title: Variable reference alignment: an improved peak alignment protocol for NMR spectral data with large intersample variation.
abstract: In an effort to address the variable correspondence problem across large sample cohorts common in metabolomic/metabonomic studies, we have developed a prealignment protocol that aims to generate spectral segments sharing a common target spectrum. Under the assumption that a single reference spectrum will not correctly represent all spectra of a data set, the goal of this approach is to perform local alignment corrections on spectral regions which share a common "most similar" spectrum. A natural beneficial outcome of this procedure is the automatic definition of spectral segments, a feature that is not common to all alignment methods. This protocol is shown to specifically improve the quality of alignment in (1)H NMR data sets exhibiting large intersample compositional variation (e.g., pH, ionic strength). As a proof-of-principle demonstration, we have utilized two recently developed alignment algorithms specific to NMR data, recursive segment-wise peak alignment and interval correlated shifting, and applied them to two data sets composed of 15 aqueous cell line extract and 20 human urine (1)H NMR profiles. Application of this protocol represents a fundamental shift from current alignment methodologies that seek to correct misalignments utilizing a single representative spectrum, with the added benefit that it can be appended to any alignment algorithm.
authors.affiliation: Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, USA.
authors.forename: Neil
authors.initials: N
authors.lastname: MacKinnon
authors.forename: Wencheng
authors.initials: W
authors.lastname: Ge
authors.forename: Amjad P
authors.initials: AP
authors.lastname: Khan
authors.forename: Bagganahalli S
authors.initials: BS
authors.lastname: Somashekar
authors.forename: Pratima
authors.initials: P
authors.lastname: Tripathi
authors.forename: Javed
authors.initials: J
authors.lastname: Siddiqui
authors.forename: John T
authors.initials: JT
authors.lastname: Wei
authors.forename: Arul M
authors.initials: AM
authors.lastname: Chinnaiyan
authors.forename: Thekkelnaycke M
authors.initials: TM
authors.lastname: Rajendiran
authors.forename: Ayyalusamy
authors.initials: A
authors.lastname: Ramamoorthy
mesh_terms: D000465:Algorithms; D002460:Cell Line; D006801:Humans; D016247:Information Storage and Retrieval; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D055432:Metabolomics; D013223:Statistics as Topic / Q000379:methods*; D016482:Urinalysis; D014867:Water / Q000737:chemistry
chemical_list: D014867:Water