= Participants Laboratories of Interfaculty Mass Spectrometry Centre - Phase 1 (Jan 2011 - Dec. 2012)= == Analytical Biochemistry == '''Head''': Rainer Bischoff[[BR]] '''Staff''': Peter Horvatovich, Natalia Govorukhina, Jos Herman[[BR]] '''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[[BR]] * 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)[[BR]] * 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)[[BR]] * 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[[BR]] Contact person: [mailto:j.h.hermans@rug.nl Jos Hermans][[BR]] === 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[[BR]] '''Availability''': [http://129.125.137.24:8080/pwi/login/login_local.jsp online][[BR]] ==== In house developed ==== '''Software''': [http://www.ncbi.nlm.nih.gov/pubmed/18715018 COW-CODA], [http://www.ncbi.nlm.nih.gov/pubmed/20070124 PTW-CODA, DTW-CODA] LC-MS time alignment algorithms using raw LC-MS data[[BR]] '''Availability''': [https://trac.nbic.nl/lcms_time_alignment_algorithms source code is available][[BR]] ---- '''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 [http://www.ncbi.nlm.nih.gov/pubmed/17237091 TOPP OpenMS], [http://www.ncbi.nlm.nih.gov/pubmed/16403790 MZmine] and [http://www.ncbi.nlm.nih.gov/pubmed/17726677 SuperHirn].[[BR]] '''Availability''': [https://trac.nbic.nl/mscompare/ source code with example data, parameters set] and [http://galaxy.nbic.nl/galaxy/ online processing service in NBIC Galaxy] is available[[BR]] ---- '''Software''': [http://www.ncbi.nlm.nih.gov/pubmed/18396914 Warp2D] tool performing time alignment of LC-MS peak lists[[BR]] '''Availability''': [http://www.nbpp.nl/warp2d.html online processing service is available] [http://www.ncbi.nlm.nih.gov/pubmed/21349866 (ref)][[BR]] ---- '''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[[BR]] '''Availability''': source code available in-house[[BR]] ---- '''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[[BR]] '''Availability''': under development[[BR]] ---- Contact person: [mailto:p.l.horvatovich@rug.nl Peter Horvatovich][[BR]]