title: An iterative block-shifting approach to retention time alignment that preserves the shape and area of gas chromatography-mass spectrometry peaks.
abstract: BACKGROUND
  Metabolomics, petroleum and biodiesel chemistry, biomarker discovery, and other fields which rely on high-resolution profiling of complex chemical mixtures generate datasets which contain millions of detector intensity readings, each uniquely addressed along dimensions of time (e.g., retention time of chemicals on a chromatographic column), a spectral value (e.g., mass-to-charge ratio of ions derived from chemicals), and the analytical run number. They also must rely on data preprocessing techniques. In particular, inter-run variance in the retention time of chemical species poses a significant hurdle that must be cleared before feature extraction, data reduction, and knowledge discovery can ensue. Alignment methods, for calibrating retention reportedly (and in our experience) can misalign matching chemicals, falsely align distinct ones, be unduly sensitive to chosen values of input parameters, and result in distortions of peak shape and area.
  
  
  RESULTS
  We present an iterative block-shifting approach for retention-time calibration that detects chromatographic features and qualifies them by retention time, spectrum, and the effect of their inclusion on the quality of alignment itself. Mass chromatograms are aligned pairwise to one selected as a reference. In tests using a 45-run GC-MS experiment, block-shifting reduced the absolute deviation of retention by greater than 30-fold. It compared favourably to COW and XCMS with respect to alignment, and was markedly superior in preservation of peak area.
  
  
  CONCLUSIONS
  Iterative block-shifting is an attractive method to align GC-MS mass chromatograms that is also generalizable to other two-dimensional techniques such as HPLC-MS.
authors.affiliation: UALR/UAMS Joint Graduate Program in Bioinformatics, University of Arkansas at Little Rock, Little Rock, AR 72204, USA. minho.chae@gmail.com
authors.forename: Minho
authors.initials: M
authors.lastname: Chae
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Shmookler Reis
authors.forename: John J
authors.initials: JJ
authors.lastname: Thaden
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D001704:Biopolymers / Q000032:analysis / Q000737:chemistry*; D008401:Gas Chromatography-Mass Spectrometry / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*
chemical_list: D001704:Biopolymers
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