December Goals (belated)
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)
- 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?
- 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
- Finish NDSEG, get letters
- AA travel awards (?)
- 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
- 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
- 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.
Written on December 12, 2017