Proteomics

• c. Questions to answer for each topic

• i. How was the instrument designed?
• ii. What are original publications and why were they significant in the development of the
• instrument?
• iii. Who designed the instruments? What are the commercially available instruments, and how much
• do they cost?
• iv. What are the sensors physically composed of? How are they designed?
• v. What is the sensitivity and how does that compare to other instruments?
• vi. What is the spatial resolution and how does that compare to other instruments?
• vii. What is the field of view and how does that compare to other instruments?
• viii. What is temporal resolution and how does that compared to other instruments?
• ix. What is the relevant and fundamental physics behind the instrumentation and what is the physical
• path towards generation of the image from source of energy?
• x. How is the raw data generated and how is the image reconstructed?
• xi. Is multiplex imaging possible with this instrument? How does it compare to other instruments?
 -Omics
• -Omics are fields of study that use powerful technologies to
analyze the massive datasets produced by living organisms.
These fields allow us to understand the intricate workings of
cells, organisms, and populations at a deeper level than ever
before.

• -omics researchers gain insights into disease, development,

evolution, and other complex biological processes. This
knowledge can then be used to develop new drugs, improve
diagnostic tools, and personalize healthcare.

• Some of the most common -omics fields include genomics,

transcriptomics, proteomics, and metabolomics.
What are Proteomics?
• Proteins can bridge the gap between genomic information and biologic
functions and disease phenotypes.
• Proteins do not function in isolation and major biological processes
are mediated through protein interactions that control metabolic and
signaling pathways, cellular processes, and organismal systems, hence
control the chaotic networks and mechanisms implicated in health and
diseases .
• Proteomics is an integrated research area that is centered on the
premise of large-scale identification and quantification of proteins in
biological specimens .
The Branches of Proteomics
Marc Wilkins

• Professor in the School of Biotechnology

and Biomolecular Sciences at the
University of New South Wales, Sydney
• PROTein complement expressed by a
genOME’.
MALDI-TOF MS
• The high sensitivity and specificity achievable by mass spectrometry
(MS) make it superior to immunoassays for analysis of several drug
types.
• MS-based clinical proteomics improve medical practice at the level of
diagnosis, characterizing new targets for drug development,
therapeutic intervention, prognosis and digging for biomarker
candidates.
• bioMérieux Vitek MALDI-TOF MS
• Costs ~250,000
• Estimated to save around $68,886.51, pays for itself in ~3 years.
 • 1. Ionize: Molecules are bombarded with energy,
turning them into charged particles.
• 2. Race time: Ions with the same charge are all
Time-of-flight mass blasted with the same force, but heavier ones are
slower.
spectrometry • 3. Measure the finish: The faster an ion reaches the
detector, the lighter it is.
• 4. Analyze the results: Identify and measure different
components in a sample based on their "flight
times."
Matrix-assisted Laser Desorption/Ionization
(MALDI) Components
• 1. Sample Preparation
• 2. Laser Irradiation
• 3. Ion Source
• 4. Flight Tube
• 5. Detector
• 6. Vacuum System:
• 7. Data Acquisition System:
 MALDI Imaging
• Solid Solution Formation:
• Excess matrix isolates analyte molecules.
• Homogeneous "solid solution" facilitates desorption.
• Matrix Excitation and Ablation:
• Laser pulse excites matrix chromophores (light-absorbing
groups).
• Rapid vibrational energy transfer leads to localized
disintegration.
• Ejected clusters contain analyte surrounded by matrix and salt
ions.
• Matrix evaporates from clusters, leaving isolated
analyte in the gas phase.
• Analyte Ionization:
• Photo-excited matrix molecules transfer protons or cations to
the analyte.
• Characteristic [M+X]+ (X = H, Na, K) ions are formed in the
desorbed plume.
Emerging In vivo techniques
• Rapid evaporative ionization MS (REIMS)
• Developed and integrated to routine clinical use for accurate identification of
tumor tissues during surgery
• High sensitivity/specificity to analyze and identify tissue samples in
vivo and ex vivo without sample preparation and in real time
Mass Spec Pen
• Uses a solid-liquid extraction mechanism and
transports the molecules to a mass
spectrometer.
• Extracted molecules can then be used to
predict if the tissue sample analyzed contains
cancerous cells using machine learning
algorithms and statistical models
• Distributed by Thermo Fisher Scientific.
The iKnife

• Electricity heats the tip of the

iKnife.
• The hot blade causes the cells in
the tissue to explode, releasing
molecules in the smoke.
• The smoke is sucked up into a
tube and fed into a mass
spectrometer.
• Generates a 'fingerprint' of the
tissue.
• ~300,000 USD
• https://www.reuters.com/article/idUSBRE96G12B/#:~:text=The%20current%20experi
mental%20version%20of,pounds%20(%24300%2C000)%20to%20build
.
• Birhanu, A.G. Mass spectrometry-based proteomics as an emerging tool in clinical
laboratories. Clin Proteom 20, 32 (2023). https://doi.org/10.1186/s12014-023-09424-x
• Graves PR, Haystead TA. Molecular biologist's guide to proteomics. Microbiol Mol
Biol Rev. 2002 Mar;66(1):39-63; table of contents. doi: 10.1128/MMBR.66.1.39-
63.2002. PMID: 11875127; PMCID: PMC120780.
• Tran A, Alby K, Kerr A, Jones M, Gilligan PH. Cost Savings Realized by
Implementation of Routine Microbiological Identification by Matrix-Assisted Laser
Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol. 2015
Aug;53(8):2473-9. doi: 10.1128/JCM.00833-15. Epub 2015 May 20. PMID:
25994167; PMCID: PMC4508454.