Assignment – 1:

Research Assignment

1- This will be the individual assignment.

2- You have to download two research articles from google scholar on the assigned topics
in addition to one paper provided.
i. (Note: Write the topic name in google scholar search bar and download
unpaid articles therefrom)
3- A data extraction sheet is given below for you to do appropriate working.
4- Write an abstract to your work

Assignment on Data Extraction (Articles)

Name. MUHAMMAD ALEEM, Roll No. 35_, Class: Biotechnology

Data Extraction Form

Article no: 01
Title: Identifying metabolites by integrating metabolome databases with mass spectrometry
cheminformatics

Author: Zijun Lai, Hiroshi Tsugawa, Gert

Wohlgemuth, Sajjan Mehta, Matthew Mueller,
Yuxuan Zheng, Atsushi Ogiwara, John Meissen Publication Date: January 2018
Megan Showalter, Kohei Takeuch,Tobias King,
Peter Beal, Masanori Arita, Oliver Foehn
Publisher (if any): Nature Publishing Group Country: USA, JAPAN, SADUI ARABIA
Volume: Issue Number: Page no:
Journal: Nature methods 15
1 53-56
IF: 10.1038 Citations: 136
Keywords/definitions: Data Mining, Mass Spectrometry, Metabolomics, Spectroscopy, Gas
Chromatography-mass Spectrometry, Gas Chromatography-tandem Mass Spectrometry, Liquid
Chromatography-tandem Mass Spectrometry, Database Search, Trimethylsilyl Derivatization,
Rearrangement, Collision-induced Dissociation, Interaction, Thin-layer Chromatography, Column
Chromatography
Objective of the Study: (Conceptual Framework):
Z.L., H.T., M.A., and O.F. designed G.W. and S.M. developed the Bin Vesicate system. HT developed
MS-DIAL 2.0 and MS-FINDER 2.0 programs. Z.L. performed sample modifications, instrument
analysis, and processing of anonymous diagnostic data. M.S. provided biological and LC-MS studies
for N-methyl-UMP detection. T.K. trained by Z.L. in cheminformatics and contributed to the validation
of MS-FINDER. M.M. wrote the previous end of Investigate. Z.L. and H.T. performance verification
and comparison of MS-DIAL 2.0 and MS-FINDER 2.0 system. Y.Z. and P. comprises N-methyl-UMP
a complex. A.O. upgraded the green file reader to ABF conversion. UJM, KT, and O.F. contributed to
the identification of Liso-MGMP and propofol derivatives. Z.L., H.T., M.A., and O.F. they discussed
the project well and wrote the manuscript.
Findings:
The novel metabolites differing in canonical methods can be identified by a combination of three
cheminformatics tools: Bin vestige, which asks Bin Base gas chromatography - mass spectrometry
(GC-MS) database metabolism to match anonymous metadata to more than 110,000 samples; MS-
DIAL 2.0, a software tool for chromatographic specification for high resolution GC-MS or liquid
chromatography - mass spectrometry (LC-MS); and MS-FINDER 2.0, a structural specification system
that uses a combination of 14 metabolic data in addition to an enzyme library of loose behavior. We
demonstrate our workflow by expressing N-methyl-uridine monophosphate (UMP),
lysomonogalactosyl-monopalmitin, N-methyl alanine, and two propofol compounds.

Methodology:
(a) Peak spotting: to determine fragment ions for GC-MS spectra, the detected m/z-RT features are
termed as 'peak spots' with computed peak quality and peak sharpness values. (b) Feature detection: all
peak spots with identical peak widths and peak top retention times are combined into single array. For
each array, peak sharpness values are totaled and a second Gaussian derivative filter is applied to
construct 'peak groups'. (c) Deconvolution and identification: MS1Dec chromatogram deconvolution
and open access Mona mass spectral database is utilized to annotate the coeluting metabolites –
phosphate, leucine, and glycerol – with 0.4-0.6 s peak top differences. The terms “Match” and
“Rematch” mean dot-product and reverse dot-product values calculated in NIST MS search program,
respectively.
The accuracy of GC-MS chromatogram deconvolution is confirmed by analyzing a biological sample
in Agilent GC-Q(MS) system.

What you have learnt from the research paper

Metabolomics such as NIH Metabolomics, Workbench and EBI Metabolites are important in
comparing metabolomic effects in relation to compound elements. However, by comparing unknown
metabolites in various biological studies, it is important to state data acquisition methods and data
processing parameters. Currently, only GC-MS (and, basically, NMR) data meet this criterion. Our
strategy makes full use of this benefit, using MS-DIAL 2.0 with Bin Vestige and MS-FINDER 2.0
which outperforms other deconvolution and software that is a diagnostic tool for unintended
metabolomics. In addition, our acquisition method found e.g., N-methyl-UMP will be significantly
increased in cancer cells and cancer cells, compared to other cell or tissue types. Recently, cellular
methylation has been shown to directly control cell proliferation in stem cell20s, increasing the chances
of concomitant processes in cancer cells or by using methylate methylated as cancer biomarkers. More
broadly, it has been shown quite often that small chemical modifications of metabolites can remove
these compounds from the main pathways of biochemistry, and that those modified metabolites,
hemimetabolies, later acquire regulatory functions, for example oxylipins. With the discovery of
hemimetabolies, the integration of Bin vestige, MS-DIAL, and MS-FINDER provides a structured
strategy to use a complete set of mass spectral information and chemical metadata to effectively detect
and measure the possible chemical composition, and will form the basis for combined and standardized
input complete metabolomics.