mzMD: A New Storage and Retrieval System for Mass Spectrometry Data

Runmin Yang; Jingjing Ma; Shu Zhang; Yu Zheng; Lusheng Wang; Daming Zhu

doi:10.1007/978-3-030-84532-2_8

mzMD: A New Storage and Retrieval System for Mass Spectrometry Data

Runmin Yang, Jingjing Ma, Shu Zhang, Yu Zheng, Lusheng Wang, Daming Zhu^*

^*Corresponding author for this work

Department of Computer Science

Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

1 Citation (Scopus)

Abstract

Viewing peaks in LC–MS data sets always happens in liquid-chromatography mass spectrometry data analysis. It is challenging to develop an LC–MS data storage and retrieval tool that can get some peaks in a data window whose image presented with their intensities in a display window resembles as closely as possible that of all peaks in the data window at a speed of real-time level. We present mzMD, a new storage system that is intended to store a set of mass spectral peaks in multiple database tables with different numbers of peaks selected from the set of peaks. We present an algorithm for visualization applications to query for summaries (representative peak sets) of given data windows. We propose criteria to evaluate the quality of summaries of data windows. Experimental statistics on real LC–MS data sets verified the high speed of mzMD in retrieving high-quality summaries of data windows. The source code is freely available at https://github.com/yrm9837/mzMD-java.

Original language	English
Title of host publication	Intelligent Computing Theories and Application
Subtitle of host publication	17th International Conference, ICIC 2021, Shenzhen, China, August 12–15, 2021, Proceedings, Part III
Place of Publication	Cham
Publisher	Springer
Pages	77-86
Volume	Part III
ISBN (Electronic)	9783030845322
ISBN (Print)	9783030845315
DOIs	https://doi.org/10.1007/978-3-030-84532-2_8
Publication status	Published - 2021
Event	17th International Conference on Intelligent Computing (ICIC 2021): Advanced Intelligent Computing Methodologies and Applications - Anthea Hotel, Shenzhen, China Duration: 12 Aug 2021 → 15 Aug 2021

Publication series

Name	Lecture Notes in Computer Science
Volume	12838
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	17th International Conference on Intelligent Computing (ICIC 2021)
Country/Territory	China
City	Shenzhen
Period	12/08/21 → 15/08/21

Research Keywords

Algorithm
Data storage
Data window
Mass spectrometry
Visualization

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10.1007/978-3-030-84532-2_8

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Yang, R., Ma, J., Zhang, S., Zheng, Y., Wang, L., & Zhu, D. (2021). mzMD: A New Storage and Retrieval System for Mass Spectrometry Data. In Intelligent Computing Theories and Application: 17th International Conference, ICIC 2021, Shenzhen, China, August 12–15, 2021, Proceedings, Part III (Vol. Part III, pp. 77-86). (Lecture Notes in Computer Science; Vol. 12838). Springer . https://doi.org/10.1007/978-3-030-84532-2_8

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title = "mzMD: A New Storage and Retrieval System for Mass Spectrometry Data",

abstract = "Viewing peaks in LC–MS data sets always happens in liquid-chromatography mass spectrometry data analysis. It is challenging to develop an LC–MS data storage and retrieval tool that can get some peaks in a data window whose image presented with their intensities in a display window resembles as closely as possible that of all peaks in the data window at a speed of real-time level. We present mzMD, a new storage system that is intended to store a set of mass spectral peaks in multiple database tables with different numbers of peaks selected from the set of peaks. We present an algorithm for visualization applications to query for summaries (representative peak sets) of given data windows. We propose criteria to evaluate the quality of summaries of data windows. Experimental statistics on real LC–MS data sets verified the high speed of mzMD in retrieving high-quality summaries of data windows. The source code is freely available at https://github.com/yrm9837/mzMD-java.",

keywords = "Algorithm, Data storage, Data window, Mass spectrometry, Visualization",

author = "Runmin Yang and Jingjing Ma and Shu Zhang and Yu Zheng and Lusheng Wang and Daming Zhu",

year = "2021",

doi = "10.1007/978-3-030-84532-2_8",

language = "English",

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series = "Lecture Notes in Computer Science",

publisher = "Springer ",

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Yang, R, Ma, J, Zhang, S, Zheng, Y, Wang, L & Zhu, D 2021, mzMD: A New Storage and Retrieval System for Mass Spectrometry Data. in Intelligent Computing Theories and Application: 17th International Conference, ICIC 2021, Shenzhen, China, August 12–15, 2021, Proceedings, Part III. vol. Part III, Lecture Notes in Computer Science, vol. 12838, Springer , Cham, pp. 77-86, 17th International Conference on Intelligent Computing (ICIC 2021), Shenzhen, China, 12/08/21. https://doi.org/10.1007/978-3-030-84532-2_8

mzMD: A New Storage and Retrieval System for Mass Spectrometry Data. / Yang, Runmin; Ma, Jingjing; Zhang, Shu et al.
Intelligent Computing Theories and Application: 17th International Conference, ICIC 2021, Shenzhen, China, August 12–15, 2021, Proceedings, Part III. Vol. Part III Cham: Springer , 2021. p. 77-86 (Lecture Notes in Computer Science; Vol. 12838).

Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

TY - GEN

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T2 - 17th International Conference on Intelligent Computing (ICIC 2021)

AU - Yang, Runmin

AU - Ma, Jingjing

AU - Zhang, Shu

AU - Zheng, Yu

AU - Wang, Lusheng

AU - Zhu, Daming

PY - 2021

Y1 - 2021

N2 - Viewing peaks in LC–MS data sets always happens in liquid-chromatography mass spectrometry data analysis. It is challenging to develop an LC–MS data storage and retrieval tool that can get some peaks in a data window whose image presented with their intensities in a display window resembles as closely as possible that of all peaks in the data window at a speed of real-time level. We present mzMD, a new storage system that is intended to store a set of mass spectral peaks in multiple database tables with different numbers of peaks selected from the set of peaks. We present an algorithm for visualization applications to query for summaries (representative peak sets) of given data windows. We propose criteria to evaluate the quality of summaries of data windows. Experimental statistics on real LC–MS data sets verified the high speed of mzMD in retrieving high-quality summaries of data windows. The source code is freely available at https://github.com/yrm9837/mzMD-java.

AB - Viewing peaks in LC–MS data sets always happens in liquid-chromatography mass spectrometry data analysis. It is challenging to develop an LC–MS data storage and retrieval tool that can get some peaks in a data window whose image presented with their intensities in a display window resembles as closely as possible that of all peaks in the data window at a speed of real-time level. We present mzMD, a new storage system that is intended to store a set of mass spectral peaks in multiple database tables with different numbers of peaks selected from the set of peaks. We present an algorithm for visualization applications to query for summaries (representative peak sets) of given data windows. We propose criteria to evaluate the quality of summaries of data windows. Experimental statistics on real LC–MS data sets verified the high speed of mzMD in retrieving high-quality summaries of data windows. The source code is freely available at https://github.com/yrm9837/mzMD-java.

KW - Algorithm

KW - Data storage

KW - Data window

KW - Mass spectrometry

KW - Visualization

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M3 - RGC 32 - Refereed conference paper (with host publication)

SN - 9783030845315

VL - Part III

T3 - Lecture Notes in Computer Science

SP - 77

EP - 86

BT - Intelligent Computing Theories and Application

PB - Springer

CY - Cham

Y2 - 12 August 2021 through 15 August 2021

ER -

Yang R, Ma J, Zhang S, Zheng Y, Wang L, Zhu D. mzMD: A New Storage and Retrieval System for Mass Spectrometry Data. In Intelligent Computing Theories and Application: 17th International Conference, ICIC 2021, Shenzhen, China, August 12–15, 2021, Proceedings, Part III. Vol. Part III. Cham: Springer . 2021. p. 77-86. (Lecture Notes in Computer Science). Epub 2021 Aug 9. doi: 10.1007/978-3-030-84532-2_8

mzMD: A New Storage and Retrieval System for Mass Spectrometry Data

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