Time flies, especially when I get various waves of data that needs analyzing, and also Thanksgiving, tests/papers from class, etc… Lots of tasks will carry over from November, BUT nevertheless, headway has been made.

Olys at dock

• Clean, measure broodstock (after hatchery meeting)

Geoduck proteomics

• Finish Results section
  • Correlation btwn various parameters, protein abundance
  • Try to use Structural Equation Model instead of linear regression model
  • QA %>1SD & %>2SD calculations
• Get more methods info from Micah, Emma
• Focus on DISCUSSION
• Identify target journals
• Determine figures for paper. Candidates:
  • Box/violin plots of protein abundances by subbasin, including 3 peptides separately. Like this, but with 4 panes for each protein:
  • NMDS plot (like what I already have) with overlaying circles by subbasin
  • 3-pane plot of pH, T, and DO (continuous)? Would be messy with all 8 traces from each site.
  • Correlation matrices for: variables identified in model (DO var, pH >1sd %, and growth)
• Remaining things that Emma said I should do:
  • 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
  • SRM dilution curve
• Idea for paper, but would take a while (probably a few days): screen all proteins in DIA Skyline data for a “menu” of targetable, detectable proteins (based on visual check of chromatograms). This could be published alongside the paper as a very usable resource.
• More lit Research
  • Growth related to protein expression - but why only some proteins were diff. expressed?
  • 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.

Prep for Oly genetics hatchery vs. wild analysis

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

Application things

• Finish NDSEG, get letters
• AA travel awards (?)

Misc.

• Submit MS paperwork to office & proposal online (pending approval from Rick, Jackie)
• Learn how to tag notebook posts
• Create README.md for proteomics data on Owl

In January:

• Determine which Oly samples to sequence from last spring/winter
• 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

On hold:

• Record podcast pilot with Megan
• Find local vendor that sells dry suits, try on to determine size, then purchase gear

Accomplishments from last month

• Checked out Oly histology data from last year’s experiment
• Cireculated MS proposal for approval from committee
• Submitted NSA abstracts, travel grant app
• Sampled experimental Olys for histology (time=0), got animals into treatments
• Received collection permit @ Mud Bay, made contact with homeowners for access, collected first batch
• Gave Oly shells to Heater @ Wood’s lab for Polydora inspection
• Got the CoEnv travel grant for AA
• Proteomics stuff:
  • Finalized SRM tech. rep filtering process
  • Tracked down tidal charts from each Geoduck Proteomics ouplant location; used to process/filter environmental data from Micah
  • Generated summary statstics on environmental data
  • Re-ran proteomics analyses on the peptide-level, where transitions within each peptide were summed. Lambda-transformed peptide abundance for normal distribution, then ran 2-way ANOVAs.
  • Learned how to run stepwise linear resgression models, ran on diff. expressed proteins with environmental summary stats.
  • Refined methods section of paper
  • Made headway on results section of paper
  • Drafted intro; will likely need to revise based on results
  • Finished parasite class things
  • Generated notebook for DIA data in Skyline
  • R-script for merging DIA results with annotations, extracting SRM targets from this dataframe
  • Generated peptide variability stats for paper
  • Discarded unecessary vials (the “just in case” vials, and autosampler vials prepped for mass spec). If I need to re-run samples, I’d prepare new autosamper vials from my digested peptides.