1. Collecting and mining mass spectrometry quality control data Wout Bittremieux, Pieter Kelchtermans, Dirk Valkenborg, Lennart Martens, Bart Goethals, Kris Laukens

2. Overview Mass spectrometry Quality control -qcML -jqcML Collecting and mining

3. Mass spectrometry ion sourcedetector generalized mass spectrometer ion selector fragmentation fragment mass analyzer protein digestion peptide separation output protein sample peptide sample spectra

4. Quality control Minimize variability Experimental design Bioinformatics workflow Tabb, D. L. et al. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. Journal of Proteome Research 9, 761–776 (2009).

5. Quality control Assess variability QC metrics Pichler, P. et al. SIMPATIQCO: A server-based software suite which facilitates monitoring the time course of LC-MS performance metrics. Journal of Proteome Research 11, 5540– 5547 (2012).

6. Quality control Assess variability QC metrics Limiting factors Compatibility Variability

7. qcML Compatibility -XML-based file format -Relational database Variability: controlled vocabularies

8. jqcML Open-source Java API Complete object model Data from several sources jqcML object model qcML file qcDB RDBMS JAXBJPA QcMLReader / QcMLWriter

9. Collecting and mining

10. Failed Calibration Miscellaneous

11. Collecting and mining QC:0000006QC:0000007QC:0000029QC:0000031QC:0000035QC:0000037QC:0000040QC:0000041QC:0000046 24761651111520,0672319812543,41634540,6205397481644 22412192156610,0711678832787,093632632,2055698121960 268265644360,0670731711264,743364841,3719376741243 23641913106580,055410352785,113191571,004819541651 12902276110,00043936716,408931713 973 2249146574390,0505119451784,435749456,1738007281288 13123417123570,0359964883190,128959683,8432498092022 1924231389540,03847816722137,56978871,877283243245 18322750113540,04109090925151,18333351,0858656461856 14193358132680,03930911337119,35372532,0891760152813

12. Conclusion Quality control for mass spectrometry experiments is crucial qcML is a new standard format for quality control metrics Data mining techniques to retrieve relevant information from the QC metrics

13. Acknowledgements ADReM / biomina Bart Cuypers Stefan Naulaerts Nghia Vu Trung Pieter Meysman Kris Laukens Bart Goethals InSPECtor Pieter Kelchtermans Lennart Martens Dirk Valkenborg biomina