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Mass Spectrometry and its application in Molecular Medicine

By Prof. Amit Kumar Mandal   |   IISER Kolkata
Learners enrolled: 324   |  Exam registration: 3
ABOUT THE COURSE:

This course provides the fundamental concepts of mass spectrometry (ESI-MS and MALDI-MS), its application in the discovery of disease biomarkers using Proteomics approach, understanding molecular mechanism of biochemical events and human diseases in terms of structural changes of protein and its posttranslational modifications using Native-MS and Hydrogen/Deuterium Exchange-MS and imaging of various cancerous tissues to generate its molecular portrait using Imaging-MS platform.

INTENDED AUDIENCE: Senior level UG students, PG students, PhD students

PREREQUISITES: Knowledge in basics of Chemistry and Biochemistry at the undergraduate level

INDUSTRY SUPPORT:
  • Dr. Reddy’s Laboratories Ltd.
  • Syngene International Ltd.
  • Biocon Limited
  • Sun Pharma
  • Intas Pharma
  • Natco Pharma
  • Torrent Pharma
  • Waters India Pvt. Ltd.
  • Bruker India Scientific Pvt Ltd.

Summary
Course Status : Upcoming
Course Type : Elective
Language for course content : English
Duration : 12 weeks
Category :
  • Biological Sciences & Bioengineering
  • Biotechnology
  • Bioprocesses
  • Biosciences
Credit Points : 3
Level : Undergraduate/Postgraduate
Start Date : 19 Jan 2026
End Date : 10 Apr 2026
Enrollment Ends : 26 Jan 2026
Exam Registration Ends : 13 Feb 2026
Exam Date : 17 Apr 2026 IST
NCrF Level   : 4.5 — 8.0

Note: This exam date is subject to change based on seat availability. You can check final exam date on your hall ticket.


Page Visits



Course layout

Week-1:
Lecture-1- Introduction to soft ionisation mass spectrometry--ESI-MS and MALDI-MS
Lecture-2- Isotopic distribution of signals in mass spectra-and-deconvolution of mass spectra
Lecture-3- Resolution of mass spectra and accuracy of mass measurement and introduction of molecular medicine
Lecture-4- Mass spectra of human hemoglobin and glycated hemoglobin as a diabetes marker glutathionyl hemoglobin as oxidative stress marker
Lecture-5- Mass spectrometry based quantification of oxidative stress in patients with chronic renal failure

Week-2:
Lecture-6- Introduction to tandem mass spectrometry and principle of de novo sequencing
Lecture-7- Chemical modification and enzyme digestion of a peptide-a step towards de novo sequencing
Lecture-8- De novo sequencing of a peptide from chemical derivatization and tandem mass spectra
Lecture-9- De novo sequencing--identification of isobaric amino acid and disulfide connectivity
Lecture-10- De novo sequencing of a tryptic peptide from tandem mass spectra

Week-3:

Lecture-11- De novo sequencing from tandem-MS and SPITC derivatization to simplify tandem-MS
Lecture-12- Routine diagnosis of Hemoglobinopathy--A disease caused by genetic variant of hemoglobin
Lecture-13- Hemoglobinopathies--Identification and characterisation using bottom up proteomics approach--Part-1
Lecture-14- Hemoglobinopathies--Identification and characterisation using bottom up proteomics approach--Part-2
Lecture-15- A genetic variant of hemoglobin causing false elevation of HbA1c and hence false diagnosis of diabetes mellitus

Week-4:
Lecture-16- Nano-LC-ESI-MS based analysis of a proteome - A bottom up proteomics approach
Lecture-17- Iron salts as food fortificants to combat Iron Deficiency Anemia
Lecture-18- Nano ferric pyrophosphate as a food fortificant in a rat model--Bioavailability and toxicity assessment
Lecture-19- Nano ferric pyrophosphate as a food fortificant in rat model--Toxicity assessment using biochemical histopathological and proteomics approach
Lecture-20- Nano ferric pyrophosphate as a food fortificant in a rat model--Exploring biomarker of toxicity using plasma proteomics

Week-5:
Lecture-21- Biomarker for nano particles induced toxicity in a rat model---nLC-ESI-MS based plasma proteomics approach
Lecture-22- Quantitative proteomics of rat plasma proteins---Absolute quantification of Fetuin B--a biomarker of nano particle toxicity
Lecture-23- 2D-gel-electrophoresis based proteomics-principle and methods
Lecture-24- Differential plasma proteomics--2D-gel based approach
Lecture-25- Analysis of 2D gel spots-in-gel digestion-identification of proteins-- MALDI-MS based approach

Week-6:
Lecture-26- Mass spectrometry based absolute quantification of human plasma proteins
Lecture-27- Absolute quantification of plasma Apolipoprotein-AIV-A probable biomarker of attempted suicide
Lecture-28- MALDI-MS based identification of microorganism in clinical samples
Lecture-29- Native mass spectrometry using nano-ESI-MS platform
Lecture-30- Analysis of an array of glycated hemoglobin in patients with poorly controlled diabetes mellitus

Week-7:
Lecture-31- Molecular mechanism of sickle hemoglobin polymerisation
Lecture-32- Inhibition of sickle hemoglobin polymerisation upon glutathionylation
Lecture-33- Structural analysis of desorbed hemoglobin from nano particle surface
Lecture-34- Functional assay of human hemoglobin and its variants
Lecture-35- Application of native mass spectrometry to calculate equilibrium constant

Week-8:
Lecture-36- Bioconjugation of para-benzoquinone-of-cigarette-smoke-and-human-hemoglobin
Lecture-37- Bioconjugation of human hemoglobin with quinone as airborne environment pollutants
Lecture-38- ion mobility-mass-spectrometry
Lecture-39- Introduction-to-hydrogen-deuterium-exchange mass spectrometry
Lecture-40- Rate law of hydrogen-deuterium-exchange kinetics

Week-9:
Lecture-41- Molecular insights in inhibition of HbS polymerisation upon oxygenation monitored by HDX-MS platform-part-I
Lecture-42- Molecular insights in inhibition of HbS polymerisation upon oxygenation monitored by HDX-MS platform-part-II
Lecture-43- Molecular insights in inhibition of HbS polymerisation upon oxygenation -part-III- and upon glutathionylation-part-I-monitored by HDX-MS platform
Lecture-44- Molecular insights in inhibition of HbS polymerisation upon glutathionylation-part-II-monitored by HDX-MS platform
Lecture-45- N-acetyl cysteine as an antisickling agent in sickle cell disease

Week-10:
Lecture-46- Effect of quinones on morphology of human RBC
Lecture-47- Effect-of-NAC-to neutralise-quinone-and-in-vivo-HDX
Lecture-48- Application of HDX-MS in structural analysis of hemoglobin in vivo
Lecture-49- Application of HDX-MS in structural analysis of hemoglobin in vivo-and-desorbed-hemoglobin from nano particle-surface
Lecture-50- Application-of-HDX-MS-and -CD-spectroscopy-to-monitor-structural changes-of hemoglobin from NP surface

Week-11:
Lecture-51- Structure-function correlation of Hb Beckman, a genetic variant of human hemoglobin, using HDX-MS
Lecture-52- Structure-function correlation of glutathionyl hemoglobin, a posttranslational variant of human hemoglobin, using HDX-MS
Lecture-53- Fundamentals of tissue imaging mass spectrometry using MALDI-MS
Lecture-54- Kidney tissue imaging in a nano particle exposed rat model
Lecture-55- Imaging of kidney tissues of NP exposed rats and imaging of human prostate tissue

Week-12:
Lecture-56- Imaging of human prostate cancer tissue using MALDI-MS
Lecture-57- Imaging of human prostate cancer tissue using MALDI-MS and analysis of tissue proteomics data
Lecture-58- Desorption Electrospray Ionisation based Mass Spectrometric Imaging of Prostate Cancer Tissue
Lecture-59- Fast photochemical oxidation of protein combined to mass spectrometry for protein footprinting both in vitro and in vivo
Lecture-60- Biosimilar-monitored through mass spectrometric techniques

Books and references

  1. Protein Sequencing and Identification Using Tandem Mass Spectrometry: Michael Kinter, Nicholas E. Sherman.
  2. Mass spectrometry: Principles and Application Edmond de Hoffmann, Vincent Stroobant.
  3. Proteomics Today Mahmoud Hamdan, Pier Giorgio Righetti.
  4. Biological Mass Spectrometry, Methods in Enzymology, Biological Mass Spectrometry, Volume 402.
  5. Hydrogen Exchange Mass Spectrometry of Proteins: Fundamental, Methods, and Applications, David D. Weis.
  6. Application of Hydrogen/Deuterium Exchange Mass Spectrometry in Structural Biology and Molecular Medicine A chapter in the Book “Advances in Biochemistry and Applications in Medicine” Volume-2; http://openaccessebooks.com/biochemistry-applications-in-medicine-volume-2.html Bindu Yadaganahalli Srinivasu, Amit Kumar Mandal.
  7. Application of Mass Spectrometry to Analyse Protein Structure within a Live Cell A chapter in the Book “Advances in Biochemistry and Applications in Medicine” Volume-3; http://openaccessebooks.com/biochemistry-applications-in-medicine-volume-3.html Bindu Yadaganahalli Srinivasu, Amit Kumar Mandal.
  8. Sickle Cell Hemoglobin A chapter in the Book “Vertebrate and Invertebrate Respiratory Proteins, Lipoproteins and other Body Fluid Proteins” Subcellular Biochemistry, 2020, Volume 94, pages 297-322, Amit Kumar Mandal, Amrita Mitra, Rajdeep Das.
  9. Mass Spectrometry Imaging: Principles and Protocols Methods in Molecular Biology, 656 Stainslav S. Rubakhin, Jonathan V. Sweedler.

Instructor bio

Prof. Amit Kumar Mandal

IISER Kolkata
Dr. Amit Kumar Mandal, Associate Professor, IISER-Kolkata, am a Chemist trained in Biophysical chemistry in PhD and Postdoctoral research level. As an independent scientist, my research is primarily based on the possibilities of using fundamental discovery based approaches in the translation space with a focus on molecular understanding of human diseases, on diagnostics and also opportunistically look at the issues of therapy. Over the past seventeen years, I am primarily involved in the investigations of the structure-function correlation of proteins that are of critical importance in different human diseases, using a combination of approaches including mass-spectrometry based clinical proteomics, native mass spectrometry, hydrogen/deuterium exchange mass spectrometry, imaging mass spectrometry and molecular spectroscopy.

Course certificate

The course is free to enroll and learn from. But if you want a certificate, you have to register and write the proctored exam conducted by us in person at any of the designated exam centres.
The exam is optional for a fee of Rs 1000/- (Rupees one thousand only).
Date and Time of Exams: April 17, 2026 Morning session 9am to 12 noon; Afternoon Session 2pm to 5pm.
Registration url: Announcements will be made when the registration form is open for registrations.
The online registration form has to be filled and the certification exam fee needs to be paid. More details will be made available when the exam registration form is published. If there are any changes, it will be mentioned then.
Please check the form for more details on the cities where the exams will be held, the conditions you agree to when you fill the form etc.

CRITERIA TO GET A CERTIFICATE

Average assignment score = 25% of average of best 8 assignments out of the total 12 assignments given in the course.
Exam score = 75% of the proctored certification exam score out of 100

Final score = Average assignment score + Exam score

Please note that assignments encompass all types (including quizzes, programming tasks, and essay submissions) available in the specific week.

YOU WILL BE ELIGIBLE FOR A CERTIFICATE ONLY IF AVERAGE ASSIGNMENT SCORE >=10/25 AND EXAM SCORE >= 30/75. If one of the 2 criteria is not met, you will not get the certificate even if the Final score >= 40/100.

Certificate will have your name, photograph and the score in the final exam with the breakup.It will have the logos of NPTEL and IISER Kolkata .It will be e-verifiable at nptel.ac.in/noc.

Only the e-certificate will be made available. Hard copies will not be dispatched.

Once again, thanks for your interest in our online courses and certification. Happy learning.

- NPTEL team
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