Peptide Mass Fingerprinting (Proteomics and Genomics)

1. PEPTIDE MASS
FINGERPRINTING
PRESENTED BY:
Shumail Shad
Rida Khalid
Arooba Baig
Muhammad Touseef
Hafiz Muhammad Zohaib
PRESENTED TO:
Dr. Fazeelat Karamat
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2. Introduction
 It is basically a technique that is used for the identification
of protein. in which the protein of interest is splitted into
smaller peptide then the mass of these peptides is
measured by mass spectrometer such as MALDI-TOF or
ESI-TOF.
 This method was first developed in 1993.
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3. Peptide – Specific protein fragment usually generated with
Trypsin.
Mass – the size of the peptide
Fingerprint – Uniqueness
 Importance
The identification of protein is one of the hardest task among
proteomics but mass spectrometry is the excellent method for
identification of protein allowing to measure with high precision
the mass/charge ratio of charged molecules such as peptides.
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4. Procedural steps
The protein of interest from a sample are separated on 2D PAGE
Protein of interest is digested by Trypsin (or any other site specific
cleavage)
Ionization of peptides in a MALDI / ESI mass spectrometer
m/z values detected and plotted as mass spectrum
PMF database search to identify the protein
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5. Sample Preparation
 Protein samples can be derived from SDS-PAGE (Sodium
dodecyl sulfate-Polyacrylamide gel electrophoresis) –
Chemical modification.
 Protein is cut into several fragments using proteolytic enzymes.
 Mostly TRYPSIN used – primarily because of its high
cleavage specificity, availability and cost.
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6.  Sample : protease = 50 : 1
 Peptides are extracted with acetonitrile and dried
under vacuum.
 Peptides dissolved in a small amount of distilled
water and are purified
 Mass spectrometric analysis
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7. Maldi analysis
Steps
 A small fraction of the peptide (usually 1 microliter or less) is pipetted onto a
MALDI target and a chemical called a matrix is added to the peptide mix
 The matrix molecules are required for the desorption of the peptide
molecules.
 Matrix and peptide molecules co-crystallize on the MALDI target and are
ready to be analyzed.
 The target is inserted into the vacuum chamber of the mass spectrometer and
the desorption and ionisation of the polypeptide fragments is initiated by a
pulsed laser beam which transfers high amounts of energy into the matrix
molecules.
 The energy transfer is sufficient to promote the ionisation and transition of
matrix molecules and peptides from the solid phase into the gas phase
 The ions are accelerated in the electric field of the mass spectrometer and fly
towards an ion detector where their arrival is detected as an electric signal.
 Their mass-to-charge ratio is proportional to their time of flight (TOF) in the
drift tube and can be calculated accordingly.
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9. Computational analysis
 The mass spectrometric analysis produces a list of molecular
weights of the fragments which is often called a peak list
 Peak list is obtained from MALD-TOF/ ESI-TOF.
 Peptide masses compared with database like Swiss-Prot.
 Insilco digestion by trypsin
 Masses of both unknown protein and database protein fragments
are compared
 Results are obtained
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10. Peak list
Calculate the absolute masses of the peptides
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11. PMF Database Search
450.2201
609.3667
698.3100
1007.5391
1199.4916
2098.9909
PEAKLIST
(EXPERIMENTAL
RESULTS)
>gi|2924450|emb|CAA17750.1| PROBABLE FATTY-ACID-CoA LIGASE FADD18 (FRAGMENT) (FATTY-ACID-CoA SYNTHETASE) (FATTY-
ACID-CoA SYNTHASE) [Mycobacterium tuberculosis H37Rv]
MAASLSENLSCHSSNMCRLSGNAATNLERPGEEPPGDRCTRRQAVRPARTLAKKGNIPVGYYKDEKKTAETFRTINGVRYAIPGDYAQVEEDGTVTMLGR
GSVSINSGGEKVYPEEVEAALKGHPDVFDALVVGVPDPRY
GQQVAAVVQARPGCRPSLAELDSFVRSEIAGYKVPRSLWFVDEVKRSPAGKPDYRWAKEQTEARPADDVH
AGHVTSGS
>gi|15610649|ref|NP_218030.1| fatty-acid-CoA ligase [Mycobacterium tuberculosis H37Rv]
MAASLSENLSCHSSNMCRLSGNAATNLERPGEEPPGDRCTRRQAVRPARTLAKKGNIPVGYYKDEKKTAE
TFRTINGVRYAIPGDYAQVEEDGTVTMLGRGSVSINSGGEKVYPEEVEAALKGHPDVFDALVVGVPDPRY
GQQVAAVVQARPGCRPSLAELDSFVRSEIAGYKVPRSLWFVDEVKRSPAGKPDYRWAKEQTEARPADDVH
AGHVTSGS
Protein FASTA
database
450.2017 (P21234)
609.2667 (P12345)
664.3300 (P89212)
1007.4251 (P12345)
1114.4416 (P89212)
1183.5266 (P12345)
1300.5116 (P21234)
1407.6462 (P21234)
1526.6211 (P89212)
1593.7101 (P89212)
1740.7501 (P21234)
2098.8909 (P12345)
in silico digestion
(THEORETICAL)
OUTPUT:
2 Unknown masses
1 hit on P21234
3 hits on P12345
RESULT:
protein is P12345
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12. Results statistically analyzed to find the best match
A PMF website (Prowl, ProFound, Mascot,
PepIdent)
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13. Advantages
 Identification of protein from Peptide Signature - only
the Masses of the peptides have to be known.
 Doesn’t require too much sample optimization
 Can be done by a moderately skilled operator (don’t
need to be an MS expert)
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14. Disadvantages
 The protein sequence has to be present in the database of interest
 Most PMF algorithms assume the peptides come from a single
protein - mixture protein can complicate the analysis and potentially
compromise the results.
 This technique is less accurate for 3+ protein mixtures
 The correct protein may not be identified even if some of the
peptides contain post-translational modifications.
 Spurious or missing critical mass peaks always lead to
problems(this could be due to mishandling sample).
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15. APPLICATION
 Proteins are being identified over large or small
phylogenetic distances across species boundaries.
 As peptide mass fingerprinting has a sample throughput
similar to AA analysis, this combined identification
approach is suitable for rapid protein identification.
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16.  Collagen is the chief proteinaceous component of vertebrate
connective tissues
 New application of peptide mass fingerprinting in the
identification of materials used in cultural objects at the Peabody
Museum of Archaeology and Ethnology
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17.  PMF uses enzymatic digestion of extracted collagen
to cleave proteins at specific amino acid sites forming
a peptide mixture.
 Markers are compared with those from known
materials to determine the species from which they
were derived.
 Since few mammalian collagen sequences are known,
species identification by PMF requires the generation
of a reference database.
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