Table 2.

Description of search file-names in the ProteomeXchange repository PXD002767 based on MaxQuant [11]. Each zip contains a range of files where the four most relevant are described above.

Search Files Filename		Description of content
MQ_Search_Kuras.zip		MaxQuant result folder “txt” of Q Exactive GelMS potato leaf samples, search against the Uniprot reference proteome databases for potato (AUP000011115) and late blight (AUP000006643).
MQ_Search_Bintje.zip		MaxQuant result folder “txt” of Q Exactive GelMS potato leaf samples, search against the Uniprot reference proteome databases for potato (AUP000011115) and late blight (AUP000006643).
MQ_Search_Sarpomira.zip		MaxQuant result folder “txt” of Q Exactive GelMS potato leaf samples, search against the Uniprot reference proteome databases for potato (AUP000011115) and late blight (AUP000006643).
MQ_Search_all_cultivars.zip		MaxQuant result folder “txt” of Q Exactive GelMS potato leaf samples from all cultivars, search against the Uniprot reference proteome databases for potato (AUP000011115) and late blight (AUP000006643).
The MaxQuant output in folder "txt" contains a range of files containing important search information. Below files are the most commonly used for post-identification analysis and quantitative analysis.
tables.pdf	A summary of all the definitions and files used for the MaxQuant search.
proteinGroups.txt	File containing all proteins with corresponding label free quantitative information to be imported into the Perseus post-analysis program [15].
summary.txt parameters.txt	Detailed description of all settings used for the MaxQuant search.