Project:
* Name: PEAKSv13_DDA_Orbitrap_QEHFX
* Description: 
* Project Version: 13 20250520
* Created at: 2025-05-27 09:28:41
+ TIC_normalisation
  Description: 
  PEAKS Version: 13 20250520
  Created at: 2025-05-27 17:37:01

  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: 1
    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 between: 7, 45
    Max Variable PTM per Peptide: 1
    Fixed Modifications: 
    - Carbamidomethylation (+57.02)
    Variable Modifications: 
    - Acetylation (Protein N-term) (+42.01)
    - Oxidation (M) (+15.99)
    Database: 
    - Proteobench
      - Taxonomy: all species
      - Searched Entries: 31889
    Deep Learning Boost: Yes
    Report Filter: 
      PSM FDR: 1.0%
      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 >= 0.0
    Retention Time Range: [0.0 - Max]
    Base Sample: Average
    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 2 Groups
      Group 1: 
        LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01;LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02;LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03;
      Group 2: 
        LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01;LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02;LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03;
    Normalization Method: Use TIC

