Writing a paper
If your research does not generate papers, it might just as well not have been done. ‘Interesting and unpublished’ is equivalent to ‘non-existent’.
George M. Whitesides
An excellent and concise guide to writing a paper by the Harvard University professor George Whitesides can be found at this DOI: 10.1002/adma.200400767
A few additional tips for our Facility users
Even if proteomics is but a small part of your project, begin by downloading instructions for authors from a major proteomics journal. These instructions are written by experts and essentially outline the experiment for you. Before you start growing cells or planting trees, read the manuscript submission checklist to find out how to account for biological and technical variability and how many and what type of replicates will conform to the statistical validation methods.
If you are going to use published work as a model for your experimental design, select only the highest-quality publications from high-impact-factor journals.
Find out whether you can access the proteome (genome) of the organism you intend to study. MS-based protein identification relies on the availability of the protein sequence databases.
Make a list of all data file formats that must be submitted with the manuscript so that these files could be generated by the Facility as part of your data processing workflow.
Each LC-MS-MS data file takes approximately 1 GB of disk space, therefore plan on copying and backing up your data shortly after it is generated. We clear out old data every 6-8 months or whenever the disk is full.
Write a paragraph describing the LC-MS/MS or MS method used in acquisition of your data. I usually have routine methods ready for you to copy. Even if you are not planning on including all experiments in a publication or thesis, this information could be useful for your group or to you on your next endeavor.
Unless you are incredibly lucky or exceptionally clever, things will go wrong and the plan will change, perhaps even more than once. Keep a careful record of all protocol changes, including MS methods, illustrated with data.
Generate figures for group meetings using the same format and quality as required by the journal and/or for your thesis. Record file names of the relevant mass spectra if you think they might be needed.
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