# July 10, 2017

`RAW` files from a Selected Reaction Monitoring project with Washington Department of Natural Resources conducted by Yaamini Venkataraman and Emma Timmins-Schiffman.

File naming convention:

2017_July_10_bivalves_{}.raw

where {} can be any of the following:

Procedural blanks: 001, 007, 013, 019, 025, 031, 037, 043, 049, 055, 061, 067, 073, 079, 088, 098, 104, 110, 116, 122, 128, 134, 138
QCs: QC{number}
Dilution curve samples: D{number}-O
Actual oyster samples: Anything else

A key to all samples can be found [here](http://owl.fish.washington.edu/spartina/DNR_SRM_20170728/Analyses/2017-07-28-SRM-Sequence-File.xlsx). 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. DIA shotgun proteomic analyses were used to select targets for the Selected Reaction Monitoring Assay to further quantify differential protein expression for 15 target proteins. 

### Sample Preparation

[Preparation](https://yaaminiv.github.io/DNR-Sample-Preparation-Round2/)
[Sonication Part 1](https://yaaminiv.github.io/DNR-Sonication-Round2/)
[BCA Assay Part 1](https://yaaminiv.github.io/DNR-BCA-Assay-Round2/)
[Mini Trypsin Digestion Part 1](https://yaaminiv.github.io/DNR-Mini-Trypsin-Digestion-Round2/)
[Sonication Part 2](https://yaaminiv.github.io/DNR-Sample-Preparation-and-Sonication-Round3/)
[BCA Assay Part 2](https://yaaminiv.github.io/DNR-BCA-Assay-Round3/)
[Mini Trypsin Digestion Part 2](https://yaaminiv.github.io/DNR-Mini-Trypsin-Digestion-Round3/)
[Speed Vacuum](https://yaaminiv.github.io/DNR-Speed-Vacuum-Round2/)
[Desalting](https://yaaminiv.github.io/DNR-Desalting-Round2/)

### Selecting SRM Targets

[Part 1](https://yaaminiv.github.io/Selecting-SRM-Targets-Part3/)
[Part 2](https://yaaminiv.github.io/Selecting-SRM-Targets-Part4/)
[Part 3](https://yaaminiv.github.io/Selecting-SRM-Targets-Part5/)
[Part 4](https://yaaminiv.github.io/Selecting-SRM-Targets-Part6/)
[Part 5](https://yaaminiv.github.io/Selecting-SRM-Targets-Part7/)

### Mass Spectrometry Methods

[Part 1](https://yaaminiv.github.io/SRM-Assay-Day1/)
[Part 2](https://yaaminiv.github.io/SRM-Assay-Day2/)
[Part 3](https://yaaminiv.github.io/SRM-Assay-Day3/)
[Part 4](https://yaaminiv.github.io/SRM-Assay-Day5/)
[Part 5](https://yaaminiv.github.io/SRM-Assay-Day6/)
[Part 6](https://yaaminiv.github.io/SRM-Assay-Day7/)
[Part 7](https://yaaminiv.github.io/SRM-Assay-Day8/)
[Part 8](https://yaaminiv.github.io/SRM-Assay-Day9/)
[Dilutions](https://yaaminiv.github.io/SRM-Dilution-Calculations2/)

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