De Novo Sequencing of Peptides from High‐Resolution Bottom‐Up Tandem Mass Spectra using Top‐Down Intended Methods. Issue 23 (20th December 2017)

• Record Type: Journal Article
• Authors: Vyatkina, Kira; Dekker, Lennard J. M.; Wu, Si; VanDuijn, Martijn M.; Liu, Xiaowen; Tolić, Nikola; Luider, Theo M.; Paša‐Tolić, Ljiljana
• Other Names: Mathivanan Suresh guestEditor.
• Is Part Of: Proteomics. Volume 17:Issue 23/24(2017)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2017-12-20
• Subjects: bottom‐up proteomics -- de novo sequencing -- high‐resolution mass spectrometry; Proteins -- Separation -- Periodicals; Bioinformatics -- Periodicals; Proteomics -- Periodicals; Genomes -- Periodicals; Molecular genetics -- Periodicals; 572.605
• DOI: 10.1002/pmic.201600321
• Languages: English
• ISSNs: 1615-9853

Abstract

Abstract: Despite 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.