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: 03
Title: Recent Advances in Targeted and Untargeted Metabolomics by NMR and
MS/NMR Methods
Author (s): Bingel, Kerem Publication Date: 2018
Publisher (if any): Multidisciplinary Digital
Country: USA
Publishing Institute
Volume: Issue Number: Page no:
Journal: High-throughput
07 02 09
IF: 10.3390 Citations: 15
Keywords/definitions: Targeted profiling; untargeted metabolomics; mass spectrometry;
nuclear magnetic resonance spectroscopy; hybrid MS/NMR methods.
Objective of the Study: (Conceptual Framework):
NMR methods can identify most of the metabolites found in a given sample, they may fail to classify
metabolites with very similar properties to chemical changes, such as creatine compared to creatine
phosphate, or uridine diphosphate and uridine triphosphate. Since these types of metabolites usually
have different mass-to-charge values (m / z), it should be possible to differentiate them by combining
NMR and MS data. To accomplish this task, the NMR / MS Translator method has been introduced.
The fully automated NMR / MS Translator method prepares candidates for baptism by metabolites by
asking for an NMR sample compared to the NMR metabolomics database. Thereafter, of the returning
candidates, there is a mass (m / z) of all their ions and adductors, as well as their isotope distribution.
Finally, it compares the expected m / z concentrations with the high-dose MS measurement for the
same sample for direct confirmation of the prescribed metabolites identified by NMR and MS. The
NMR / MS Translator method has been used in human urine, tomato extract, and the Arabidopsis
thaliana metabolome, by increasing self-identification using only the NMR or MS method.

Findings:
Metabolomics has made significant progress in many areas over the past 18 months. This small
overview aims to provide an overview of these developments in terms of their contribution to targeted
and targeted metabolomics. New computational methods have emerged to overcome the complete
manual computation of metabolites in a single spectrum (1D) 1H nuclear resonance (NMR) spectra.
This provides additional consistency between comparisons between labs. The combination of two (2D)
NMR metabolic data under the integrated web server allowed for the most accurate identification of the
metabolites listed in the list of these repositories. With the remaining unregistered and unknown
metabolites, new cheminformatics methods have been developed by combining NMR with mass
spectrometry (MS). These combined MS / NMR methods accelerate the detection of anonymity in
unintended studies, and now allow for the detection of a large number of metabolites in in-app studies

Methodology:
Untargeted studies focus on measuring and comparing as many signals as possible across a sample set,
followed by the assignment of these signal to metabolite ID’s by using metabolomics databases.
Although excellent progress has been made in expanding metabolomics databases with new
metabolites, a significant portion of signals detected in untargeted studies still cannot be identified
through this approach due to the absence of their spectra in the databases. Untargeted studies are highly
interested in the identification of unknown metabolites, especially when they are the biomarkers of a
study. Identification of unknowns is generally accepted as the bottleneck of untargeted metabolomics.
Traditionally, their identification has been performed by extensive isolation of the molecule from
extracts in sufficient amount for detailed analysis by MS, NMR, X-ray, circular dichroism, and other
analytical techniques. While this approach has been proven to be useful, complete fractionation is time-
consuming. Moreover, a low yield of purification may not allow for the downstream structure
elucidation process for low-abundance metabolites. Alternatively, structure elucidation can be
performed in the mixture environment, such as in crude extract or the partially fractionated sample.
There are three main approaches that are proposed for unknown identification in mixtures; the first
approach uses only mass spectrometry techniques. This approach compares the experimental
fragmentation spectra of unknown metabolite with the predicted fragmentation of all the possible
candidate isomeric structures to find the best match.
The second strategy, on the other hand, only relies on NMR, in which the experimental chemical shifts
of unknown metabolites are sequentially assigned and deconvoluted by multidimensional NMR. These
assignments are further verified through comparison against their quantum NMR chemical shift
predictions. While these MS and NMR-based approaches greatly facilitate the structural
characterization, they have limited power. Since they only rely on a single technique. Recently, several
hybrid MS/NMR metabolite identification strategies have been proposed.

What you have learnt from the research paper

The field of metabolomics is rapidly evolving, with strong applications in line with path development.
Most of the recent developments in NMR and MS / NMR methods are covered in this minor overview
with some emphasis on their contribution to targeted and unintended metabolomics. Fast, accurate, and
automatic detection technology, and the size of the material has improved over the past 18 months. We
expect this trend to continue. For targeted metabolomics, continuous increase in automation, speed, and
accuracy of complete metabolite calculations are essential. On the diagnostic side, there are currently
about 1,000 metabolites available in NMR software database libraries and web servers. This number is
much smaller than the estimated hundreds of naturally occurring metabolites. Therefore, these libraries
need to continue to grow by adding more metabolites, such as purchasing and recording actual levels,
by extracting data from books, and by plotting the formation of novel metabolites, which will make it
clear that MS / NMR methods are a potent compound. Overall, these efforts will help in predicting
several growing numbers of metabolites in app studies.