example input

Example input

1-2 are MaxQuant files that add modification site probabilities and are optional
3 is qpmerge metadata flat file format (it needs to be converted to xml with the TemplateMetaData importer)
4 is progenesis quantification

Dataset 1: Mus musculus (mouse, mammalian model organism)

Find the following files in the Download section under examples/mouse

1. MaxQuant_Output_Phospho (ST)Sites.txt
2. MaxQuant_Output_Phospho (Y)Sites.txt
3. METADATA.txt
4. Progenesis_Output_pr140319_ms090319ph_mo_peptide.csv

Dataset 2: Arabidopsis thaliana (plant model organism)

Find the following files in the Download section under examples/arabidopsis

1. MaxQuant_Output_Phospho (ST)Sites.txt
2. MaxQuant_Output_Phospho (Y)Sites.txt
3. METADATA.txt
4. Progenesis_Output_pr140404_at_ms131108_OGethyl-SDSethyl_all.csv

Dataset 3: Ostreococcus tauri (algae, smallest free living eukaryote)

Find the following files in the Download section under examples/ostreococcus

1. MaxQuant_Output_Phospho (ST)Sites.txt
2. MaxQuant_Output_Phospho (Y)Sites.txt
3. METADATA.txt
4. Progenesis_Output_08_PR120907_MS120906_ot_CK1phospho_peptide_cca1-IC261.csv