Ion

Proteobench · Jan 7, 2025 · 32c18c2 · 32c18c2
1 parent ff9bfdc
commit 32c18c2
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Showing 4 changed files with 41 additions and 0 deletions.
diff --git a/proteobench/io/parsing/io_parse_settings/Quant/lfq/ion/DDA/parse_settings_peaks.toml b/proteobench/io/parsing/io_parse_settings/Quant/lfq/ion/DDA/parse_settings_peaks.toml
@@ -0,0 +1,37 @@
+[mapper]
+"Accession" = "Proteins"
+"Peptide" = "Sequence"
+"z" = "Charge"
+
+[condition_mapper]
+"Group 1 Normalized Area" = "A"
+"Group 2 Normalized Area" = "A"
+"Group 3 Normalized Area" = "A"
+"Group 4 Normalized Area" = "B"
+"Group 5 Normalized Area" = "B"
+"Group 6 Normalized Area" = "B"
+
+[run_mapper]
+"Group 1 Normalized Area" = "Condition_A_Sample_Alpha_01"
+"Group 2 Normalized Area" = "Condition_A_Sample_Alpha_02"
+"Group 3 Normalized Area" = "Condition_A_Sample_Alpha_03"
+"Group 4 Normalized Area" = "Condition_B_Sample_Alpha_01"
+"Group 5 Normalized Area" = "Condition_B_Sample_Alpha_02"
+"Group 6 Normalized Area" = "Condition_B_Sample_Alpha_03"
+
+[species_mapper]
+"_YEAST" = "YEAST"
+"_ECOLI" = "ECOLI"
+"_HUMAN" = "HUMAN"
+
+[modifications_parser]
+"parse_column" = "Sequence"
+"before_aa" = false
+"isalpha" = true
+"isupper" = true
+"pattern"="(?<=\\().+?(?=\\))"
+"modification_dict" = {"+57.02" = "Carbamidomethyl", "+15.99" = "Oxidation", "-17.026548" = "Gln->pyro-Glu", "-18.010565" = "Glu->pyro-Glu", "+42.01" = "Acetyl"}
+
+[general]
+"contaminant_flag" = "Cont_"
+"decoy_flag" = false
diff --git a/proteobench/io/parsing/io_parse_settings/parse_settings_files.toml b/proteobench/io/parsing/io_parse_settings/parse_settings_files.toml
@@ -6,6 +6,7 @@
 "ProlineStudio" = "parse_settings_proline.toml"
 "MSAngel" = "parse_settings_msangel.toml"
 "Sage" = "parse_settings_sage.toml"
+"PEAKS" = "parse_settings_peaks.toml"
 "Custom" = "parse_settings_custom.toml"
 
 [quant_lfq_peptidoform_DDA]

diff --git a/proteobench/io/parsing/parse_ion.py b/proteobench/io/parsing/parse_ion.py
@@ -107,6 +107,8 @@ def load_input_file(input_csv: str, input_format: str) -> pd.DataFrame:
         input_data_frame["PG.ProteinGroups"] = input_data_frame["PG.ProteinGroups"].str.join(";")
     elif input_format == "MSAID":
         input_data_frame = pd.read_csv(input_csv, low_memory=False, sep="\t")
+    elif input_format == "PEAKS":
+        input_data_frame = pd.read_csv(input_csv, low_memory=False, sep=",")
 
     return input_data_frame
 

diff --git a/proteobench/plotting/plot_quant.py b/proteobench/plotting/plot_quant.py
@@ -88,6 +88,7 @@ def plot_metric(
             "FragPipe (DIA-NN quant)": "#ff7f00",
             "MSAID": "#afff57",
             "Proteome Discoverer": "#8c564b",
+            "PEAKS": "#f781bf",
         },
         mapping: Dict[str, int] = {"old": 10, "new": 20},
         highlight_color: str = "#d30067",