title: FTDR 2.0: a tool to achieve sub-ppm level recalibrated accuracy in routine LC-MS analysis.
abstract: Advances in proteomics research involve the use of high-precision and high-resolution mass spectrometry instruments. Although hardware improvements are the main impetus for the acquisition of high-quality data, enhancements in software tools are also needed. In this study, recalibration was verified as an important way to improve data accuracy. A new version tool, known as FTDR 2.0, was developed to recalibrate the mass-to-charge ratio error of most observed parent ions to the sub part per million level in routine experiments. First, many new parameters were introduced and screened as features online to reduce systematic error and to adapt to various data sets. Second, a support vector regression model was trained to characterize the complex nonlinear maps from features to mass-to-charge ratio measurement errors. Third, a specific mass-to-charge ratio error tolerance for each parent ion was estimated by considering the impact of signal intensity. FTDR 2.0 is a user-friendly tool that supports most commonly used data standards and formats. A C++ library and the source code are provided to support the redevelopment and integration into other mass spectrometry data processing tools. The performance of FTDR 2.0 was verified using several experimental data sets from different research programs. Recalibration with FTDR 2.0 has been proved to improve the peptide identification in qualitative, quantitative, and post-translational modification analyses.
authors.affiliation: College of Mechatronic Engineering and Automatic Control, National University of Defense Technology, Changsha, 410073, China.
authors.forename: Jiyang
authors.initials: J
authors.lastname: Zhang
authors.forename: Jie
authors.initials: J
authors.lastname: Ma
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.forename: Changming
authors.initials: C
authors.lastname: Xu
authors.forename: Yunping
authors.initials: Y
authors.lastname: Zhu
authors.forename: Hongwei
authors.initials: H
authors.lastname: Xie
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D002138:Calibration; D002852:Chromatography, Ion Exchange; D030562:Databases, Protein; D006801:Humans; D008099:Liver / Q000378:metabolism; D010446:Peptide Fragments / Q000737:chemistry / Q000302:isolation & purification; D010449:Peptide Mapping; D010750:Phosphoproteins / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D011499:Protein Processing, Post-Translational; D059748:Proteolysis; D020543:Proteome / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D057386:Search Engine; D012680:Sensitivity and Specificity; D012984:Software
chemical_list: D019843:Archaeal Proteins; D010446:Peptide Fragments; D010750:Phosphoproteins; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins