title: A statistical method for chromatographic alignment of LC-MS data.
abstract: Integrated liquid-chromatography mass-spectrometry (LC-MS) is becoming a widely used approach for quantifying the protein composition of complex samples. The output of the LC-MS system measures the intensity of a peptide with a specific mass-charge ratio and retention time. In the last few years, this technology has been used to compare complex biological samples across multiple conditions. One challenge for comparative proteomic profiling with LC-MS is to match corresponding peptide features from different experiments. In this paper, we propose a new method--Peptide Element Alignment (PETAL) that uses raw spectrum data and detected peak to simultaneously align features from multiple LC-MS experiments. PETAL creates spectrum elements, each of which represents the mass spectrum of a single peptide in a single scan. Peptides detected in different LC-MS data are aligned if they can be represented by the same elements. By considering each peptide separately, PETAL enjoys greater flexibility than time warping methods. While most existing methods process multiple data sets by sequentially aligning each data set to an arbitrarily chosen template data set, PETAL treats all experiments symmetrically and can analyze all experiments simultaneously. We illustrate the performance of PETAL on example data sets.
authors.affiliation: Fred Hutchinson Cancer Research Center, Seattle, WA, USA. pwang@fhcrc.org
authors.forename: Pei
authors.initials: P
authors.lastname: Wang
authors.forename: Hua
authors.initials: H
authors.lastname: Tang
authors.forename: Matthew P
authors.initials: MP
authors.lastname: Fitzgibbon
authors.forename: Martin
authors.initials: M
authors.lastname: McIntosh
authors.forename: Marc
authors.initials: M
authors.lastname: Coram
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
authors.forename: Eugene
authors.initials: E
authors.lastname: Yi
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D000818:Animals; D001798:Blood Proteins / Q000032:analysis / Q000737:chemistry; D002417:Cattle; D002853:Chromatography, Liquid / Q000379:methods*; D003627:Data Interpretation, Statistical; D006023:Glycoproteins / Q000032:analysis / Q000097:blood / Q000737:chemistry; D006801:Humans; D010455:Peptides / Q000032:analysis* / Q000737:chemistry; D011506:Proteins / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*
chemical_list: D001798:Blood Proteins; D006023:Glycoproteins; D010455:Peptides; D011506:Proteins