (directly or by mail). It will take us a few days to analyse your samples, and we will report high confidence protein identifications to you in the form of a QC Scaffold results file (typically within one week).
To view your results file you will need to download the latest version of Free Scaffold Viewer from Proteome Software* on your computer. The Free Scaffold Viewer lets you:
- display a complete, side-by-side view of the proteins identified in all your samples
- balance the number of proteins and calculate the experiment-wide false discovery rate
- filter protein identifications by protein or peptide probability scores
- validate protein and PTM identifications by drilling down to the sequence coverage
- inspect peptide matches and evidence spectra supporting the identification
- organise your replicate samples into categories reflecting your experimental conditions
- compare the number of proteins, peptides or spectra in different samples or categories
- organise and share results and key MS/MS data with colleagues
- capture all the information journals require in a paper’s methods section
- prepare for publication by automatically formatting data for submission
Please contact us (Tom Nebl/Lisa Connolly) if you have any questions regarding the use of Scaffold Viewer.
*We are not responsible for third party website content/downloads.