Unit tests for QuiXoT

We present here four experiments you may use to check QuiXoT, as well as testing it is working as expected in your machine:

Test 1: 18O quantification and statistical analysis from Proteome Discoverer results

1. Download the zip with the files from here.
2. After unzipping the files, you should have three folders: dir, inv, and raw.

• The dir folder should contain an XML file called modifications.xml and and MSF file called 110112_VSMC_EN_OG21.msf (the latter being an SQLite file containing identifications of the target SEQUEST search from Proteome Discoverer 1.4; the decoy search).
• The inv folder should contain an MSF file called 110112_VSMC_EN_OG21-01.msf (an SQLite file containing the corresponding decoy SEQUEST search).
• The raw folder should contain a Thermo RAW file called 110112_VSMC_EN_OG21.RAW, containing all the spectral information saved by the spectrometre.

1. After opening pRatio, drag and drop the dir and inv folders in the Target search and Decoy search fields, respectively. Press the button Run!.
2. After finishing, seven files should be saved in the dir folder, including four tab-separated text files (with XLS ending), and XML file (the QuiXML file), and two TXT files.
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Test 2: 18O quantification statistical analysis starting from QuiXML file + binStack

In the following examples, we start with QuiXML/binStack files, so we can skip some of the initial steps.

1. Download the zip with the files from here.

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Test 3: iTRAQ statistical analysis starting from QuiXML file + binStack

1. Download the zip with the files from here.

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Test 4: SILAC statistical analysis starting from QuiXML file + binStack

1. Download the zip with the files from here.

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