FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics

Kyowon Jeong; Jihyung Kim; Manasi Gaikwad; Siti Nurul Hidayah; Laura Heikaus; Hartmut Schlüter; Oliver Kohlbacher

doi:10.1016/j.cels.2020.01.003

FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics

Standard

FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics. / Jeong, Kyowon; Kim, Jihyung; Gaikwad, Manasi; Hidayah, Siti Nurul; Heikaus, Laura; Schlüter, Hartmut; Kohlbacher, Oliver.

In: CELL SYST, Vol. 10, No. 2, 26.02.2020, p. 213-218.e6.

Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

Harvard

Jeong, K, Kim, J, Gaikwad, M, Hidayah, SN, Heikaus, L, Schlüter, H & Kohlbacher, O 2020, 'FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics', CELL SYST, vol. 10, no. 2, pp. 213-218.e6. https://doi.org/10.1016/j.cels.2020.01.003

APA

Jeong, K., Kim, J., Gaikwad, M., Hidayah, S. N., Heikaus, L., Schlüter, H., & Kohlbacher, O. (2020). FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics. CELL SYST, 10(2), 213-218.e6. https://doi.org/10.1016/j.cels.2020.01.003

Vancouver

Jeong K, Kim J, Gaikwad M, Hidayah SN, Heikaus L, Schlüter H et al. FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics. CELL SYST. 2020 Feb 26;10(2):213-218.e6. https://doi.org/10.1016/j.cels.2020.01.003

Bibtex

@article{422beeb8f9bd45dcbeb4d615e7b3ff9e,

title = "FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics",

abstract = "Top-down mass spectrometry (TD-MS)-based proteomics analyzes intact proteoforms and thus preserves information about individual protein species. The MS signal of these high-mass analytes is complex and challenges the accurate determination of proteoform masses. Fast and accurate feature deconvolution (i.e., the determination of intact proteoform masses) is, therefore, an essential step for TD data analysis. Here, we present FLASHDeconv, an algorithm achieving higher deconvolution quality, with an execution speed two orders of magnitude faster than existing approaches. FLASHDeconv transforms peak positions (m/z) within spectra into log m/z space. This simple transformation turns the deconvolution problem into a search for constant patterns, thereby greatly accelerating the process. In both simple and complex samples, FLASHDeconv reports more genuine feature masses and substantially fewer artifacts than other existing methods. FLASHDeconv is freely available for download here: https://www.openms.org/flashdeconv/. A record of this paper's Transparent Peer Review process is included in the Supplemental Information.",

author = "Kyowon Jeong and Jihyung Kim and Manasi Gaikwad and Hidayah, {Siti Nurul} and Laura Heikaus and Hartmut Schl{\"u}ter and Oliver Kohlbacher",

year = "2020",

month = feb,

day = "26",

doi = "10.1016/j.cels.2020.01.003",

language = "English",

volume = "10",

pages = "213--218.e6",

journal = "CELL SYST",

issn = "2405-4712",

publisher = "Cell Press",

number = "2",

}

RIS

TY - JOUR

T1 - FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics

AU - Jeong, Kyowon

AU - Kim, Jihyung

AU - Gaikwad, Manasi

AU - Hidayah, Siti Nurul

AU - Heikaus, Laura

AU - Schlüter, Hartmut

AU - Kohlbacher, Oliver

PY - 2020/2/26

Y1 - 2020/2/26

N2 - Top-down mass spectrometry (TD-MS)-based proteomics analyzes intact proteoforms and thus preserves information about individual protein species. The MS signal of these high-mass analytes is complex and challenges the accurate determination of proteoform masses. Fast and accurate feature deconvolution (i.e., the determination of intact proteoform masses) is, therefore, an essential step for TD data analysis. Here, we present FLASHDeconv, an algorithm achieving higher deconvolution quality, with an execution speed two orders of magnitude faster than existing approaches. FLASHDeconv transforms peak positions (m/z) within spectra into log m/z space. This simple transformation turns the deconvolution problem into a search for constant patterns, thereby greatly accelerating the process. In both simple and complex samples, FLASHDeconv reports more genuine feature masses and substantially fewer artifacts than other existing methods. FLASHDeconv is freely available for download here: https://www.openms.org/flashdeconv/. A record of this paper's Transparent Peer Review process is included in the Supplemental Information.

AB - Top-down mass spectrometry (TD-MS)-based proteomics analyzes intact proteoforms and thus preserves information about individual protein species. The MS signal of these high-mass analytes is complex and challenges the accurate determination of proteoform masses. Fast and accurate feature deconvolution (i.e., the determination of intact proteoform masses) is, therefore, an essential step for TD data analysis. Here, we present FLASHDeconv, an algorithm achieving higher deconvolution quality, with an execution speed two orders of magnitude faster than existing approaches. FLASHDeconv transforms peak positions (m/z) within spectra into log m/z space. This simple transformation turns the deconvolution problem into a search for constant patterns, thereby greatly accelerating the process. In both simple and complex samples, FLASHDeconv reports more genuine feature masses and substantially fewer artifacts than other existing methods. FLASHDeconv is freely available for download here: https://www.openms.org/flashdeconv/. A record of this paper's Transparent Peer Review process is included in the Supplemental Information.

U2 - 10.1016/j.cels.2020.01.003

DO - 10.1016/j.cels.2020.01.003

M3 - SCORING: Journal article

C2 - 32078799

VL - 10

SP - 213-218.e6

JO - CELL SYST

JF - CELL SYST

SN - 2405-4712

IS - 2

ER -