Good Morning and welcome to
Core Facility — Proteomic Mass Spectrometry
Nature Milestones: This is a series of articles which follows the historical progress and development of Biological Mass Spectrometry over the last century through a series of groundbreaking articles covering milestone events and discoveries in Nature Journals.
A researcher’s guide to mass spectrometry-based proteomics: This article gives in-depth information regarding the processes and functioning of three major types of mass spectrometer – the LIT, the Triple-Quad, and the Orbitrap. Included are discussions of basic MS ion physics principles including the variable electrical fields, ion optics and mass filters, amongst others.
Quantitative mass spectrometry in proteomics (a review: 2007-2012): This is an excellent review into the progress mass spectrometry has made into investigating biological processes in complex cells. Included topics are chemical labelling of proteins and peptides, label-free and absolute quantification, and analyses of quantitative MS data
A pair of videos from Matthew Padula from the Technical University Sydney which nicely describes the fundamental principles in mass spectrometry, such as mass over charge and peptide fragmentation, and how they are applied to proteomics.
Q. How soon can I expect my results?
A. This is a difficult question to answer fully, however we strive to return data to users as soon as we possibly can – ‘in a timely manner’. To explain – there is a significant difference in processing time between receiving 2-3 gel bands (something we would expect to process in 24 hours) through to a quantitative analysis of 6 cell lysates (which may need fractionation and/or substantial (3-5 hour each) LC-MS runs, followed by database searches – a process which may take over a week.) However, barring unexpected instrument downtime, we plan to give all users an expected data delivery time at the time of sample submission.
Q. How do I get my data?
A. In order to accommodate stringent data safety procedures, we have developed a protocol whereby we are cannibalising the secure data share feature of the open source Nextcloud server program. What this means is that the core facility has a firewalled, single-user-only instance of Nextcloud installed in ITZ, where results files will be placed. A time-limited https link to the file is then generated with password-protection, and emailed to the user. The user then clicks on the link opening an https tunnel to the server, whereby the files can be downloaded. Passwords will be previously arranged with the user via a separate email.
Q. What happens to my samples after MS analysis?
A. As part of a material transfer agreement (MTA), and legal considerations, the samples remain the property of the user at all times. Hence it is the responsibility of the user to reclaim samples. However, the user must be aware that samples will degrade over time, even when stored at -80. As such we will store samples for a maximum of 6 months, unless instructed otherwise. If a user decides that the sample can be disposed of inside this period, then this must be submitted in writing (email).