User Guide

• Installation
  • Git repository
  • Dependencies
• Output Data
  • Calibration Data
  • Quantification Data
• Example Usage
  • Calibration
  • INQuant
  • Combined calibration and quantification:

The status file

The status file will always be output by the INQuant, and this contains information about the script run, time usage, the user specifications and the output of the run.

Status file example

Status for script run for experiment: example_data_unfiltered

Script purpose:
Example runthrough of INQuant with auto generated example data

Script started at: 2025-04-29 16:13:38

Time spent on entire script: 1.62 seconds
- Time elapsed for time-flags called underway in the script:
-- Finished running mzml file no. 1: 1.081 second(s)
-- Finished running mzml file no. 2: 1.309 second(s)
-- Finished running mzml file no. 3: 1.537 second(s)
-- Normalization by median: 1.598 second(s)
-- Loading proteome file: 1.599 second(s)
-- Running protein alignment: 1.604 second(s)
-- Finished protein alignment: 1.612 second(s)
-- Creating protein table: 1.612 second(s)
-- Processed proteins, starting grouping: 1.613 second(s)
-- Found master proteins: 1.613 second(s)
-- Grouped proteins: 1.614 second(s)

Mass charge tolerance: 50 ppm
Confidence filter: None
Intensity tolerance: 20.0%
Retention time window tolerance: 1.0%
Empty values in output files: 
Ran MBR: True
MBR tolerance: 90.0%
Normalization by median
Protein quantification method: mean
Number of peptides per protein (N) for quantification: 5

Files loaded in this script (excluding mzML):
-- Predictions file: predictions.csv
---- Line count: 2892
-- Proteome file: example_proteome.fasta
---- Line count: 614

mzML files loaded in running of this script:
ID: 1, filename: file_1
ID: 2, filename: file_2
ID: 3, filename: file_3

Noise calculations in this script based on MS2 lowest 5.0% intensities:
ID: 1, noise: 3098.363525390625
ID: 2, noise: 3100.0302734375
ID: 3, noise: 3094.64013671875

In this script, the following data files were created:
-- Protein table: example_data_unfiltered_protein_table.csv
---- Line count: 52
-- Peptide table: example_data_unfiltered_peptide_table.csv
---- Line count: 126
-- PSM table: example_data_unfiltered_psm_table.csv
---- Line count: 178