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Proteomics Tools and Databases

• APEX Protocol - Perl scripts for APEX calculations
• APEX Quantitative Proteomics Tool - developed by John Braisted and colleagues at the J. Craig Venter Insitute, Rockville, MD.
• Mass Spectrometry Data Repository - Proteomics RAW data
• MSpresso - Supplementary information
• PeptideProphet, ProteinProphet - as part of the Transproteomic Pipeline software for mass spectrometry data analysis
• Proteogest - in silico protein digest and description of biophysical peptide properties
• Peptide Detectability Predictor - for LC/MS Ion Traps
• Publication by Mallick et al. on sequence features determining peptide MS detectability
• AAindex - database of amino acid properties

Collaborators (former and current)

• Dr. Dan Finley (Harvard, USA)
• Dr. Hyungwon Choi (Singapore National University, Singapore)
• Dr. Joel McManus (Carnegie Mellon University, Pittsburgh, USA)
• Dr. Markus Landthaler (Max-Delbrueck-Center Berlin, Germany)
• Dr. Edward M. Marcotte (University of Texas at Austin, USA)
• Dr. Luiz O. Penalva (University of Texas at San Antonio, USA)
• Dr. George Georgiou (University of Texas at Austin, USA)
• Dr. William Press (University of Texas at Austin, USA)
• Dr. Dan Miranker (University of Texas at Austin, USA)
• Dr. Alexander Brodzky (Brown University, USA)
• Dr. John Braisted, Dr. Srilatha Kuntumalla (JC Venter Institute, USA)

PhD and Postdoc scholarship opportunities

• Boehringer Ingelheim Foundation (not only for Germans)
• DAAD (for Germans to go abroad, for others to go to Germany)
• DFG (for Germans to go abroad, for others to go to Germany)
• in the US - Life Science Research Foundation
• in Europe - EMBO
• worldwide - Human Frontier Science Program
• Surviving grad school (useful not just for PhD students)

Faculty job search for postdocs (random advice)

When starting the job search / while applying/interviewing:

• Read the respective sections in the HHMI book on "Making the right moves"
• Read "At the Helm" by Kathy Barker
• Organize (with your fellow postdocs) a lunchmeeting with some professors and ask them all your questions
• Ask if you can sit in in Chalk Talks
• Organize mock Chalk Talks with your fellow postdocs
• Lots of advice here: https://tomprof.stanford.edu/

Once you have a lab/job offer/etc

• Go to the CSHL course on Leadership in Bioscience, it's great!
• Sign up to this email list: https://tomprof.stanford.edu/
• Go to one of the EMBO workshops
• Read the respective book by Carl Cohen on "Lab Dynamics"
• Go to Carl Cohen's website
• Read "At the Helm" by Kathy Barker
• Read the respective sections in the HHMI Book on "Making the right moves"
• Read Mohammed Noor's book "You are hired! Now what?"
• Read "Every other Thursday" and see if you want to start a 'self-help' group like that
• Talk talk talk to your colleagues
• If you don't have much teaching experience or are not from the US, take a course prior to be thrown into it. I highly recommend Barbara Houtz's Scientists Teaching Science online course, e.g. via the New York Academy of Sciences!
• You have just landed a fantastic job. Enjoy! :)

Miscellaneous

• OpenWetWare.org - for sharing protocols etc
• Quartzy - for lab organization
• Christine's thoughts on How to Write a Paper
• Ten Simple Rules on How to Write a Paper
• Ten Simple Rules on How to Review a Paper
• Ten Simple Rules for Getting a Grant