Dataset description
-------------------
This dataset contains spots data from 10 patients receiving a peritoneal dialysis treatment. Peritoneal dialysis effluent (PDE) samples were collected from patients following a peritoneal equilibrium test in different time points. Each patient's sample was analyzed using 2D-gel electrophoresis. Then, the 'Progenesis SameSpots' software was used to compare each patient's samples. Differentially expressed spots (those in 'Samespots Report' directory) were excised and analysed through MALDI-TOF mass spectrometry. Obtained spectra were submitted to Mascot in order to obtain a list of protein identifications.

Dataset contents
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- `Samespots Report`: HTML files corresponding to the reports generated by Progenesis Samespots ("Export report" option). Each report can be individually imported into S2P using menu `Import/Samespots/Single HTM report`.
- `Spots`: contains files that store spots data (saved with the `Export to CSV` option of the Samespots Report editor in S2P).
- `Maldi plate`: contains files related with Maldi plates.
- `Mascot identifications`: contains files related with the Mascot identifications.
- `Processed Spots`: contains files that store procerssed spots data (i.e. created from files in `Spots` in order to add the Mascot identifications) in CSV and Excel formats. This files can't be opened with S2P but with third party software (e.g. R, LibreOffice, Excel, etc.).
	
### Spots
`Spots` directory contains one CSV file corresponding to each HTML report in the `Samespots Report` directory. Each file is the result of saving as CSV the report files contained in the `Samespots Report` directory using a fold value of 1.0, a p-value of 0.05 and the patient identifier (e.g. `IE`, `JM`, etc.) as spots suffix.

CSV files in this directory have a `Custom format` where fields are not quoted, `,` is the column separator, `.` is the decimal separator, and `Windows` is the line break.

### Maldi plate
`Maldi plate` directory contents:
- `2015.12.21_PDE_peptidos_longitudinal_study.mpl`: one of the MALDI plates used in this experiment to analyze the identified spots in the MALDI-TOF mass spectrometer.
- `2015.06.02_LP_patient_longitudinal_study.mpl`: one of the MALDI plates in this experiment to analyze the identified spots in the MALDI-TOF mass spectrometer.

### Mascot identifications
`Mascot identifications` directory contents:
- `2015.12.21_PDE_Peptidos_Longitudinal_Study.BTR.HTM`: Mascot HTML report file.
- `2015.12.21_PDE_Peptidos_Longitudinal_Study.csv`: Mascot identifications from `2015.12.21_PDE_Peptidos_Longitudinal_Study.BTR.HTM` in CSV format. This file is the result of saving as CSV the Mascot HTML report file using a minimum mascot score of 56, removing duplicates and removing identifications of Keratins. This CSV has a `Custom format` where fields are quoted, `,` is the column separator, `.` is the decimal separator, and `Windows` is the line break.
- `LP_2015.06.02.BTR.HTM`: Mascot HTML report file.
- `LP_2015.06.02.csv`: Mascot identifications from `LP_2015.06.02.BTR.HTM` in CSV format. This file is the result of saving as CSV the Mascot HTML report file using a minimum mascot score of 56, removing duplicates and removing identifications of Keratins. This CSV has a `Custom format` where fields are quoted, `,` is the column separator, `.` is the decimal separator, and `Windows` is the line break.
- `MascotIdentifications_WithSpots.csv`: Spot Mascot identifications in CSV format. This file is the result of merging both Maldi plates within the corresponding Mascot HTML report files using a minimum mascot score of 56, removing duplicates and removing identifications of Keratins. This CSV has a `Custom format` where fields are quoted, `,` is the column separator, `.` is the decimal separator, and `Windows` is the line break. This CSV file can be loaded into S2P using the menu `Load/Load spot identifications`.