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New QCQuan Job

Job name:

 


Design of Experiment (DoE) file:

  To create a DoE file, click here.


Quick Start (short)

When in doubt, download example input data / output data / report.

  1. Correctly format your (peptide-spectrum matches) PSMs in .txt, .csv/tsv or .xlsx files. The 'Sequence', 'Master Protein Accession' and quantification columns (see DoE step) are absolutely required (bold in image), others (example file for TMT 6-plex) are optional but add functionality.
    These should be in separate files: one per LC-MS/MS run.
    For Proteome Discoverer: export PSM files. For other software, simply use a wrapper file.
    QCQuan example PSM file

    Example PSM file. TMT 6-plex quantification columns are called '126' through '131', but you can use any number and name them anything you like (specify names in DoE step).

  2. Create a 'design of experiment' (DoE) file here.
    Give names to your different LC-MS/MS runs and groups (biological conditions), and specify the names of the quantification labels as they appear in the headers of your PSM files.
  3. Upload the DoE file in the "New Job" form.
  4. Fill out the Job Settings form.
    In case you wish to include 'shared peptides', check the box under "Advanced settings". QCQuan will run automatically run once excluding shared peptides and once including them.
    In case you used multiple search engines to generate PSMs, the information from the Master engine will be preferred over that of the Slave(s).

  5. Press "Submit job" and save the job ID, just in case (use it in the "Job Lookup" page).
    When the job is done, the Job Info page will provide you with download links for the report file as well a .zip file.

Quick Start

This step-by-step tutorial will let QCQuan analyze your labeled LC-MS/MS proteomics differential expression experiment and provide you with output files on both the non-redundant-peptide level as well as protein level, including a quality control and differential expression report in PDF format.

  1. You'll need the peptide-spectrum matches in .txt, .csv/tsv or .xlsx format. These should be in separate files: one per LC-MS/MS run. Please verify that all required data 'observables' or 'columns' are present in your PSM files and have valid contents, especially if you're not using files generated by Proteome Discoverer (PD).
    The required columns should have these exact names and {possible values}:
    • Sequence: {string} the peptide sequence.
    • Master Protein Accessions: {string;string;...} accession numbers of the proteins associated with a PSM, separated by semi-colons.
    • First Scan: {integer} identifier for the MS scan in which the peptide was detected. If you don't have such a column, just create one with all values set to a unique integer. PSMs detected by multiple times by different PSM Algorithms should have the same value.
    • (???): {string} names of the reporter labels or channel names you provided in the DoE file.
    If this is not the case, simply create a text file (wrapper) with on each line YOUR_NAME for the observable, as well as OUR_NAME, separated by a TAB character.
    If you have any additional columns or observables you would like QCQuan to use, please refer to the complete set of compatible column names.
  2. You'll also need a 'design of experiment' (DoE) file. Create one by going to the "DoE Creator" and following the instructions. You'll have to give names to your different 'LC-MS/MS runs', specify which biological/chemical conditions were used in which MS run, and indicate for each MS run which 'channels' or 'reporter labels' (as they appear in the headers of your PSM files) belong to which of those conditions. At the end of the procedure, you can download the DoE file you need. This file can easily be modified with a text editor if you want to correct a mistake, or quickly generate your own new DoE file.
  3. Got your PSM files and DoE file? Great, in the "New Job" form, choose a job name. Then, upload your DoE file.
  4. Fill out the Job Settings form. Please remark:
    • If you are not using Proteome Discoverer for generating PSM files, you will be warned to provide the wrapper file(s) you (should have) created in the PSM file verification step by uploading one under the "Advanced" button for each PSM data file.
    • In case you used multiple search engines to generate PSMs, the information from the Master engine will be preferred over that of the Slave(s).
    • QCQuan will refrain from using 'shared peptides' (peptides that may correspond to multiple proteins) unless you check the box under "Advanced settings". In that case a second analysis will be done for the assuming that all proteins make (full) use of every peptide they share with another protein.
  5. Press "Submit job" and make sure you land on the "Job Info" page which states your job is running. If you didn't provide an e-mail address, be sure to copy and save the job ID. You can use your job ID to retrieve your job information from the "Job Lookup" page in case you close your Job Info page.
  6. As soon as the job is done, the Job Info page will provide you with download links for the report file as well a .zip file containing:
    • normalized data on the non-redundant, modified peptide level (1 file per LC-MS/MS run)
    • differential expression analysis on the protein level (in 1 comprehensive file as well as split out in 1 file per condition)
Found a bug? Send us the details and job ID at qcquan@vito.be.