title: An adaptive alignment algorithm for quality-controlled label-free LC-MS.
abstract: Label-free quantification using precursor-based intensities is a versatile workflow for large-scale proteomics studies. The method however requires extensive computational analysis and is therefore in need of robust quality control during the data mining stage. We present a new label-free data analysis workflow integrated into a multiuser software platform. A novel adaptive alignment algorithm has been developed to minimize the possible systematic bias introduced into the analysis. Parameters are estimated on the fly from the data at hand, producing a user-friendly analysis suite. Quality metrics are output in every step of the analysis as well as actively incorporated into the parameter estimation. We furthermore show the improvement of this system by comprehensive comparison to classical label-free analysis methodology as well as current state-of-the-art software.
authors.affiliation: Department of Immunotechnology, Lund University, BMC D13, 22184 Lund, Sweden.
authors.forename: Marianne
authors.initials: M
authors.lastname: Sandin
authors.forename: Ashfaq
authors.initials: A
authors.lastname: Ali
authors.forename: Karin
authors.initials: K
authors.lastname: Hansson
authors.forename: Olle
authors.initials: O
authors.lastname: Månsson
authors.forename: Erik
authors.initials: E
authors.lastname: Andreasson
authors.forename: Svante
authors.initials: S
authors.lastname: Resjö
authors.forename: Fredrik
authors.initials: F
authors.lastname: Levander
mesh_terms: D000465:Algorithms; D002853:Chromatography, Liquid / Q000379:methods / Q000592:standards; D055750:Phytophthora infestans / Q000502:physiology; D010935:Plant Diseases / Q000469:parasitology; D010940:Plant Proteins / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D020543:Proteome / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D040901:Proteomics; D011786:Quality Control; D012984:Software; D011198:Solanum tuberosum / Q000378:metabolism / Q000469:parasitology; D053719:Tandem Mass Spectrometry / Q000379:methods / Q000592:standards*
chemical_list: D010940:Plant Proteins; D020543:Proteome