Project:
* Name: ProteobenchModule2_DDA
* Description: 
* Created at: 2025-01-03 19:05:59
+ Proteobench_PEAKS
  Description: 
  Created at: 2025-01-03 19:05:59

  Data Refinement Parameters:
    Skip Preprocessing: false
    Mass Correction: true
    Chimera Association: true

  De Novo Parameters:
    Precursor Mass Error Tolerance: 10.00ppm
    Fragment Mass Error Tolerance: 0.02Da
    Enzyme: Trypsin
    Max Variable PTM per Peptide: 2
    Fixed Modifications: 
    - Carbamidomethylation (+57.02)
    Variable Modifications: 
    - Acetylation (Protein N-term) (+42.01)
    - Oxidation (M) (+15.99)

  Database Search Parameters:
    Precursor Mass Error Tolerance: 10.00ppm
    Fragment Mass Error Tolerance: 0.02Da
    Enzyme: Trypsin
    Max Missed Cleavage: 2
    Digest Mode: Specific
    Peptide Length Range: 7 - 50
    Max Variable PTM per Peptide: 2
    Fixed Modifications: 
    - Carbamidomethylation (+57.02)
    Variable Modifications: 
    - Acetylation (Protein N-term) (+42.01)
    - Oxidation (M) (+15.99)
    Database: 
    - ProteobenchModule2
      - Taxonomy: all species
      - Searched Entries: 31887
    Deep Learning Boost: Yes
    Report Filter: 
      PSM -10LgP >= 20.0
      Proteins -10LgP >= 15.0
      Proteins Unique Peptides >= 1
      De Novo Only ALC >= 50.0%
      De Novo Only Tag Sharing: Disabled
      De Novo Only Fully Matched: No
      Confident Amino Acid Threshold: 2.00%

  LFQ Parameters:
    Quantification Type: Label Free Quantification
    LFQ Method: Identification Directed Quantification
    Mass Error Tolerance: 10.00ppm
    Retention Time Shift Tolerance: Auto detected
    Feature Intensity >= 100000.0
    Retention Time Range: [0.0 - Max]
    Base Sample: Sample 1
    Peptide Feature Filter:
      Avg Area >= 0.0
      Quality >= 0.0
      Charge between: [1 - 5]
      Peptide ID Count >= 0 per group
      Detected in at least 0 samples per group
      Use in Group Coefficient of Variation Filter: No
    Protein:
      Significance Method: ANOVA
      Modified Form Exclusion: Yes
      Remove Outlier: Yes
      Use Top 3 Peptide
      Significance >= 0.0
      Fold Change between: [1.0 - 64.0]
      Has at least 1 Used Peptide
    Samples: 6 Samples in 6 Groups
      Group 1: 
        Sample 1;
      Group 2: 
        Sample 2;
      Group 3: 
        Sample 3;
      Group 4: 
        Sample 4;
      Group 5: 
        Sample 5;
      Group 6: 
        Sample 6;
    Normalization Method: Use TIC

  QC Parameters:
    Corresponding Result: LFQ
    Number Of Samples: 6
    Control Sample: Sample 1
    Acceptance Tolerance: 10.0%
    QC Attributes:
        # MS1
        # MS2
        MS2/MS1 Rate
        # Features
        Full Width (min)
        FWHM (sec)
        BPC
        TIC Correlation
        # PSM
        # MS2 Scans
        # Identified Features
        # Peptides
        # Sequences
        # Protein Groups
        # Top Proteins
        # All Proteins
        ID Rate
        # PSM/# Peptides
        MS1 Error Mean (S.D)
        MS2 Error Mean (S.D)
        Missed Cleavage Ratio
        Enzyme Specificity Ratio
        Quantified Peptides
        Quantified Protein Groups
        Quantified Features
