IDEAL-Q is an automated analysis tool for label-free quantitative proteomics. It accepts mzXML raw data format and Mascot xml and ProtXML/PepXML for identification result. IDEAL-Q uses an elution time prediction and peak alignment algorithms to quantify peptides across different LC-MS runs and increase quantitation coverage. Furthermore, the tool adopts an stringent validation step on Signal-to-noise ratio, Charge state, Isotopic distribution (SCI validation) to ensure quantitation accuracy. IDEAL-Q provides variously optional normalization tools for flexible workflow design such as addition of fractionation strategies and multiple spiked internal standards.

Important Notices

  • To run IDEAL-Q, raw data in mzXML format and protein identification result are required. (User Guide for Preparing Input Data)
  • Parameter Setting Introduction (pdf)
  • Options for determination of protein ratio (pdf)
  • For users who are using Windows Vista or Windows 7, please make sure first to execute the program in "Run as administrator" mode. (pdf)
  • Currently, IDEAL-Q does not accept mzXML files in the binary encoding precision of 64.
    Please use the binary encoding precision of 32 when converting data to mzXML files.
The recommended system environment is:
  1. Operating System: Windows XP, Windows 7 or higher
  2. CPU: Intel ® CPU 2.40 GHz
  3. HDD: 50GB or more free space
  4. Memory: 4GB or more
  5. Microsoft .Net Framework: .Net 4.0 or higher
  6. Screen Resolution: 1024*768 or higher


Chih-Chiang Tsou et al. , IDEAL-Q: An automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation Molecular & Cellular Proteomics, Vol. 9, pp. 131-144, 2010.

Update Information


V1.065 is available

  • Add a new parser to parse the scan titles elaborated from Thermo Scientific.

V1.064 is available

  • Add a new parser to parse the scan titles elaborated from Bruker DataAnalysis 4.1.

V1.063 is available

  • Users do NOT have to request for activation key.

V1.062 is available

  • Fix the bug for adopting Linear Regression Normalization (If you have used this function for adjusting your result, please update the program and reapply the function to get correct adjustment)

V1.061 is available

  • Support mzML standard spectral format (So far only the file from AB SCIEX TripleTOF 5600 is tested, we are welcome to providing test sample mzML files for other instruments)
  • Fix the bugs for showing peptide abundance result

V1.051 is available

  • Fix the problem of underestimating S/N for centroid data

V1.050 is available

  • Fix the bugs for parsing PepXML result of PepArML that some modified peptides were not successfully parsed.
  • Merry X'mas and Happy New Year

V1.048 is available

  • Fix the bugs of peak processing in v1.047

V1.047 is available

  • Fix PepXML loading bugs for PepArML's result

V1.046 is available

  • Add an option in "Apply changes and recalculate ratio" to report estimated protein abundance for each sample using top N high abundances peptides.
  • Accelerate the processing of showing tables after applying re-quantitation module.

V1.035 is available

  • Add performing B-spline for signal smoothing before peak detection. B-spline better estimates peak shape for centroid-converted data.
  • Change format of description for peptide's modification site
    • Mascot:
    • Previous format: Sequence (YSPSQNSPIHHIPSR), Site(0.300000200000000.0),
    • Change to : Site (Y[Phospho (Y)]SPSQNS[Phospho (ST)]PIHHIPSR)
    • PeptideProphet /ProteinProphet
    • Previous format: Sequence (GILLASR), Site (n[43]GILLASR[166] )
    • Change to: Site ([43(N-term)]GILLASR[166(R)])

V1.025 is available

  • Support Mascot XML format generated from using Bruker instrument. More details please check Data Preparation User Manual

V1.024 is available

  • Added features:
    • Parameters of signal processing can be adjusted according to different instrument characteristics. Two default parameter sets are available for a. QTOF/QSTAR and b. Orbitrap/FT-ICR. The default parameters were empirically tuned, might be not optimal, please advise us if you have a better setting, suggestions, or advices.
    • Options of different strategies to determine protein ratio, a. by the peptide ratios after outlier elimination, and b. by the ratios of top-N high abundance peptides.
    • Options for the stringency of determining a peptide abundance, a. by setting a minimum number of replicates having the peptide identified, b. by setting a minimum proportion of replicates where the peptide is successfully quantified and passed the SCI validation.

V1.013 is available


V1.012is available

  • Bug fixed (bug that after internal standard normalization is adopted, ratios weren't updated)

V1.011 is available

  • Bugs fixed (bugs on generation of commonly expressed protein list)

V1.01 is available

  • Improved requantitation module (processes in multi-threading manner)
  • Added function to filter proteins with specified expression pattern. (Added in "functions"
  • Added function to filter peptides with specified modification. (Added in "functions"
  • Added option in peptide list to select/deselect peptides used for protein ratio calculation
  • Remove expiration date check

V1.000 is available

  • Added test functions to support MS1 data acquired by centroid mode, increased No. of threading for multi-core machine. Added option to save Elution 3D, XIC, PIMS images while processing quantitation.

V 0.993 is available

  • Fixed bugs of parsing PepXML files

V 0.990 is available

  • The added functions are viewing annotated MS/MS spectrum and result exporting in EXCEL .xls format

Publications which use IDEAL-Q