#Peptide Extractor (PepEx) 0.01

PepEx is a proteomics/peptidomics visualization tool that allows the representation of quantitative data. The program localizes the position of each peptide in their respective proteins and returns the total abundances associated with each amino acid of the sequence by summing the peptides that contains them. The output file can be easily represented (i.e with Excel). The resulting plot or proteolytic map shows the areas of preferential proteolysis within the protein.

The current version of Pepex requires python 2.7 and no further dependencies.

####Chromatographic Input file It is a .csv file located at the csv_input_file folder. The file format is five columns:

• Name: Peptide sequence in one letter format
• Volumen: Peptide quantitative information (i.e number of counts)
• Notes: Protein ID in uniprot format (i.e sp|Q9TUM6|PLIN2_BOVIN)
• Sample: When multiple samples are included on the file, a name for each one is required
• Phospho: Number of phosphorylated residues (or any other PTM or peptide attribute). PepEx can filter and analyze the data containing specific values or ranges of values for this column.

####Protein files Protein sequences should be included on the fasta_input_files folder in .fasta format and named with the uniprot number (i.e Q9TUM6.fasta). If one protein included on the input file (“Notes” column) is not on the folder the analysis will stop.

####Configuration file SamplewiseSequenceAlignerConfig.xml can be opened with a text editor. Two options:

• Route and name of the input file: can be changed at the third line.
• Phosphorylation: can filter the data according to column “Phospho” from the input file. Can be changed at the fifth line.

####Running PepEx Once the input file, protein fasta files and the configuration file have been set, the analysis can be performed clicking on testScript.py.

####Output file

Output file will be generated at the csv_output_files folder. The file will have multiple tables, one table per protein and each table will have the following format.

AA Index	AA	Volume	Exp1.d	Exp2.d	Exp3.d	Exp4.d	Exp5.d
16	R	15329260	775302	2446862	1145531	5781107	574183
17	E	16982790	1219449	2582336	1404984	5781107	627134
18	L	17385701	1364979	2744509	1481942	5781107	627134
19	E	17560980	1364979	2795431	1481942	5781107	627134
20	E	17560980	1364979	2795431	1481942	5781107	627134
21	L	17651764	1364979	2822736	1481942	5781107	627134
22	N	18696031	1364979	3002235	1481942	6229211	627134
23	V	18696031	1364979	3002235	1481942	6229211	627134
24	P	18696031	1364979	3002235	1481942	6229211	627134
25	G	18696031	1364979	3002235	1481942	6229211	627134

The column named “AA Index” for the amino acid (AA) numeration, a second column named “AA” for the amino acid single-letter code, a third column named “Volume” contains the sum of the subsequent columns and a number of columns, one for each experiment included on the analysis, with their corresponding names. The followings columns contain the corresponding abundances of the displayed peptide range within the labeled experiment. Amino acid sequence is listed from the N-terminus (top) to the C-terminus (bottom).