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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.

In: Proteomics, Vol. 17, No. 23-24, 1600321, 12.2017.

Research output: Contribution to journalArticlepeer-review

Harvard

Vyatkina, K, Dekker, LJM, Wu, S, VanDuijn, MM, Liu, X, Tolić, N, Luider, TM & Paša-Tolić, L 2017, 'De Novo Sequencing of Peptides from High-Resolution Bottom-Up Tandem Mass Spectra using Top-Down Intended Methods', Proteomics, vol. 17, no. 23-24, 1600321. https://doi.org/10.1002/pmic.201600321, https://doi.org/10.1002/pmic.201600321

APA

Vyatkina, K., Dekker, L. J. M., Wu, S., VanDuijn, M. M., Liu, X., Tolić, N., Luider, T. M., & 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]. https://doi.org/10.1002/pmic.201600321, https://doi.org/10.1002/pmic.201600321

Vancouver

Author

Vyatkina, Kira ; Dekker, Lennard J.M. ; Wu, Si ; VanDuijn, Martijn M. ; Liu, Xiaowen ; Tolić, Nikola ; Luider, Theo M. ; Paša-Tolić, Ljiljana. / De Novo Sequencing of Peptides from High-Resolution Bottom-Up Tandem Mass Spectra using Top-Down Intended Methods. In: Proteomics. 2017 ; Vol. 17, No. 23-24.

BibTeX

@article{226df5d08eb241b3b7fc198b8f5662be,
title = "De Novo Sequencing of Peptides from High-Resolution Bottom-Up Tandem Mass Spectra using Top-Down Intended Methods",
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.",
keywords = "bottom-up proteomics, de novo sequencing, high-resolution mass spectrometry, ALGORITHM, MS/MS, DATABASE SEARCH, PROTEIN IDENTIFICATION, SOFTWARE, ORBITRAP, DECONVOLUTION, SPECTROMETRY, TAGS, PROTEOMICS",
author = "Kira Vyatkina and Dekker, {Lennard J.M.} and Si Wu and VanDuijn, {Martijn M.} and Xiaowen Liu and Nikola Toli{\'c} and Luider, {Theo M.} and Ljiljana Pa{\v s}a-Toli{\'c}",
note = "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",
year = "2017",
month = dec,
doi = "10.1002/pmic.201600321",
language = "English",
volume = "17",
journal = "Proteomics",
issn = "1615-9853",
publisher = "Wiley-Blackwell",
number = "23-24",

}

RIS

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