Participants Laboratories of Interfaculty Mass Spectrometry Centre - Phase 1 (Jan 2011 - Dec. 2012)

Analytical Biochemistry

Head: Rainer Bischoff
Staff: Peter Horvatovich, Natalia Govorukhina, Jos Herman
Location: Building 3211, Antonius Deusinglaan 1, 9713 AV Groningen

Main MS Equipments

• Agilent 6510 QTOF equipped with chipcube and Agilent 1200 HPLC system equipped with nano and capillary pumps and thermostated autosampler, acquisition software: MassHunter? B02.00
  
• Agilent 1100 series LC/MSD-SL iontrap with chipcube and Agilent 1100 HPLC system equipped with nano and capillary pumps and thermostated autosampler, acquisition software: Chemstation B01.03 (for LC) and LC/MSD Trap Software and Data Analyst 3.5 (for MS)
  
• Agilent 1100 series LC/MSD-SL iontrap with Agilent 1100 HPLC system equipped with nano and capillary pumps and thermostated autosampler, acquisition software: Chemstation B01.03 (for LC) and LC/MSD Trap Software and Data Analyst 3.5 (for MS)
  
• Agilent 6410 Triple quad LC-MS equipped with chipcube, Prospect 2 switching valve system & autosampler, and Agilent 1200 HPLC system equipped with nano and capillary pumps and thermostated autosampler, acquisition software: MassHunter? B06.01
  

Contact person: Jos Hermans

Main Bioinformatics tools

Commercial

Software: Phenyx 2.6.2 peptide and protein identification platform running on dual Xeon server (8 cores) with 16 GB RAM
Availability: ​online

In house developed

Software: ​COW-CODA, ​PTW-CODA, DTW-CODA LC-MS time alignment algorithms using raw LC-MS data
Availability: ​source code is available

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Software: msComapre is a framework for quantitative processing of label-free LC-MS data including feature extraction/quantification and feature matching modules from popular opensource programs such as ​TOPP OpenMS, ​MZmine and ​SuperHirn.
Availability: ​source code with example data, parameters set and ​online processing service in NBIC Galaxy is available

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Software: ​Warp2D tool performing time alignment of LC-MS peak lists
Availability: ​online processing service is available ​(ref)

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Software: several discriminating compound selection methods such as t-test, Mann-Whitney-Wilcoxon-test, Nearest Shrunken Centroid, linear Support Vector Machine – Recursive Features Elimination, Principal Component Discriminant Analysis and Partial Least Squares Discriminant Analysis
Availability: source code available in-house

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Software: Data Analysis Framework (DAF) can be used to integrate data processing tools, design workflows and provides data processing services using the Dutch Life Science Grid
Availability: under development

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Contact person: Peter Horvatovich