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MPI für Biochemie  

Protein Analysis
Friedrich Lottspeich

ICPLQuant

 

ICPLQuant is a quantitative proteomics software package (freeware) designed to automatically analyze large mass spectrometric data sets from ICPL based proteomics experiments.


ICPLQuant has been developed to accurately quantify ICPL-labeled peptides on the MS level during LC-MALDI and peptide mass fingerprint experiments.  The tool is able to generate a list of differentially regulated peptide precursors for subsequent MS/MS experiments, minimizing time consuming acquisition and interpretation of MS/MS data. ICPLQuant is based on two independent units. Unit 1 performs ICPL multiplex detection and quantification and proposes peptides to be identified by MS/MS. Unit 2 combines MASCOT MS/MS protein identification with the quantitative data and produces a protein/peptide list with all the relevant information accessible for further data mining.

 

ICPL-ESIQuant has been developed to accurately quantify ICPL-labeled peptides on the MS level in ESI-MS runs.  Raw MS data files have to be converted into the commonly accepted mzXML file format before running ICPL-ESIQuant (see ICPL-ESIQuant  tutorial).
            

Features:

 

  • Peak picking and deisotoping of MS1 raw peak data
  • Recognition of ICPL multiplets (even incomplete ones) in medium complex spectra
  • Quantification of all ICPL multiplets correcting for isotopic impurities of reagents.
  • Preparation of a precursor list containing peptides with user defined regulation factors
     for MS/MS analysis.
  • MASCOT .dat file parser
  • Merging of quantification  information and identification information
  • Protein and peptide output lists in open formats, easily accessible for data mining programs
  • Support of ICPL quantitation.
  • Visual display of LC profiles.
  • Visual display of 2D peak maps.
  • Computation of protein quantitation ratios (with standard deviation estimation).
  • Export of results to files, Excel and to databases.
  • Support of data formats for 2 different MALDI mass spectrometers : Applied Biosystems 4700/4800 TOF/TOF; Bruker Ultraflex II.
  • Support for ESI:  vendor Thermo Electron/Finnigan; Orbitrap; software package XCalibur (.raw file).
     
EsiQuant_Chromato        ESIQuant_PeakMap

Fig. 1: ICPL quadruplet TIC of ovalbumin (ratio of 1:1:2:5)         Fig. 2: Peak map of ICPL-ESIQuant (detected ICPL multiplets in red)        


References

Brunner A, Keidel E, Dosch D, Kellermann J, Lottspeich F. ICPLQuant – a software for non-isobaric isotope labeling proteomics. Proteomics 10 (2010), 315-323
 

License Agreement

Please read carefully the ICPLQuant and ICPL-ESIQuant Freeware Software License Agreement before downloading or using the software.

 

 

News,  file releases

2011-09-25 ICPL-ESIQuant version 2.0 now available!
                   

2010-02-26 ICPL-ESIQuant version 1.1.3 now available!
                   
This version is more stable than 1.0 and 1.1 and is able to process greater data amounts.

2010-01-27 New Video Tutorials for ICPLQuant and ICPL-ESIQuant are available!
                   
Windows media Player is needed to join the videos.

2010-01-14. Video Tutorials for ICPL-ESIQuant and ICPLQuant are provided.
                   
Windows media Player is needed to join the videos.
A voice supported version of the videos will follow.

 

2009-12-23. ICPL-ESIQuant, Version 1.0 for ORBITRAP data is available in its first version.

RAW files have to be deconvoluted and deisotoped by the QualBrowser software included in the Xcalibur software and converted into mzXML format before
running ICPL-ESIQuant (see ICPL-ESIQuant  tutorial).

2009-12-15. New Release, Version 1.61

  • A new MASCOT DAT Parser was implemented (http://www.matrixscience.com/msparser.html)
  • The minimum compound size (in how many fractions must a mass peak appear to be accepted as a compound?) is now adjustable in the SETTINGS section

2009-11-16. The ICPLQuant paper "ICPLQuant – a software for non-isobaric isotope labeling proteomics" is accepted for publication in Proteomics (DOI 10.1002/pmic.200900174)

2009-10-12. We are working on a Orbitrap version of ICPLQuant . Users who are interested in the software, please contact brunner@biochem.mpg.de

 

Tutorials:

ICPLQuant tutorial (Microsoft Word)

ICPL-ESIQuant tutorial (Microsoft Word)

Video tutorials are available here.

 

Software download:

ICPLQuant

ICPL-ESIQuant

 

Developer information

ICPLQuant  and ICPL-ESIQuant are written in JAVA and can be used platform independent. The runtime is installed by default in later versions of Windows.

Contact

Please feel free to contact our Bioinformatics group!

email: brunner@biochem.mpg.de