Dataset description
-------------------
This dataset contains Mascot quantification reports corresponding to the LC-MS/MS analysis of the blood serum of a patient with osteoarthritis. From this blood serum, four samples were taken. These four samples were divided into two groups: ON, with two samples whose proteins were digested using the classic overnight method [1]; and US, with two samples whose proteins were digested using the ultrasonic accelerated method using the microplate horn assembly device [2].

The Mascot search engine was used for protein identification and to determine the emPAI values for each identified protein. Mascot reports containing emPAI values were exported using the “Export” option in Mascot Search Results, which creates a CSV file of each LC-MS/MS run (i.e. 8 files in this case).

Samples are organized in three different ways in order to perform three different comparisons: (i) Overnight sample 1 vs. Overnight sample 2; (i) Ultrasonic sample 1 vs. Ultrasonic sample 2; and (iii) Overnight vs. Ultrasonic samples.

Dataset contents
--------------------
- `S2P-Data`: Mascot quantification reports prepared to be loaded with S2P.
- `Results`: case study result files.
	
### S2P-Data
`S2P-Data` directory contents:
- `S2P-parameters.txt`: the parameter settings to load the other directories in this one using S2P.
- `Samples ON`: ON samples following the layout required by S2P. This folder can be loaded using the `Import/Import Mascot quantifications` operation using the parameters specified in `S2P-parameters.txt`.
- `Samples US`: US samples following the layout required by S2P. This folder can be loaded using the `Import/Import Mascot quantifications` operation using the parameters specified in `S2P-parameters.txt`.
- `US versus ON`: US and ON samples following the layout required by S2P so that they can be compared by condition. This folder can be loaded using the `Import/Import Mascot quantifications` operation using the parameters specified in `S2P-parameters.txt`.

### Results
`Results` directory contents:
- `Samples ON.csv`: `Conditions` table exported when the `Samples ON` directory is loaded.
- `Samples US.csv`: `Conditions` table exported when the `Samples US` directory is loaded.
- `US versus ON.csv`: `Conditions` table exported when the `US versus ON` directory is loaded.
- `Results.xlxs`: Excel spreadsheet containing the three previous tables with additional calculations.

References
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- [1] H.M. Santos, R. Rial-Otero, L. Fernandes, G. Vale, M.G. Rivas, I. Moura, J.L. Capelo, Improving Sample Treatment for In-Solution Protein Identification by Peptide Mass Fingerprint Using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry, J. Proteome Res. 6 (2007) 3393–3399. doi:10.1021/pr0702518.
- [2] S. Jorge, J.E. Araújo, F.M. Pimentel-Santos, J.C. Branco, H.M. Santos, C. Lodeiro, J.L. Capelo, Unparalleled Sample Treatment Throughput for Proteomics Workflows Relying on Ultrasonic Energy, Talanta. (2017). doi:10.1016/j.talanta.2017.07.079.
