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Proprietary software for MS analysis

The software described below is dedicated for relative quantiative analysis of protein expression with label-free or iTRAQ (Isobaric Tag for Relative and Absolute Quantitation) methods.

Software for qualitative analysis:

  • MScan - dedicated for qualitative analysis of protein/peptide lists generated by the Mascot search engine. An additional feature is the export of data in a format suitable for further quantitative analysis, both with table isotope labeling and label-free methods.
  • DatViewer - the pre-processing software for collections of fragmentation spectra intended for identification of proteins and peptides present in samples measured with MS. The goal of pre-processing procedures is maximizing the number of reliable identifications and optimizing the time of database search performed by the identification software.
  • Decoy - this software allows to prepare target/decoy databases of protein sequences, used for the estimation of false positive rate in the results of protein/peptide identification.

Software for label-free quantification:

  • MSconvert - the software allows for conversion of raw LC-MS spectra into universal 2D heatmaps, independent from the vendor or type of MS instrument. The heatmaps can be used for quantification of peptides/proteins present in the samples.
  • MSparky - this software is capable of extracting quantitative values from the LC-MS spectra of peptides, using 2D heatmap representation of LC-MS data and theoretical models of isotopic envelopes from peptide ions. This process is essential for the label-free analysis.  

Software for statistical analysis of MS data:

  • Diffprot - software dedicated to the statistical analysis of the quantitative values derived from proteomic experiments performed with label-free or iTRAQ methods. This tool is particularly efficient with small number of samples and very robust in terms of protein identification errors.
  • MStat - this software implements the algorithms for visualization, normalization and mutlidimensional statistical analysis and classification of quantitative dara derived from MS. It can be used for analysis of both proteomic and peptidomic data derived from stable isotope labeling-based or label-free data. 


  •  M. Bakun, J. Karczmarski, J. Poznański, T. Rubel, M. Rózga, A. Malinowska, D. Sands, E. Hennig, J. Olędzki, J. Ostrowski, M. Dadlez: An integrated LC-ESI-MS platform for quantitation of serum peptide ladders. Application for colon carcinoma study. Proteomics - Clinical Applications, 2009, 8, 932-946 
  • J. Sikora, J. Towpik, D. Graczyk, M. Kistowski, T. Rubel, J. Poznanski, J. Langridge, C. Hughes, M. Dadlez, M. Boguta: Yeast prion [PSI+] lowers the levels of mitochondrial prohibitins. Biochim Biophys Acta - Molecular Cell Research, 2009, 1793 (11), 1703-1709 
  • M. Mikula, P. Gaj, K. Dzwonek, T. Rubel, J. Karczmarski, A. Paziewska, A. Dzwonek, P. Bragoszewski, M. Dadlez, J. Ostrowski: Comprehensive analysis of the palindromic motif TCTCGCGAGA, a regulatory element of the HNRNPK promoter. DNA Research, 2010, 17 (4), 245-260

  • Mikula, T. Rubel, J. Karczmarski, K. Goryca, M. Dadlez J. Ostrowski: Integrating proteomic and transcriptomic high throughput surveys for search of new biomarkers of colon tumors. Functional & Integrative Genomics

  • A. Malinowska, M. Kistowski, M. Bakun, T. Rubel, M. Tkaczyk, J. Mierzejewska, M. Dadlez: Diffprot—software for non-parametric statistical analysis of differential proteomics data. Journal of proteomics, 2012, 75(13), 4062-4073.



  •  mgr Michał Kistowski (IBB PAN)
  •  mgr inż. Lech Raczyński (IRE PW)
  •  dr inż. Tymon Rubel (IRE PW)


  •  mgr Magdalena Bakun (IBB PAN)
  •  dr Jakub Karczmarski (COI Warszawa)
  •  mgr Agata Malinowska (IBB PAN)
  •  dr Jacek Sikora (IBB PAN)
  •  dr Magdalena Skrzypczak (COI Warszawa)


 Software development was financed from the R&D grant 0612/R/P01/2007/03 (R13 010 03) - "Nowe narzędzia do analizy danych spektrometrii mas w zastosowaniu do diagnostyki medycznej" (New tools for the analysis of mass spectrometry data in medical diagnostics).