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: http://www.wdhof.org/wdhof-scholarshipDesc.aspx
- 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?
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
Written on November 7, 2017