title: Generic workflow for quality assessment of quantitative label-free LC-MS analysis.
abstract: As high-resolution instruments are becoming standard in proteomics laboratories, label-free quantification using precursor measurements is becoming a viable option, and is consequently rapidly gaining popularity. Several software solutions have been presented for label-free analysis, but to our knowledge no conclusive studies regarding the sensitivity and reliability of each step of the analysis procedure has been described. Here, we use real complex samples to assess the reliability of label-free quantification using four different software solutions. A generic approach to quality test quantitative label-free LC-MS is introduced. Measures for evaluation are defined for feature detection, alignment and quantification. All steps of the analysis could be considered adequately performed by the utilized software solutions, although differences and possibilities for improvement could be identified. The described method provides an effective testing procedure, which can help the user to quickly pinpoint where in the workflow changes are needed.
authors.affiliation: Department of Immunotechnology, Lund University, BMC D13, Lund, Sweden.
authors.forename: Marianne
authors.initials: M
authors.lastname: Sandin
authors.forename: Morten
authors.initials: M
authors.lastname: Krogh
authors.forename: Karin
authors.initials: K
authors.lastname: Hansson
authors.forename: Fredrik
authors.initials: F
authors.lastname: Levander
mesh_terms: D000465:Algorithms; D002853:Chromatography, Liquid / Q000592:standards / Q000706:statistics & numerical data; D019295:Computational Biology; D003627:Data Interpretation, Statistical; D030562:Databases, Protein / Q000706:statistics & numerical data; D006801:Humans; D011506:Proteins / Q000302:isolation & purification; D040901:Proteomics / Q000592:standards* / Q000706:statistics & numerical data*; D011786:Quality Control; D015203:Reproducibility of Results; D016415:Sequence Alignment / Q000592:standards / Q000706:statistics & numerical data; D012984:Software; D053719:Tandem Mass Spectrometry / Q000592:standards* / Q000706:statistics & numerical data*; D057188:Workflow
chemical_list: D011506:Proteins