Proteomics%20Technology%20and%20Protein%20Identification

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Proteomics Technology and Protein Identification

• Nathan Edwards
• Center for Bioinformatics and Computational
  Biology

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Outline

• Proteomics
• Mass Spectrometry
• Protein Quantitation
• Protein Identification
• Computer Lab

3
Proteomics

• Proteins are the machines that drive much of
  biology
• Genes are merely the recipe
• The direct characterization of a samples
  proteins en masse.
• What proteins are present?
• What isoform of each protein is present?
• How much of each protein is present?

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Systems Biology

• Establish relationships by
• Choosing related samples,
• Global characterization, and
• Comparison.

Gene / Transcript / Protein Gene / Transcript / Protein
Measurement Predetermined Unknown
Discrete (DNA) Genotyping Sequencing
Continuous Gene Expression Proteomics
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Samples

• Healthy / Diseased
• Cancerous / Benign
• Drug resistant / Drug susceptible
• Bound / Unbound
• Tissue specific
• Cellular location specific
• Mitochondria, Membrane

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Protein Chemistry Assay Techniques

• Gel Electrophoresis
• Isoelectric point
• Molecular weight
• Liquid Chromatography
• Hydrophobicity
• Digestion Enzymes
• Cut protein at motif
• Fluorescence
• Staining

• Affinity capture
• Phosphorylation
• Protein Binding
• Receptors
• Complexes
• Flow Cytometry
• Mass Spectrometry
• Accurate molecular weight

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2D Gel-Electrophoresis

• Protein separation
• Molecular weight (Mw)
• Isoelectric point (pI)
• Staining
• Birds-eye view of protein abundance

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2D Gel-Electrophoresis
Bécamel et al., Biol. Proced. Online 2002494-104
.
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Paradigm Shift

• Traditional protein chemistry assay methods
  struggle to establish identity.
• Identity requires
• Specificity of measurement (Precision)
• Mass spectrometry
• A reference for comparison (Measurement ?
  Identity)
• Protein sequence databases

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Mass Spectrometer

• ElectronMultiplier(EM)

• Time-Of-Flight (TOF)
• Quadrapole
• Ion-Trap

• MALDI
• Electro-SprayIonization (ESI)

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Mass Spectrometer(MALDI-TOF)
(b) M_at_LDITM LR by Micromass, UK
Detector (linear mode)
Reflectron
N2 Laser
Lens
Detector (reflectron mode)
Target plate with sample
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Mass Spectrometer (MALDI-TOF)
UV (337 nm)
Microchannel plate detector
Field-free drift zone
Source
Pulse voltage
Analyte/matrix
Ed 0
Length D
Length s
Backing plate (grounded)
Extraction grid (source voltage -Vs)
Detector grid -Vs
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Mass Spectrum
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Mass is fundamental
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Mass Spectrum
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Mass Spectrum

• Isotope Cluster
• 12C 99
• 13C 1

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Peptide Mass Fingerprint
Cut out 2D-GelSpot
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Peptide Mass Fingerprint
Trypsin Digest
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Peptide Mass Fingerprint

• Trypsin digestion enzyme
• Highly specific
• Cuts after K R except if followed by P
• Protein sequence from sequence database
• In silico digest
• Mass computation
• For each protein sequence in turn
• Compare computer generated masses with observed
  spectrum

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Mass Spectrometry

• Strengths
• Precise molecular weight
• Fragmentation
• Automated
• Weaknesses
• Best for a few molecules at a time
• Best for small molecules
• Mass-to-charge ratio, not mass
• Intensity ? Abundance

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Proteomics Quantitation

• 2D-Gel Electrophoresis
• Replicate LC/MS acquisitions
• Stable Isotope Labeling
• Protein profiling

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LC/MS for Peptide Abundance
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LC/MS for Peptide Abundance
Mass Spectrometry
LC/MS 1 MS spectrum every 1-2 seconds
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LC/MS for Peptide Abundance
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LC/MS for Peptide Abundance
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Stable Isotope Labeling
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Stable Isotope Labeling

• SILAC Lysine with 12C6 vs 13C6

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MALDI Protein Profiling

• Hundreds of healthy and diseased samples
• Single MS spectrum per sample
• Statistical datamining to find biomarkers
• Commercialization for ovarian cancer under name
  Ovacheck

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MALDI Protein ProfilingMale Spectra
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MALDI Protein ProfilingFemale Spectra
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Protein Profiling Statgram
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MALDI Protein Profiling
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MALDI Protein Profiling
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Peptide Identification by MS/MS

• Most mature proteomics workflow
• Sample preparation
• Instruments
• Software
• Compatible with quantitation by
• Replicate LC/MS acquisitions
• Stable isotope labeling
• 2D-Gels (but essentially unnecessary)

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Sample Preparation for MS/MS
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Single Stage MS
MS
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Tandem Mass Spectrometry(MS/MS)
Precursor selection
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Tandem Mass Spectrometry(MS/MS)
Precursor selection collision induced
dissociation (CID)
MS/MS
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Peptide Fragmentation
Peptides consist of amino-acids arranged in a
linear backbone.
N-terminus
H-HN-CH-CO-NH-CH-CO-NH-CH-CO-OH
Ri-1
Ri
Ri1
C-terminus
AA residuei-1
AA residuei
AA residuei1
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Peptide Fragmentation
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Peptide Fragmentation
yn-i-1
-HN-CH-CO-NH-CH-CO-NH-
CH-R
Ri
i1
R
i1
bi1
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Peptide Fragmentation
xn-i
yn-i-1
-HN-CH-CO-NH-CH-CO-NH-
CH-R
Ri
i1
R
ai
i1
bi1
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Peptide Fragmentation
Peptide S-G-F-L-E-E-D-E-L-K
MW ion ion MW
88 b1 S GFLEEDELK y9 1080
145 b2 SG FLEEDELK y8 1022
292 b3 SGF LEEDELK y7 875
405 b4 SGFL EEDELK y6 762
534 b5 SGFLE EDELK y5 633
663 b6 SGFLEE DELK y4 504
778 b7 SGFLEED ELK y3 389
907 b8 SGFLEEDE LK y2 260
1020 b9 SGFLEEDEL K y1 147
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Peptide Fragmentation
1166
1020
907
778
663
534
405
292
145
88
b ions
K
L
E
D
E
E
L
F
G
S
147
260
389
504
633
762
875
1022
1080
1166
y ions
100
Intensity
0
m/z
250
500
750
1000
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Peptide Fragmentation
1166
1020
907
778
663
534
405
292
145
88
b ions
S
K
L
E
D
E
E
L
F
G
147
260
389
504
633
762
875
1022
1080
1166
y ions
y6
100
y7
Intensity
y5
y2
y3
y8
y4
y9
0
m/z
250
500
750
1000
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Peptide Fragmentation
1166
1020
907
778
663
534
405
292
145
88
b ions
K
L
E
D
E
E
L
F
G
S
147
260
389
504
633
762
875
1022
1080
1166
y ions
y6
100
y7
Intensity
y5
b3
b4
y2
y3
b5
y8
y4
b8
y9
b6
b7
b9
0
m/z
250
500
750
1000
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Peptide Identification

• Given
• The mass of the precursor ion, and
• The MS/MS spectrum
• Output
• The amino-acid sequence of the peptide

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Peptide Identification

• Two paradigms
• De novo interpretation
• Sequence database search

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De Novo Interpretation
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De Novo Interpretation
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De Novo Interpretation
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De Novo Interpretation
Amino-Acid Residual MW Amino-Acid Residual MW
A Alanine 71.03712 M Methionine 131.04049
C Cysteine 103.00919 N Asparagine 114.04293
D Aspartic acid 115.02695 P Proline 97.05277
E Glutamic acid 129.04260 Q Glutamine 128.05858
F Phenylalanine 147.06842 R Arginine 156.10112
G Glycine 57.02147 S Serine 87.03203
H Histidine 137.05891 T Threonine 101.04768
I Isoleucine 113.08407 V Valine 99.06842
K Lysine 128.09497 W Tryptophan 186.07932
L Leucine 113.08407 Y Tyrosine 163.06333
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De Novo Interpretation
from Lu and Chen (2003), JCB 101
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De Novo Interpretation
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De Novo Interpretation
from Lu and Chen (2003), JCB 101
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De Novo Interpretation

• Find good paths in spectrum graph
• Cant use same peak twice
• Forbidden pairs NP-hard
• Nested forbidden pairs Dynamic Prog.
• Simple peptide fragmentation model
• Usually many apparently good solutions
• Needs better fragmentation model
• Needs better path scoring

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De Novo Interpretation

• Amino-acids have duplicate masses!
• Incomplete ladders create ambiguity.
• Noise peaks and unmodeled fragments create
  ambiguity
• Best de novo interpretation may have no
  biological relevance
• Current algorithms cannot model many aspects of
  peptide fragmentation
• Identifies relatively few peptides in
  high-throughput workflows

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Sequence Database Search

• Compares peptides from a protein sequence
  database with spectra
• Filter peptide candidates by
• Precursor mass
• Digest motif
• Score each peptide against spectrum
• Generate all possible peptide fragments
• Match putative fragments with peaks
• Score and rank

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Peptide Fragmentation
K
L
E
D
E
E
L
F
G
S
100
Intensity
0
m/z
250
500
750
1000
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Peptide Fragmentation
1166
1020
907
778
663
534
405
292
145
88
b ions
K
L
E
D
E
E
L
F
G
S
147
260
389
504
633
762
875
1022
1080
1166
y ions
100
Intensity
0
m/z
250
500
750
1000
61
Peptide Fragmentation
1166
1020
907
778
663
534
405
292
145
88
b ions
K
L
E
D
E
E
L
F
G
S
147
260
389
504
633
762
875
1022
1080
1166
y ions
y6
100
y7
Intensity
y5
b3
b4
y2
y3
b5
y8
y4
b8
y9
b6
b7
b9
0
m/z
250
500
750
1000
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Sequence Database Search

• No need for complete ladders
• Possible to model all known peptide fragments
• Sequence permutations eliminated
• All candidates have some biological relevance
• Practical for high-throughput peptide
  identification
• Correct peptide might be missing from database!

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Peptide Candidate Filtering

• Digestion Enzyme Trypsin
• Cuts just after K or R unless followed by a P.
• Basic residues (K R) at C-terminal attract
  ionizing charge, leading to strong y-ions
• Average peptide length about 10-15 amino-acids
• Must allow for missed cleavage sites

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Peptide Candidate Filtering

• gtALBU_HUMAN MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDL
  GEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAK

No missed cleavage sites
MK WVTFISLLFLFSSAYSR GVFR R DAHK SEVAHR FK DLGEENF
K ALVLIAFAQYLQQCPFEDHVK LVNEVTEFAK
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Peptide Candidate Filtering

• gtALBU_HUMAN MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDL
  GEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAK

One missed cleavage site
MKWVTFISLLFLFSSAYSR WVTFISLLFLFSSAYSRGVFR GVFRR RD
AHK DAHKSEVAHR SEVAHRFK FKDLGEENFK DLGEENFKALVLIAF
AQYLQQCPFEDHVK ALVLIAFAQYLQQCPFEDHVKLVNEVTEFAK
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Peptide Candidate Filtering

• Peptide molecular weight
• Only have m/z value
• Need to determine charge state
• Ion selection tolerance
• Mass for each amino-acid symbol?
• Monoisotopic vs. Average
• Default residual mass
• Depends on sample preparation protocol
• Cysteine almost always modified

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Peptide Molecular Weight
i0
Same peptide,i of C13 isotope
i1
i2
i3
i4
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Peptide Molecular Weight
i0
Same peptide,i of C13 isotope
i1
i2
i3
i4
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Peptide Molecular Weight
from Isotopes An IonSource.Com Tutorial
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Peptide Molecular Weight

• Peptide sequence WVTFISLLFLFSSAYSR
• Potential phosphorylation?
• S,T,Y 80 Da

WVTFISLLFLFSSAYSR 2018.06
WVTFISLLFLFSSAYSR 2098.06
WVTFISLLFLFSSAYSR 2098.06
WVTFISLLFLFSSAYSR 2098.06
WVTFISLLFLFSSAYSR 2098.06
WVTFISLLFLFSSAYSR 2098.06
WVTFISLLFLFSSAYSR 2098.06
WVTFISLLFLFSSAYSR 2178.06
WVTFISLLFLFSSAYSR 2178.06

WVTFISLLFLFSSAYSR 2418.06

• 7 Molecular Weights
• 64 Peptides

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Peptide Scoring

• Peptide fragments vary based on
• The instrument
• The peptides amino-acid sequence
• The peptides charge state
• Etc
• Search engines model peptide fragmentation to
  various degrees.
• Speed vs. sensitivity tradeoff
• y-ions b-ions occur most frequently

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Mascot Search Engine
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Mascot MS/MS Ions Search
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Sequence Database SearchTraps and Pitfalls

• Search options may eliminate the correct peptide
• Parent mass tolerance too small
• Fragment m/z tolerance too small
• Incorrect parent ion charge state
• Non-tryptic or semi-tryptic peptide
• Incorrect or unexpected modification
• Sequence database too conservative
• Unreliable taxonomy annotation

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Sequence Database SearchTraps and Pitfalls

• Search options can cause infinite search times
• Variable modifications increase search times
  exponentially
• Non-tryptic search increases search time by two
  orders of magnitude
• Large sequence databases contain many irrelevant
  peptide candidates

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Sequence Database SearchTraps and Pitfalls

• Best available peptide isnt necessarily correct!
• Score statistics (e-values) are essential!
• What is the chance a peptide could score this
  well by chance alone?
• The wrong peptide can look correct if the right
  peptide is missing!
• Need scores (or e-values) that are invariant to
  spectrum quality and peptide properties

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Sequence Database SearchTraps and Pitfalls

• Search engines often make incorrect assumptions
  about sample prep
• Proteins with lots of identified peptides are not
  more likely to be present
• Peptide identifications do not represent
  independent observations
• All proteins are not equally interesting to report

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Sequence Database SearchTraps and Pitfalls

• Good spectral processing can make a big
  difference
• Poorly calibrated spectra require large m/z
  tolerances
• Poorly baselined spectra make small peaks hard to
  believe
• Poorly de-isotoped spectra have extra peaks and
  misleading charge state assignments

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Summary

• Protein identification from tandem mass spectra
  is a key proteomics technology.
• Protein identifications should be treated with
  healthy skepticism.
• Look at all the evidence!
• Spectra remain unidentified for a variety of
  reasons.
• Lots of open algorithmic problems!

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Further Reading

• Matrix Science (Mascot) Web Site
• www.matrixscience.com
• Seattle Proteome Center (ISB)
• www.proteomecenter.org
• Proteomic Mass Spectrometry Lab at The Scripps
  Research Institute
• fields.scripps.edu
• UCSF ProteinProspector
• prospector.ucsf.edu