New QCQuan Job

Job name:


Design of Experiment (DoE) file:

  To create a DoE file, click here.

What does QCQuan do?

QCQuan is for "separating the wheat from the chaff", i.e. quickly assessing whether or not your experiment(s) produced useful information. The differential expression analysis is based on simple statistical procedures, but any protein found to be differential using QCQuan should also be found differential by other, more complex methods.

QCQuan analyzes your labeled LC-MS/MS proteomics differential expression experiment and provides you with (normalized) 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.

QCQuan is for separating the wheat from the chaff.

Initial QCQuan publication: VAN HOUTVEN, Joris, et al. QCQuan: a web tool for the automated assessment of protein expression and data quality of labeled mass spectrometry experiments. Journal of proteome research, 2019.
Initial CONSTANd publicaton: Maes, E., Hadiwikarta, W. W., Mertens, I., Baggerman, G., Hooyberghs, J., & Valkenborg, D. (2016). CONSTANd: A normalization method for isobaric labeled spectra by constrained optimization. Molecular & Cellular Proteomics, 15(8), 2779-2790.

I just want CONSTANd normalization.

Then simply 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 have 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.
Found a bug? Send us the details and job ID at qcquan@vito.be.