quantms runs

proteobench/io/parsing/io_parse_settings/Quant/lfq/ion/DDA/parse_settings_msstats.toml

@@ -0,0 +1,33 @@
+[mapper]
+"ProteinName" = "Proteins"
+"Sequence" = "Sequence"
+"PrecursorCharge" = "Charge"
+"Reference" = "Raw file"
+"PeptideSequence" = "Modified sequence"
+
+[condition_mapper]
+"LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML" = "A"
+"LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML" = "A"
+"LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.mzML" = "A"
+"LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML" = "B"
+"LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML" = "B"
+"LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML" = "B"
+
+[run_mapper]
+"LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML" = "Condition_A_Sample_Alpha_01"
+"LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML" = "Condition_A_Sample_Alpha_02"
+"LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.mzML" = "Condition_A_Sample_Alpha_03"
+"LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML" = "Condition_B_Sample_Alpha_01"
+"LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML" = "Condition_B_Sample_Alpha_02"
+"LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML" = "Condition_B_Sample_Alpha_03"
+
+
+[species_mapper]
+"_YEAST" = "YEAST"
+"_ECOLI" = "ECOLI"
+"_HUMAN" = "HUMAN"
+
+
+[general]
+"contaminant_flag" = "Cont_"
+"decoy_flag" = false

proteobench/io/parsing/io_parse_settings/parse_settings_files.toml

@@ -7,6 +7,7 @@
 "MSAngel" = "parse_settings_msangel.toml"
 "Sage" = "parse_settings_sage.toml"
 "PEAKS" = "parse_settings_peaks.toml"
+"quantms" = "parse_settings_msstats.toml"
 "Custom" = "parse_settings_custom.toml"
 
 [quant_lfq_peptidoform_DDA]

proteobench/io/parsing/parse_ion.py

@@ -1,7 +1,6 @@
 import math
 import os
 import re
-from typing import Dict, List, Optional
 
 import pandas as pd
 
@@ -109,7 +108,18 @@ def load_input_file(input_csv: str, input_format: str) -> pd.DataFrame:
         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=",")
-
+    elif input_format == "quantms":
+        input_data_frame = pd.read_csv(input_csv, low_memory=False)
+        input_data_frame = input_data_frame.assign(
+            proforma=input_data_frame["PeptideSequence"].str.replace(
+                r"\(([^)]+)\)",
+                r"",
+                regex=True,
+            ),
+        )
+        input_data_frame["Sequence"] = input_data_frame["PeptideSequence"].str.replace(r"\(([^)]+)\)", r"", regex=True)
+    else:
+        raise ValueError(f"Input format '{input_format}' not recognized.")
     return input_data_frame
 
 

proteobench/io/parsing/parse_settings.py

@@ -171,14 +171,16 @@ def convert_to_standard_format(self, df: pd.DataFrame) -> tuple[pd.DataFrame, Di
                     df_filtered_melted["proforma"] + "|Z=" + df_filtered_melted["Charge"].astype(str)
                 )
             else:
-                print("Not all columns required for making the ion are available.")
+                # ! raise ValueError
+                print("Not all columns required for making the ion are available: 'proforma' and 'Charge'.")
             return df_filtered_melted, replicate_to_raw
 
         elif self.analysis_level == "peptidoform":
             if "proforma" in df_filtered_melted.columns:
                 df_filtered_melted["peptidoform"] = df_filtered_melted["proforma"]
             else:
-                print("Not all columns required for making the peptidoform are available.")
+                # ! raise ValueError
+                print("Not all columns required for making the peptidoform are available: 'proforma'.")
             return df_filtered_melted, replicate_to_raw
 
         else:
@@ -244,11 +246,11 @@ def convert_to_standard_format(self, df: pd.DataFrame) -> tuple[pd.DataFrame, Di
         if self.parser.analysis_level == "ion":
             try:
                 df["precursor ion"] = df["proforma"] + "|Z=" + df["Charge"].astype(str)
-            except KeyError:
+            except KeyError as e:
                 raise KeyError(
                     "Not all columns required for making the ion are available."
                     " Is the charge available in the input file?"
-                )
+                ) from e
 
             return df, replicate_to_raw
 

proteobench/modules/quant/lfq/ion/DDA/quant_lfq_ion_DDA.py

@@ -113,42 +113,45 @@ def benchmarking(
         except pd.errors.ParserError as e:
             raise ParseError(
                 f"Error parsing {input_format} file, please make sure the format is correct and the correct software tool is chosen: {e}"
-            )
+            ) from e
         except Exception as e:
-            raise ParseSettingsError(f"Error parsing the input file: {e}")
+            raise ParseSettingsError("Error parsing the input file.") from e
 
+        msg = f"Folder: {self.parse_settings_dir}, Module: {self.module_id}"
         # Parse settings file
         try:
             parse_settings = ParseSettingsBuilder(
                 parse_settings_dir=self.parse_settings_dir, module_id=self.module_id
             ).build_parser(input_format)
         except KeyError as e:
-            raise ParseSettingsError(f"Error parsing settings file for parsing, settings seem to be missing: {e}")
+            raise ParseSettingsError(
+                f"Error parsing settings file for parsing, settings seem to be missing: {msg}"
+            ) from e
         except FileNotFoundError as e:
-            raise ParseSettingsError(f"Could not find the parsing settings file: {e}")
+            raise ParseSettingsError(f"Could not find the parsing settings file: {msg}") from e
         except Exception as e:
-            raise ParseSettingsError(f"Error parsing settings file for parsing: {e}")
+            raise ParseSettingsError(f"Error parsing settings file for parsing: {msg}") from e
 
         try:
             standard_format, replicate_to_raw = parse_settings.convert_to_standard_format(input_df)
         except KeyError as e:
-            raise ConvertStandardFormatError(f"Error converting to standard format, key missing: {e}")
+            raise ConvertStandardFormatError("Error converting to standard format, key missing.") from e
         except Exception as e:
-            raise ConvertStandardFormatError(f"Error converting to standard format: {e}")
+            raise ConvertStandardFormatError("Error converting to standard format.") from e
 
-        # calculate quantification scores
+        # instantiate quantification scores
         try:
             quant_score = QuantScores(
                 self.precursor_name, parse_settings.species_expected_ratio(), parse_settings.species_dict()
             )
         except Exception as e:
-            raise QuantificationError(f"Error generating quantification scores: {e}")
+            raise QuantificationError("Error generating quantification scores.") from e
 
         # generate intermediate data structure
         try:
             intermediate_data_structure = quant_score.generate_intermediate(standard_format, replicate_to_raw)
         except Exception as e:
-            raise IntermediateFormatGenerationError(f"Error generating intermediate data structure: {e}")
+            raise IntermediateFormatGenerationError("Error generating intermediate data structure.") from e
 
         # try:
         current_datapoint = Datapoint.generate_datapoint(

proteobench/plotting/plot_quant.py

@@ -89,6 +89,7 @@ def plot_metric(
             "MSAID": "#afff57",
             "Proteome Discoverer": "#8c564b",
             "PEAKS": "#f781bf",
+            "quantms": "#03fc39",
         },
         mapping: Dict[str, int] = {"old": 10, "new": 20},
         highlight_color: str = "#d30067",

test/data/dda_quant/sample_dda_quantms.sdrf_openms_design_msstats_in.csv

@@ -0,0 +1,101 @@
+ProteinName,PeptideSequence,PrecursorCharge,FragmentIon,ProductCharge,IsotopeLabelType,Condition,BioReplicate,Run,Intensity,Reference
+sp|P09733|TBA1_YEAST,DLFHPEQLISGK,3,,0,L,cond_A,1,1,131708800.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|P32119|PRDX2_HUMAN,TDEGIAYR,2,,0,L,cond_B,4,4,845348600.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|P49321|NASP_HUMAN,EQVYDAMGEK,2,,0,L,cond_B,4,4,48666640.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|P50990|TCPQ_HUMAN,TVGATALPR,2,,0,L,cond_A,1,1,958554700.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|Q99832|TCPH_HUMAN,SLHDAIMIVR,3,,0,L,cond_B,4,4,329470100.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|P58004|SESN2_HUMAN,GPSAFIPVEEVLR,2,,0,L,cond_B,5,5,29033340.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML
+sp|P02545|LMNA_HUMAN,ASASGSGAQVGGPISSGSSASSVTVTR,3,,0,L,cond_B,4,4,97719470.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|Q8WWM7|ATX2L_HUMAN,FTDSAIAMNSK,2,,0,L,cond_B,6,6,47579640.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML
+sp|P50552|VASP_HUMAN,QQPGPSEHIER,3,,0,L,cond_B,4,4,118654400.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|Q7L014|DDX46_HUMAN,ASYPC(Carbamidomethyl)MSLHGGIDQYDR,3,,0,L,cond_B,4,4,38434830.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|P30154|2AAB_HUMAN,MAGDQVANVR,2,,0,L,cond_A,1,1,47908580.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|Q04726|TLE3_HUMAN,AELTSSAPAC(Carbamidomethyl)YALAISPDAK,2,,0,L,cond_A,2,2,22015490.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML
+sp|P35658|NU214_HUMAN,SSLLAVSNK,2,,0,L,cond_A,1,1,91677080.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|Q8WUM4|PDC6I_HUMAN,LLDEEEATDNDLR,2,,0,L,cond_A,1,1,245312700.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|P38910|CH10_YEAST,LNQAEVVAVGPGFTDANGNK,3,,0,L,cond_B,4,4,81358820.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|Q9UQR0|SCML2_HUMAN,SEAPSYIAVPDPSVLK,2,,0,L,cond_A,2,2,43908620.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML
+sp|O43390|HNRPR_HUMAN,LC(Carbamidomethyl)DSYEIRPGK,2,,0,L,cond_A,1,1,50041590.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|P05373|HEM2_YEAST,GLINANLAHK,2,,0,L,cond_B,5,5,32199620.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML
+sp|Q04438|SPG4_YEAST,NVDISNMSQGEFLR,2,,0,L,cond_B,4,4,70438430.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|Q9NUQ3|TXLNG_HUMAN,ALGAHLEAEPK,3,,0,L,cond_A,1,1,83372190.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|P49411|EFTU_HUMAN,NMITGTAPLDGC(Carbamidomethyl)ILVVAANDGPMPQTR,3,,0,L,cond_A,1,1,128703300.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|Q14657|LAGE3_HUMAN,FGPPVSR,2,,0,L,cond_B,6,6,57360970.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML
+sp|P38426|TPS3_YEAST,NPNLSFDSHPPR,3,,0,L,cond_A,1,1,61451870.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|P21333|FLNA_HUMAN,SPFEVYVDK,2,,0,L,cond_B,5,5,297051000.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML
+sp|Q14684|RRP1B_HUMAN,AGPGSLELC(Carbamidomethyl)GLPSQK,2,,0,L,cond_B,6,6,60428020.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML
+sp|Q07666|KHDR1_HUMAN,ILGPQGNTIK,2,,0,L,cond_A,1,1,507243000.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|P48735|IDHP_HUMAN,VC(Carbamidomethyl)VETVESGAMTK,2,,0,L,cond_B,4,4,49347380.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|Q15645|PCH2_HUMAN,IDVAFVDR,2,,0,L,cond_A,2,2,70441630.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML
+sp|P00558|PGK1_HUMAN,AC(Carbamidomethyl)ANPAAGSVILLENLR,3,,0,L,cond_A,3,3,639706700.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.mzML
+sp|P46367|ALDH4_YEAST,HIYQSAAAGLK,2,,0,L,cond_A,2,2,190671900.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML
+sp|Q5T653|RM02_HUMAN,QMQVLETC(Carbamidomethyl)VATVGR,2,,0,L,cond_A,2,2,38343660.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML
+sp|Q9NWV4|CZIB_HUMAN,TIVEFEC(Carbamidomethyl)R,2,,0,L,cond_A,1,1,82191550.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|P09972|ALDOC_HUMAN,YTPEEIAMATVTALR,2,,0,L,cond_B,6,6,351006400.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML
+sp|P42696|RBM34_HUMAN,IQINQEEER,2,,0,L,cond_B,5,5,17101070.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML
+sp|Q8WUM4|PDC6I_HUMAN,FYNELTEILVR,2,,0,L,cond_A,2,2,220731500.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML
+sp|Q15833|STXB2_HUMAN,EPIPSLEAIYLLSPTEK,2,,0,L,cond_A,3,3,26323180.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.mzML
+sp|Q9BWS9|CHID1_HUMAN,GLVVTDLK,2,,0,L,cond_A,3,3,25301540.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.mzML
+sp|Q02486|ABF2_YEAST,LYSEYQK,2,,0,L,cond_B,5,5,48212330.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML
+sp|Cont_Q3SX14|GELS_BOVIN,AQPVQVAEGSEPDSFWEALGGK,2,,0,L,cond_A,1,1,29316550.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|Q92841|DDX17_HUMAN,FVINYDYPNSSEDYVHR,3,,0,L,cond_B,4,4,331407500.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|Q13428|TCOF_HUMAN,LGAGEGGEASVSPEK,2,,0,L,cond_B,6,6,37681520.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML
+sp|P11177|ODPB_HUMAN,DAINQGMDEELERDEK,3,,0,L,cond_A,2,2,69755510.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML
+sp|P08758|ANXA5_HUMAN,ALLLLC(Carbamidomethyl)GEDD,2,,0,L,cond_A,1,1,41767580.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|Q9UHD8|SEPT9_HUMAN,FINDQYEK,2,,0,L,cond_A,2,2,93834380.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML
+sp|Q9UNZ2|NSF1C_HUMAN,SPNELVDDLFK,2,,0,L,cond_A,2,2,38462320.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML
+sp|Q1KMD3|HNRL2_HUMAN,NGEDLGVAFWISK,2,,0,L,cond_B,4,4,124289300.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|P16157|ANK1_HUMAN,LGYISVTDVLK,2,,0,L,cond_B,4,4,78834210.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|P30050|RL12_HUMAN,QAQIEVVPSASALIIK,2,,0,L,cond_A,1,1,610790300.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|P15880|RS2_HUMAN,LSIVPVR,2,,0,L,cond_B,4,4,618046500.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|P27616|PUR7_YEAST,TELDGILPLVAR,2,,0,L,cond_A,3,3,435745100.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.mzML
+sp|P26641|EF1G_HUMAN,STFVLDEFK,2,,0,L,cond_B,4,4,1932950000.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|O15498|YKT6_HUMAN,VAFTLLEK,2,,0,L,cond_B,5,5,38799580.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML
+sp|P38088|SYG_YEAST,YDIGNPVTGETLESPR,2,,0,L,cond_B,4,4,186166200.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|P49589|SYCC_HUMAN,VSEYVPEIVNFVQK,3,,0,L,cond_B,5,5,26276280.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML
+sp|P38764|RPN1_YEAST,VGQAVETVGQAGRPK,2,,0,L,cond_A,3,3,22935790.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.mzML
+sp|P28482|MK01_HUMAN,VADPDHDHTGFLTEYVATR,4,,0,L,cond_B,4,4,230327400.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|P23381|SYWC_HUMAN,MSASDPNSSIFLTDTAK,2,,0,L,cond_A,3,3,346003800.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.mzML
+sp|P38701|RS20_YEAST,YIDLEAPVQIVK,3,,0,L,cond_A,1,1,49868200.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|P16120|THRC_YEAST,ADVELVK,2,,0,L,cond_B,6,6,3600227000.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML
+sp|P09110|THIK_HUMAN,QDTFALASQQK,2,,0,L,cond_A,3,3,84843690.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.mzML
+sp|P30044|PRDX5_HUMAN,THLPGFVEQAEALK,3,,0,L,cond_B,5,5,286970800.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML
+sp|P35197|GCS1_YEAST,NFNGNAEDSSTAGNTTHTEYQK,3,,0,L,cond_A,1,1,30576350.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|Q99567|NUP88_HUMAN,NQSPTEAEKPASSSLPSSPPPQLLTR,3,,0,L,cond_B,6,6,122309400.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML
+sp|P0A6G7|CLPP_ECOLI,FLSAPEAVEYGLVDSILTHR,3,,0,L,cond_A,3,3,97005950.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.mzML
+sp|Q14690|RRP5_HUMAN,VVILNVDLLK,2,,0,L,cond_B,5,5,15405070.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML
+sp|P0A6P1|EFTS_ECOLI,VAALEGDVLGSYQHGAR,2,,0,L,cond_B,5,5,68910670.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML
+sp|O43583|DENR_HUMAN,QEAGISEGQGTAGEEEEK,2,,0,L,cond_B,6,6,74275150.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML
+sp|Q6PJ69|TRI65_HUMAN,ASLEVTQQQATQAEGQLLELR,3,,0,L,cond_A,2,2,14652530.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML
+sp|O15397|IPO8_HUMAN,ETENDDVTNVIQK,2,,0,L,cond_A,3,3,41540000.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.mzML
+sp|P0A9G6|ACEA_ECOLI,ADQIQWSAGIEPGDPR,2,,0,L,cond_B,5,5,106234000.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML
+sp|Q15393|SF3B3_HUMAN,MQGQEAVLAMSSR,2,,0,L,cond_B,6,6,285025400.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML
+sp|P07814|SYEP_HUMAN,EAPC(Carbamidomethyl)VLIYIPDGHTK,2,,0,L,cond_A,3,3,49156330.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.mzML
+sp|Q9H9A7|RMI1_HUMAN,DLEHPLLPDGILEIPK,3,,0,L,cond_B,4,4,13267190.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|O94880|PHF14_HUMAN,LNIPAILR,2,,0,L,cond_B,6,6,18349690.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML
+sp|Q08J23|NSUN2_HUMAN,LAQEGIYTLYPFINSR,3,,0,L,cond_B,5,5,41253360.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML
+sp|P32929|CGL_HUMAN,VIYPGLPSHPQHELVK,3,,0,L,cond_B,6,6,96001410.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML
+sp|P0AGE9|SUCD_ECOLI,SGTLTYEAVK,2,,0,L,cond_B,4,4,131380700.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|O15355|PPM1G_HUMAN,GTEAGQVGEPGIPTGEAGPSC(Carbamidomethyl)SSASDK,2,,0,L,cond_A,2,2,32767620.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML
+sp|Q99614|TTC1_HUMAN,SNEDVNSSELDEEYLIELEK,2,,0,L,cond_B,4,4,44210590.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|P62316|SMD2_HUMAN,REEEEFNTGPLSVLTQSVK,2,,0,L,cond_A,3,3,216058000.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.mzML
+sp|O14828|SCAM3_HUMAN,ELQHAALGGTATR,2,,0,L,cond_B,4,4,8710374.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|Q9BX10|GTPB2_HUMAN,VGADITVLR,2,,0,L,cond_B,5,5,30394810.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML
+sp|P31539|HS104_YEAST,YAIDMTEQAR,2,,0,L,cond_A,2,2,309601800.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML
+sp|Q08723|RPN8_YEAST,VTNSFALPFEEDEK,2,,0,L,cond_A,1,1,53689080.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|P53250|TWF1_YEAST,SFEELVQLASQER,2,,0,L,cond_B,6,6,17220740.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML
+sp|P14922|CYC8_YEAST,ANEIYFR,2,,0,L,cond_A,1,1,19421460.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|Q9UJV9|DDX41_HUMAN,GVEAVAIHGGK,2,,0,L,cond_B,4,4,12814100.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|Q99856|ARI3A_HUMAN,MALVADEQQR,2,,0,L,cond_A,1,1,207930200.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|Q9Y613|FHOD1_HUMAN,FSGVAGEAPSNPSVPVAVSSGPGR,2,,0,L,cond_B,4,4,14475940.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|P46778|RL21_HUMAN,VYNVTQHAVGIVVNK,3,,0,L,cond_A,1,1,817014100.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|P31939|PUR9_HUMAN,NLTALGLNLVASGGTAK,2,,0,L,cond_B,6,6,409515000.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML
+sp|P09105|HBAT_HUMAN,LGSNVGVYTTEALER,2,,0,L,cond_A,2,2,47899360.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML
+sp|Q96T37|RBM15_HUMAN,SSGAASSAPGGGDGAEYK,2,,0,L,cond_B,5,5,20204150.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML
+sp|Q96G03|PGM2_HUMAN,MNDLTIIQTTQGFC(Carbamidomethyl)R,2,,0,L,cond_B,4,4,44245960.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|Q9BXP5|SRRT_HUMAN,EEEWEKPK,2,,0,L,cond_B,4,4,25720120.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|P42704|LPPRC_HUMAN,MEEANIQPNR,2,,0,L,cond_B,4,4,104089900.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|Q86V81|THOC4_HUMAN,SLGTADVHFER,3,,0,L,cond_B,4,4,527266100.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML
+sp|P22336|RFA1_YEAST,EEDPNEFTK,2,,0,L,cond_A,1,1,20258070.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML
+sp|Cont_Q7SIH1|A2MG_BOVIN,NEESLVFVQTDKPIYKPEQTVK,4,,0,L,cond_A,2,2,120535100.0,LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML
+sp|Q8WUM4|PDC6I_HUMAN,DTIVLLC(Carbamidomethyl)KPEPELNAAIPSANPAK,2,,0,L,cond_B,5,5,27655920.0,LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML

test/test_module_dda_quant.py

@@ -28,6 +28,7 @@
     "ProlineStudio": os.path.join(TESTDATA_DIR, "Proline_DDA_quan_ions_subset.xlsx"),
     "MSAngel": os.path.join(TESTDATA_DIR, "MSAngel_DDA_quan_ions_subset.xlsx"),
     "i2MassChroQ": os.path.join(TESTDATA_DIR, "i2MassChroQ_DDA_quant_ions_test_new_random_subset.tsv"),
+    "quantms": os.path.join(TESTDATA_DIR, "sample_dda_quantms.sdrf_openms_design_msstats_in.csv"),
 }