title: Inversion of peak elution order prevents uniform time alignment of complex liquid-chromatography coupled to mass spectrometry datasets.
abstract: Retention time alignment is one of the most challenging steps in processing LC-MS datasets of complex proteomics samples acquired within a differential profiling study. A large number of time alignment methods have been developed for accurate pre-processing of such datasets. These methods generally assume that common compounds elute in the same order but they do not test whether this assumption holds. If this assumption is not valid, alignments based on a monotonic retention time function will lose accuracy for peaks that depart from the expected order of the retention time correspondence function. To address this issue, we propose a quality control method that assesses if a pair of complex LC-MS datasets can be aligned with the same alignment performance based on statistical tests before correcting retention time shifts. The algorithm first confirms the presence of an adequate number of common peaks (>∼100 accurately matched peak pairs), then determines if the probability for a conserved elution order of those common peaks is sufficiently high (>0.01) and finally performs retention time alignment of two LC-MS chromatograms. This procedure was applied to LC-MS and LC-MS/MS datasets from two different inter-laboratory proteomics studies showing that a large number of common peaks in chromatograms acquired by different laboratories change elution order with considerable retention time differences.
authors.affiliation: Analytical Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands; Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors.forename: Vikram
authors.initials: V
authors.lastname: Mitra
authors.affiliation: Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
authors.forename: Age
authors.initials: A
authors.lastname: Smilde
authors.affiliation: Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
authors.forename: Huub
authors.initials: H
authors.lastname: Hoefsloot
authors.affiliation: IBM T.J. Watson Research Centre, 1101 Kitchawan Road, Yorktown Heights, 10598 NY, USA.
authors.forename: Frank
authors.initials: F
authors.lastname: Suits
authors.affiliation: Analytical Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands; Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors.forename: Rainer
authors.initials: R
authors.lastname: Bischoff
authors.affiliation: Analytical Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands; Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands. Electronic address: p.l.horvatovich@rug.nl.
authors.forename: Péter
authors.initials: P
authors.lastname: Horvatovich
mesh_terms: D000465:Algorithms; D002851:Chromatography, High Pressure Liquid / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods*; D009010:Monte Carlo Method; D011336:Probability; D040901:Proteomics / Q000379:methods; D013997:Time Factors
keywords: Data pre-processing; Inversion of peak elution order; Liquid chromatography; Orthogonal separation; Retention time alignment; Shotgun proteomics