# January 23, 2017

`RAW` files from a DIA shotgun proteomics project with Washington Department of Natural Resources conducted by Yaamini Venkataraman and Emma Timmins-Schiffman. 

Files are sorted in two categories, oyster samples and blanks, using the following file naming convention:

2017_January_23_envtstress_{}.raw

where {} can be:

Procedural blanks: blank{number}
Oyster samples: oyster{number}

A key to all samples can be found [here](http://owl.fish.washington.edu/spartina/January_2017_DNR_Raw_Data/Other_files/2017_January_23_sequence_file.csv). The folder "Other_files" has files important for mass spectrometry methods. Below are other relevant links about the project.

### [Background](https://yaaminiv.github.io/DNR-Project-Introduction/)

150 sibling *C. gigas* were outplanted at five different locations in and around Puget Sound (Case Inlet, Fidalgo Bay, Port Gamble Bay, Skokomish River Delta and Willapa Bay). At each site, oysters were placed in both bare and eelgrass patches. After one month, gill tissue samples were collected and frozen. The purpose of this project is to examine differential protein expression between sites and habitat. Using DIA shotgun proteomics analyses, baseline protein expression was characterized for ten oysters. Each oyster represented a unique site and habitat condition. 

### Sample Preparation

[Preparation](https://yaaminiv.github.io/First-Day/)
[Sonication](https://yaaminiv.github.io/Sonication/)
[BCA Assay](https://yaaminiv.github.io/BCA-Assay-Trial-2/)
[Mini Trypsin Digestion](https://yaaminiv.github.io/Mini-Trypsin-Digestion/)
[Speed Vacuum](https://yaaminiv.github.io/Speed-Vacuum/)
[Desalting](https://yaaminiv.github.io/Desalting/)
[PRTC Preparation](https://yaaminiv.github.io/PRTC-preparation/)

### Mass Spectrometry Methods

[MZ ratio selection](https://yaaminiv.github.io/MZ-ratios/)
[Set-up](https://yaaminiv.github.io/Mass-Spec-Setup/)
[Mass Spectrometry Start](https://yaaminiv.github.io/Mass-Spec-Start/)
[Update 1](https://yaaminiv.github.io/Mass-Spec-Updates/)
[Update 2](https://yaaminiv.github.io/Mass-Spec-Update-2/)
[Update 3](https://yaaminiv.github.io/Mass-Spec-Update-3/)

### [Associated Downstream Analyses](https://github.com/sr320/LabDocs/wiki/DIA-data-Analyses)

Data was used to inform a Selected Monitoring Reaction Assay, or targetted assay for higher quality proteomic data to examine differential protein expression.