Vyatkina, KiraDekker, Lennard J. M.Wu, SiVanDuijn, Martijn M.Liu, XiaowenTolić, NikolaLuider, Theo M.Paša-Tolić, Ljiljana2017-12-212017-12-212017-12Vyatkina, K., Dekker, L. J. M., Wu, S., VanDuijn, M. M., Liu, X., Tolić, N., Luider, T. M. and Paša-Tolić, L. (2017), De Novo Sequencing of Peptides from High-Resolution Bottom-Up Tandem Mass Spectra using Top-Down Intended Methods. Proteomics, 17(23-24), 1600321. http://dx.doi.org/10.1002/pmic.201600321https://hdl.handle.net/1805/14873Despite high-resolution mass spectrometers are becoming accessible for more and more laboratories, tandem (MS/MS) mass spectra are still often collected at a low resolution. And even if acquired at a high resolution, software tools used for their processing do not tend to benefit from that in full, and an ability to specify a relative mass tolerance in this case often remains the only feature the respective algorithms take advantage of. We argue that a more efficient way to analyze high-resolution MS/MS spectra should be with methods more explicitly accounting for the precision level, and sustain this claim through demonstrating that a de novo sequencing framework originally developed for (high-resolution) top-down MS/MS data is perfectly suitable for processing high-resolution bottom-up datasets, even though a top-down like deconvolution performed as the first step will leave in many spectra at most a few peaks.enPublisher Policybottom-up proteomicshigh-resolution mass spectrometryde novo sequencingArticle