MaxQuant.Live Enables Global Targeting of More Than 25,000 Peptides

• Published in: Molecular & cellular proteomics Vol. 18; no. 5; pp. 982 - 994
• Main Authors: Wichmann, Christoph, Meier, Florian, Virreira Winter, Sebastian, Brunner, Andreas-David, Cox, Jürgen, Mann, Matthias
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.05.2019; The American Society for Biochemistry and Molecular Biology
• Subjects: Algorithms; Amino Acid Sequence; Bioinformatics software; Computational Biology; Global targeting; HeLa Cells; Humans; Label-free quantification; Parallel reaction monitoring; Peptides - chemistry; Peptides - metabolism; Protein Identification; Proteome - analysis; Proteomics; Quality control and metrics; Quantification; Real time control; Reproducibility of Results; Software; Targeted mass spectrometry; Technological Innovation and Resources; Global targeting; Targeted mass spectrometry; Quantification; Real time control; Computational Biology; Bioinformatics software; Parallel reaction monitoring; Protein Identification; Quality control and metrics; Label-free quantification
• DOI: 10.1074/mcp.TIR118.001131
• ISSN: 1535-9476

MaxQuant.Live builds on the fast application programming interface of quadrupole Orbitrap mass analyzers to control data acquisition in real-time (freely available at www.maxquant.live). Its graphical user interface enables advanced data acquisition strategies, such as in-depth characterization of peptides of interest. Online recalibration in mass, retention time, and intensity dimensions extends this concept to more than 25,000 peptides per run. Our “global targeting” strategy combines the best of targeted and shotgun approaches. [Display omitted] Highlights •MaxQuant.Live controls Orbitrap mass analyzers in real-time.•Freely available apps enable advanced data acquisition strategies.•On-the-fly mass, retention time and intensity recalibration.•Global targeting unifies shotgun and targeted proteomics. Mass spectrometry (MS)-based proteomics is often performed in a shotgun format, in which as many peptide precursors as possible are selected from full or MS1 scans so that their fragment spectra can be recorded in MS2 scans. Although achieving great proteome depths, shotgun proteomics cannot guarantee that each precursor will be fragmented in each run. In contrast, targeted proteomics aims to reproducibly and sensitively record a restricted number of precursor/fragment combinations in each run, based on prescheduled mass-to-charge and retention time windows. Here we set out to unify these two concepts by a global targeting approach in which an arbitrary number of precursors of interest are detected in real-time, followed by standard fragmentation or advanced peptide-specific analyses. We made use of a fast application programming interface to a quadrupole Orbitrap instrument and real-time recalibration in mass, retention time and intensity dimensions to predict precursor identity. MaxQuant.Live is freely available (www.maxquant.live) and has a graphical user interface to specify many predefined data acquisition strategies. Acquisition speed is as fast as with the vendor software and the power of our approach is demonstrated with the acquisition of breakdown curves for hundreds of precursors of interest. We also uncover precursors that are not even visible in MS1 scans, using elution time prediction based on the auto-adjusted retention time alone. Finally, we successfully recognized and targeted more than 25,000 peptides in single LC-MS runs. Global targeting combines the advantages of two classical approaches in MS-based proteomics, whereas greatly expanding the analytical toolbox. MaxQuant.Live builds on the fast application programming interface of quadrupole Orbitrap mass analyzers to control data acquisition in real-time (freely available at www.maxquant.live). Its graphical user interface enables advanced data acquisition strategies, such as in-depth characterization of peptides of interest. Online recalibration in mass, retention time, and intensity dimensions extends this concept to more than 25,000 peptides per run. Our “global targeting” strategy combines the best of targeted and shotgun approaches.