November Goals

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:
  • 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:

  • 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?


  • Learn how to tag notebook posts
  • Throw away some geoduck vials (D, E, autosampler vials) & organize others (original samples, quantified proteins, digested peptides)
  • Create for proteomics data on Owl
Written on November 7, 2017