process_maxquant/maxquant_settings.json at master · joerivstrien/process_maxquant · GitHub

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{
"steps_dict":
    {
        "filtering_step":1,
        "uniprot_step":1,
        "mitocarta_step":1,
        "clustering_step":1,
        "make_excel_file_step":1
    },

"filtering_step":
    {
        "EXACT_MATCHES":[
            "Number of proteins",
            "Razor + unique peptides",
            "Fasta headers",
            "PEP",
            "Intensity",
            "Mol. weight [kDa]",
            "Sequence length",
            "MS/MS Count",
            "iBAQ"
        ],
        "CONTAINS":[
            "iBAQ "
        ],
        "PROTEIN_FILTERS":[
            "REV",
            "CON"
        ]
    },

"uniprot_step":
    {
        "uniprot_options":
            {
                "get_gene_name":1,
                "get_protein_name":1,
                "get_organism_name":1,
                "get_uniprot_hyperlink": 1,
                "get_cell_compartment": 1,
                "get_string_linkout": 1
            },

            "uniprot_base_url":"https://www.ebi.ac.uk/proteins/api/proteins?",
            "uniprot_request_url":"offset=0&size=100&accession=",
            "request_idle_time":4,
            "batch_amount":100,
            "uniprot_protein_base_url":"https://www.uniprot.org/uniprot/",
	    "known_gene_names": ["name", "orfNames", "olnNames"],
	    "known_protein_names": ["recommendedName","submittedName","alternativeName"],
            "string_linkout_parameters":
                {
                    "string_base_url":"https://string-db.org/network/",
                    "uniprot_mapping_service_url":"https://www.uniprot.org/uploadlists/",
                    "regex_pattern":"\\-[0-9]{1}$"
                }
        },

"mitocarta_step":
    {
        "mitocarta_human_ftp_link":"ftp://ftp.broadinstitute.org/distribution/metabolic/papers/Pagliarini/MitoCarta3.0/Human.MitoCarta3.0.xls",
        "mitocarta_mouse_ftp_link":"ftp://ftp.broadinstitute.org/distribution/metabolic/papers/Pagliarini/MitoCarta3.0/Mouse.MitoCarta3.0.xls",
        "human_sheet_name":"A Human MitoCarta3.0",
        "mouse_sheet_name":"A Mouse MitoCarta3.0",
	"mitocarta_symbol_column":"Symbol",
	"mitocarta_additional_symbol_column":"Synonyms",
	"evaluate_symbol_column":0,
	"evaluate_additional_symbol_column":1
    },

"clustering_step":
    {
        "method":"average",
        "metric":"correlation"
    },

"make_excel_file_step":
    {
        "excel_file_name":"processed_maxquant_file.xlsx",
        "identifier_column_names":["Majority protein IDs", "Protein IDs", "Fasta headers"],
	"output_column_order":["Fasta headers", "Majority protein IDs", "Razor + unique peptides", "identifier", "Sequence length", "Mol. weight [kDa]", "PEP", "iBAQ", "MS/MS Count", "Intensity", "Number of proteins"]
    }
}