November tasks

Geoduck proteomics

  • Data analysis continued
    • [ ] Finalize SRM tech. rep filter process
    • [ ] Generate Linear Response Plot, as per Emma: Peak area on the y, amount of peptide (moles) on the x. Don’t know absolute quantity of experimental peptides, could make the x-axis relative quantity or something. Can generate plots like these in MSstats.
    • [ ] DIA error rate
  • Notebooks
    • [ ] DIA Skyline document, error rate checking
    • [ ] DIA analysis
    • [ ] SRM dilution curve notebook
  • Researh
    • [ ] Consider implications: HSP70 is not highly specific, since some interference w/ gigas in dilution curve
    • [ ] More lit review – bioassays
    • [ ] Determine if abundance difference is “biologically relevant.” If I can find SRM abundance good (haven’t found good references yet), OR find citable % diff.
  • Writing Timeline:
  Analysis Writing
Nov 1-5 Additional SRM data analysis (follow-up to ANOSIM), dilution curve analysis notebook More lit research & draft introduction
Nov 6-12 Re-do DIA analysis in R with notebook documentation SRM results DIA results
Nov 13-19 DIA error rate, ROC curve, linear response plot Edits to introduction, and start Discussion
Nov 20-26 Refine protein box plots More discussion
Nov 27-Dec 1 Environmental data analysis & plots Clean-up/edits

Oly genetics hatchery vs. wild

  • [ ] Read Fischer et al. 2012
  • [ ] Get most current data set from Crystal
  • [ ] ID best program to use

Application things

  • [ ] GROW
  • [ ] Finish NDSEG
  • [ ] NSA travel grant, other?
  • [ ] Dive grant: http://ift.tt/2hhG91E
  • [ ] NSA travel award
  • [ ] AA travel awards

Oly 2017 experiment:

  • [ ] Organize data
  • [ ] Analyze histology data
  • [ ] Determine which samples to sequence
  • [ ] Meet with STATS resource to figure out how to analyze Oly larval survival – parse out survival data to 224um, to juvenile, by time for reps

Oly 2018 experiment:

  • [X] Help collect & clean FB
  • [ ] Order histology supplies
  • [ ] Sample broodstock for histology, send off
  • [ ] Get broodstock into temp treatments

For Committee:

  • [ ] Circulate proposal for approval
  • [ ] Submit paperwork to office & proposal online

Scientific Diving

  • [ ] Find local vendor that sells dry suits, try on to determine size
  • [ ] Purchase gear

Record podcast pilot with Megan

  • [ ] Read Megan’s paper
  • [ ] Rent mic from UW tech resources for this
  • [ ] Where to record?

Misc.

  • [ ] Learn how to tag notebook posts
  • [ ] Throw away some geoduck vials (D, E, autosampler vials) & organize others (original samples, quantified proteins, digested peptides)
  • [ ] Create README.md for proteomics data on Owl

from LabNotebook http://ift.tt/2m1Mi49
via IFTTT

November Goals
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