Результаты исследований: Научные публикации в периодических изданиях › статья › Рецензирование
De Novo Sequencing of Peptides from High-Resolution Bottom-Up Tandem Mass Spectra using Top-Down Intended Methods. / Vyatkina, Kira; Dekker, Lennard J.M.; Wu, Si; VanDuijn, Martijn M.; Liu, Xiaowen; Tolić, Nikola; Luider, Theo M.; Paša-Tolić, Ljiljana.
в: Proteomics, Том 17, № 23-24, 1600321, 12.2017.Результаты исследований: Научные публикации в периодических изданиях › статья › Рецензирование
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TY - JOUR
T1 - De Novo Sequencing of Peptides from High-Resolution Bottom-Up Tandem Mass Spectra using Top-Down Intended Methods
AU - Vyatkina, Kira
AU - Dekker, Lennard J.M.
AU - Wu, Si
AU - VanDuijn, Martijn M.
AU - Liu, Xiaowen
AU - Tolić, Nikola
AU - Luider, Theo M.
AU - Paša-Tolić, Ljiljana
N1 - Funding Information: The research by K.V. was partially supported by Government of Russian Federation (Grant 11.G34.31.0018, until December 2014) and Russian Science Foundation (Grant 14-50-00069, since February 2015). L.D. and M.V. are financially supported by The Netherlands Organization for Scientific Research (NWO), Zenith Grant 93511034. We are extremely grateful to Dr. Pavel Pevzner for fruitful discussions related to our work, and for the anonymous referees for their fruitful comments and suggestions
PY - 2017/12
Y1 - 2017/12
N2 - 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.
AB - 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.
KW - bottom-up proteomics
KW - de novo sequencing
KW - high-resolution mass spectrometry
KW - ALGORITHM
KW - MS/MS
KW - DATABASE SEARCH
KW - PROTEIN IDENTIFICATION
KW - SOFTWARE
KW - ORBITRAP
KW - DECONVOLUTION
KW - SPECTROMETRY
KW - TAGS
KW - PROTEOMICS
UR - http://www.scopus.com/inward/record.url?scp=85038428458&partnerID=8YFLogxK
UR - http://www.mendeley.com/research/novo-sequencing-peptides-highresolution-bottomup-tandem-mass-spectra-using-topdown-intended-methods
U2 - 10.1002/pmic.201600321
DO - 10.1002/pmic.201600321
M3 - Article
C2 - 29110399
AN - SCOPUS:85038428458
VL - 17
JO - Proteomics
JF - Proteomics
SN - 1615-9853
IS - 23-24
M1 - 1600321
ER -
ID: 27002527