Download CHAPTER G5 PEPTIDES AND PROTEINS ANALYSIS BY MS

B ac k t o B a sic s
Peptides and Proteins Analysis by MS
Back to Basics Section G: Applications
CHAPTER G5
PEPTIDES AND PROTEINS
ANALYSIS BY MS
TABLE OF CONTENTS
Quick Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . 587
Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 589
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 591
Fast Atom Bombardment (FAB) . . . . . . . . . . . . 591
Dynamic FAB . . . . . . . . . . . . . . . . . . . . . . . . . . 593
Mass Spectrometry Mass Spectrometry (MS-MS) . . . . . . . . . . . . . . 593
Other Ion Sources . . . . . . . . . . . . . . . . . . . . . . . 595
Laser Desorption Mass Spectrometry (LDMS) . 597
Electrospray (ES) . . . . . . . . . . . . . . . . . . . . . . . 597
Proteins of Large Molecular Mass . . . . . . . . . . . 601
Analysis of Peptide Mixtures . . . . . . . . . . . . . . . 603
Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . 603
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Quick Guide
Peptides and Proteins Analysis by MS
• Amino acids are the molecular building blocks of peptides and
proteins. About 20 common amino acids are known.
• Peptides and proteins are formed by linking successive amino acids
into chains or rings. The order (sequence) and types of amino
acids determine the chemical and physical properties of peptides
and proteins.
• An enzyme is a special protein which acts as a catalyst for
biochemical reactions.
• Fast Atom Bombardment (FAB) is an ionization technique which
produces a protonated or deprotonated molecular ion and hence
a molecular mass for the sample.
• Liquid Secondary Ion Mass Spectrometry (LSIMS) is a similar but
more recent technique than FAB, and produces indistinguishable
data.
• Dynamic/Continuous Flow FAB allows a continuous stream of
liquid into the FAB source, and hence constitutes an LC-MS
interface.
• An enzyme digest is the term applied to a process whereby a
peptide or protein is mixed with a selected enzyme under
favourable conditions to allow reaction to occur. The enzyme
splits the peptide or protein into smaller units which are easier to
identify.
• Post-translational modifications to proteins are biochemical in
origin and alter the measured molecular mass relative to that
calculated for an untranslated sequence.
• Laser Desorption Mass Spectrometry (LDMS) coupled to a
Time-of-Flight analyser produces an unresolved protonated or
deprotonated molecular ion cluster with virtually no upper mass
limit.
• Electrospray (ES) produces a series of multiply charged ions which
is transformed into an accurate molecular mass profile with
virtually no upper mass range limit.
• Peptides and proteins can be analysed by mass spectrometry.
Molecular mass information can be found by FAB or LSIMS for
samples up to 10 kDa in mass. Laser Desorption and electrospray
can analyse much higher molecular mass samples.
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556
100%
90
Tyr-Gly-Gly-Phe-Leu
MW = 555
80
556 = [M+H]+
70
60
50
40
30
397
20
10
336
317
0
300
Figure 1
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350
425
400
450
500
550
600
mass
650
For this FAB experiment, a sample of the pentapeptidic enkephalin,
Tyr.Gly.Gly.Phe.Leu., dissolved in glycerol was bombarded by
xenon atoms. The resulting mass spectrum shows abundant
protonated molecular ions at m/z 556.
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• Tandem Mass Spectrometry (MS-MS) produces precise structural
or sequence information by selective and specific induced
fragmentation, routinely on samples up to 2500 Da. For samples
of greater molecular mass than this, an enzyme digest will usually
produce several peptides of molecular mass suitable for mass
spectrometry.
• Samples containing mixtures of peptides can be analysed directly
by electrospray. Alternatively they can be separated and analysed
by LC-MS coupling techniques such as Dynamic/Continuous Flow
FAB, or Electrospray.
Summary
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The use of mass spectrometry for the analysis of peptides, proteins
and enzymes has been summarized. This guide should be read in
conjunction with others in the ‘Back to Basics’ series including
‘Biotechnology’ and those describing specific ionization techniques in
detail.
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5
[ 1 ; R = acetyl
1) Acetyl
2) 8-hydroxybutyryl
3) Propionyl
4) Crotonyl
5) Butyryl + Isobutyryl
6) Isovaleryl
7) Octanoyl ]
6
1
3
4
2
4:4
8:2
7
12
15:4
TIME (min)
(a)
NH 2
N
N
303
-
=
=
O
NH
OH CH3
-
-
-
=
O
-
-
CH3
OH
OH
C - CH2 - CH2 - NH - C - CH - C - CH2 - O - P - O - P - O
-
O
=
O
508
CH2
N
136
CH2
O
-
428
O OH
-
S
HO - P - OH
-
=
-
CH2
136
N
330
R
O
( 1; R = acetyl)
303
MH+
810
428
508
330
100
500
800
(b)
Figure 2
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(a) LC-FAB-MS analysis of short and medium chain acyl coenzyme
A compounds (1, = 1-7; 0.5 nmol of each). These compounds carry
acyl groups for enzyme reactions and a number of metabolic
diseases can be traced to enzyme deficiencies which result in the
accumulation of toxic coenzyme A thioesters. (b) The FAB mass
spectrum of acetyl coenzyme A (component 1.1 from the trace
shown in (a). The likely origin of major fragment ions is indicated.
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ANALYSIS OF PEPTIDES AND PROTEINS BY MASS SPECTROMETRY
Introduction
Until 1981, mass spectrometry was limited, generally, to the analysis
of volatile, relatively low molecular mass samples and was difficult to
apply to involatile peptides and proteins without first cutting them
chemically into smaller volatile segments. During the past decade the
situation has changed radically with the advent of new ionization
techniques and the development of tandem mass spectrometry. Now,
the mass spectrometer has a well-deserved place in any laboratory
interested in the analysis of peptides and proteins.
Fast Atom
Bombardment
(FAB)
The first breakthrough came with the development of FAB which
enabled polar compounds of large molecular mass to be ionized
without application of heat for volatilization of the sample.
In FAB (see ‘Back to Basics’ guide), the sample is dissolved in a suitable
solvent (also called a matrix) of low volatility (e.g. glycerol,
thioglycerol, m-nitrobenzyl alcohol) and is bombarded by a beam of
fast xenon or argon atoms. Ionization produces protonated [M+H+]
or deprotonated ([M-H]-) molecular ions, sometimes accompanied by
a little fragmentation. The matrix reproducibly gives background ion
peaks but these can interfere with sample ion peaks and usually
dominate the low mass end of the spectrum (Figure 1). Different
samples exhibit different levels of response to FAB and, with a
mixture of components, it is feasible that not all will be detected; in
some cases, the minor components of a sample appear more
prominently in the mass spectrum than the major ones.
Despite these limitations, FAB is in widespread use and is an excellent
technique for determining the molecular masses of peptides up to
10,000 Daltons, with an accuracy of 0.5 Da.
FAB has evolved and fast atoms are being replaced by fast ions, such
as Caesium (Cs+). This variation is called Liquid Secondary Ion Mass
Spectrometry (LSIMS) because the sample solution affords the
secondary ion beam whilst the bombarding ions constitute the
primary beam. Spectra produced by FAB and LSIMS are virtually
identical, although higher sensitivity at high mass (10 kDa) is claimed
for the latter.
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ION
SOURCE
Figure 3
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MS(1)
CC
MS(2)
A typical MS-MS configuration. Ions produced from a source (e.g.
dynamic-FAB) are analysed by MS(1). Molecular ions (M+ or
[M+H]+ or [M-H]- etc.) are selected in MS(1) and passed through a
collision cell (CC) where they are activated by collision with a
neutral gas. The activation causes some of the molecular ions to
break up and the resulting fragment ions provide evidence of the
original molecular structure. The spectrum of fragment ions is mass
analysed in the second mass spectrometer, MS(2).
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Dynamic FAB
Another development arising from FAB has been its transformation
from a static to a dynamic technique, by allowing a continuous flow of
a solution to travel from a reservoir through a capillary to the probe
tip. Samples are injected either directly, or through a liquid
chromatography (LC) column. The technique is known as Dynamic or
Continuous Flow FAB/LSIMS and provides a convenient direct LC-MS
coupling for the on-line analysis of mixtures, (Figure 2). Mixtures, as
with the acyl coenzyme A factors shown in Figure 2, can be separated
and analysed on-line. In peptide and protein work, the peptidic
substance is often reacted (digested) with enzymes which cleave the
peptide or protein at places along its backbone to give smaller
peptides. This digest (mixture of peptides) must be separated into its
components and the newly-formed peptides identified so that the
original structure can be deduced (this is called ‘mapping’ and is
something like assembling a linear jigsaw). LC-FAB-MS is well-suited
to the separation of such mixtures and the identification of
components through their molecular masses. However, not only the
molecular mass of a peptide is important. The actual sequence (order)
of amino acid residues making up the peptide chain is also important
and FAB, which gives predominantly molecular mass information and
few structural pointers, must be supplemented by another technique,
MS-MS or tandem MS.
Mass SpectrometryMass Spectrometry
(MS-MS)
Typically, a sample is analysed by FAB-MS to obtain a relative
molecular mass and then by FAB-MS-MS to achieve structural
information by fragmenting the molecular ion and examining the
fragment ions. This is achieved by passing the molecular ion from the
first mass analyser into a collision cell (Figure 3). Here collision gas
(e.g. argon) is used to fragment this ion. The fragment ions produced
are analysed by a second mass spectrometer.
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100%
90
80
70
60
50
40
30
20
10
0
m/z 300
915
H-Arg-Val-Tyr le-His-Pro-Phe-OH
669
532
784
400
mass
400
500
600
700
800
900
NH3
Phe
Phe-Pro-H2 O
Phe-Pro-His-H2O
Arg-Val-Tyr-Ile
Figure 4
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A typical FAB-MS-MS experiment on a peptide. The FAB-MS
spectrum of angiotensin III is dominated by the protonated
molecular ion [M+H]+ at m/z 932, confirming the molecular mass
of 931. In an MS-MS experiment only the ion at m/z 932 was
allowed to pass through the first mass analyser into the collision cell
(Figure 3). On passing through the collision cell several fragment
ions were produced and were all analysed by the second mass
analyser to produce the spectrum shown here. The ion at m/z 915
arises by loss of NH3 from 932. The ions at m/z 784, 669, 532 and
400 arise respectively by loss of a phenylalanine residue;
phenylalanine, proline and a water molecule; phenylalanine, proline,
histidine and a water molecule; and arginine, valine, tyrosine and
isoleucine, from 932. These fragments verify the expected sequence
of amino acid residues in Angiotensin III.
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The fragments can only arise directly from the molecular ion and so
provide useful sequence information for peptides. Peptides have been
found to fragment by predictable pathways along their backbone from
the C-terminus and/or the N-terminus, as shown by the example of
angiotensin III (Figure 4).
Tandem mass spectrometers most commonly used for MS-MS studies
include the following analyser combinations, although many others
are possible:
1. quadrupole - collision cell - quadrupole
2. magnetic/electrostatic analyser - collision cell - quadrupole
3. magnetic/electrostatic analyser - collision cell
- magnetic/electrostatic analyser
The collision cell used with the first two types (1, 2) is an RF-only
quadrupole or a hexapole. This type of cell adds only a relatively small
amount of energy to an ion during its collision with the cell gas. The
third type uses a high energy collision cell which has the advantage of
producing fragmentation of amino acid side chains as well as the
‘backbone’ fragmentation shown in Figure 4. This extra fragmentation
gives information which permits differentiation of the two isomeric
amino acid residues, leucine and isoleucine. Sequence information has
been obtained by MS-MS on samples up to 2500 Da, which covers
most enzyme digest generated peptides, often at low pmole levels,
and usually in just a few minutes.
Other Ion Sources
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The techniques described thus far cope well with samples up to
10 kDa. Molecular mass determinations on peptides can be used to
identify modifications occurring after the protein has been assembled
according to its DNA code (post-translation), to map a protein
structure, or simply to confirm the composition of a peptide. For
samples with molecular masses in excess of this, the sensitivity of FAB
is quite low and such analyses are far from routine. Two new
developments have extended the scope of mass spectrometry even
further to the analysis of peptides and proteins of high mass.
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100
Peptides and Proteins Analysis by MS
893.2
(a)
942.7
(n+1) +
m1
998.1
1060.5
1131.1
848.6
n+
m2
1211.8
1304.9
808.2
1413.6
0
m/z
100
0
m/z
700
800
900
1000
1100
1200
1300
1400
1500
1600
16951.1
(c)
16200
16400
16600
16800
17000
17200
17400
17600
17800
(b)
Mass to
Charge Ratio (m/z)
1542.04
1413.59
1304.93
1211.80
1131.12
1060.46
998.11
942.75
893.15
848.57
808.21
771.49
No. of
charges (n)
11
12
13
14
15
16
17
18
19
20
21
22
Mean
S.D.
Molecular
Mass (RMM)
16951.40
16950.95
16950.94
16951.11
16951.62
16951.26
16950.67
16951.30
16950.71
16951.25
16951.14
16950.72
16951.09
±0.30
Figure 5 A sample of the protein, horse heart myoglobin, was dissolved in acidified aqueous
acetonitrile (1% formic acid in H2O/CH3CN, 1:1 v/v) at a concentration of 20 pmol/l.
This sample was injected into a flow of the same solvent passing at 5 µl/min. into the
electrospray source to give the mass spectrum of protonated molecular ions
[M+nH]+ shown in (a). The measured m/z values are given in the table (b), along with
the number of protons (charges; n) associated with each. The mean relative
molecular mass (RMM) is 16951.09 ± 0.3 Da. Finally, the transformed spectrum,
corresponding to the true relative molecular mass is shown in (c); the observed value
is close to that calculated (16951.4), an error of only 0.002%.
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Laser Desorption
Mass Spectrometry
(LDMS)
Peptides and Proteins Analysis by MS
This technique depends on the use of solid matrices (e.g., cinnamic
acid derivatives) to absorb energy from a laser pulse so as to volatilize
and ionize proteins premixed with the matrix. Mass analysis is
achieved by a Time-of-Flight analyser which, as the name suggests,
measures precisely the time taken for the ions to travel from the
source through the flight tube to the detector. The heavier the ion,
the longer the flight time. The spectrum generally contains a
protonated [M+H+] or deprotonated [M-H]- molecular ion cluster,
together with a doubly-charged and perhaps further multiply charged
ions. Fragmentation, and hence sequence information, is usually
absent.
In principle there is no upper limit to the mass range and proteins as
large as 200 kDa have been measured using as little as 1 pmole of
material, making this one of the most sensitive techniques available.
However, the resolution of this technique is low compared with
other mass spectrometric methods, and the ions constituting the
molecular mass cluster are unresolved. Heterogeneous proteins can
present a problem, as the mass accuracy of 0.1% (e.g. 50 Da at
50 kDa) means that some post-translational modifications go
undetected and mass changes associated with a single amino acid
substitution would be unnoticed.
Electrospray (ES)
This second development has radically increased the use of mass
spectrometry in biotechnology by providing an ionization technique
capable of analysing large polar, thermally-sensitive biomolecules with
unprecedented mass accuracy and good sensitivity.
In ES, the sample, in solution, is passed through a narrow capillary and
reaches an atmospheric pressure ionization source as a liquid spray.
The voltage at the end of the capillary is significantly higher (3 kV)
than that of the mass analyser and so the sample emerging is dispersed
into an aerosol of highly charged droplets known as the electrospray.
Evaporation of solvent, aided by a stream of nitrogen, causes a
decrease in the size of the droplets until eventually multiply-charged
ions from individual protein molecules, free from solvent, are
released and can be mass analysed.
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(a)
13+ etc.
α13 = ( α globin + 13H)
γ 13 = ( γ globin + 13H) 13+ etc.
α15
α14
γ 16
γ 15
γ14
α13
γ13
β's
α12
β's
1000
β's
β 's
1100
1200
1300
(b)
Normal α
(15126.4)
Gγ
(15995.3)
Normal β
(15867.2)
Aγ
(16009.3)
Sickle β
(15837. 2)
0
mass
Figure 6
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15200
15400
15600
16000
16200
(a) Part of an electrospray spectrum of globins from the cord blood
of a sickle cell carrier baby and, (b) the same after computer
transformation onto a true molecular mass scale. Normal α, β and
γ globins are clearly visible, along with the sickle cell variant, β. The
two γ-globins (A, G), although having a mass difference of only
14 Da in 16,00 0Da, are easily distinguished from each other.
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The ions so produced are separated by their mass-to-charge (m/z)
ratios. For peptides and proteins, the intact molecules become
protonated with a number (n) of protons (H+). Thus, in place of the
true molecular mass (M), molecular ions have a mass of [M+nH].
More importantly, the ion has n positive charges resulting from
addition of the n protons (H+). Since the mass spectrometer does not
measure mass directly but, rather, mass-to-charge (m/z) ratio the
measured m/z value is [M+nH]/n. This last value is less than the true
molecular mass, depending on the value of n. If the ion of true mass
20,000 Da carries 10 protons, for example, then the m/z value
measured would be (20,000+10)/10 = 2001.
This last m/z value is easy to measure accurately and, if its relationship
to the true mass is known (n = 10), this means the true mass can be
measured very accurately also. The multiply-charged ions have typical
m/z values of <3000 Da, which means that conventional quadrupole
or magnetic sector analysers can be used for mass measurement.
Actually, the spectrum consists of a series of multiply-charged
protonated molecular ions [M+nH]n+ for each component present in
the sample. Each ion in the series differs by plus and minus one charge
from adjacent ions ([M+nH]n+; n = an integer series for example,
1,2,3.... etc). Mathematical transformation of the spectrum produces
a true molecular mass profile of the sample (Figure 5).
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(a)
100
Peptides and Proteins Analysis by MS
Normal α
CHILD
β Montreal - Chori
β Sickle
(β 6:Glu
0
mass
(b)
100
15000
15200
Normal α
15400
15600
15000
Figure 7
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IIe)
Val
15800
16000
MOTHER
Normal β
0
mass
( β 87:Thr
15200
15400
15600
15800
β Montreal - Chori
16000
Electrospray mass spectra of globins from the blood of (a), a child
diagnosed as having the sickle cell anaemia trait and (b) its mother.
As well as the usual β-globin sickle cell variant at m/z 15837.2, a new
variant (β-Montreal-Chori) appears at m/z 15879.3 and is observed
in both the child and the mother.
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Proteins of Large
Molecular Mass
Peptides and Proteins Analysis by MS
Whilst electrospray can be and is used for molecules of all molecular
masses, it has had an especially marked impact on the measurement
of accurate molecular mass for proteins. Traditionally, direct
molecular mass measurement on proteins has been difficult, with
values being obtained which were accurate to only tens or even
hundreds of Daltons. The advent of electrospray now means that
molecular masses of 20,000 Da and upwards can be measured with
unprecedented accuracy (Figure 6). This level of accuracy means that
it is also possible to identify post-translational modifications of
proteins (e.g. glycosylation, acetylation, methylation, hydroxylation,
etc.) and to detect mass changes associated with substitution or
deletion of a single amino acid.
A typical electrospray analysis can be completed in 15 minutes with
as little as 1 pmole of protein. An analysis of the globins from the cord
blood of a baby (Figure 6) showed quite clearly that five globins were
present, viz., the normal ones (α, β, Gγ and Aγ) and a sickle cell
variant (β). The last one is easily revealed in the mass spectrum even
at a level of only 4% in the blood analysed.
Whilst this example shows that small differences in large masses are
easily discerned by electrospray methodology, it should be noted that
absolute accuracy of mass measurement is unprecedentedly high. The
accuracy is sufficiently high that substitution of one amino acid by
another can be detected with ease. Figure 7 illustrates this following
the discovery of a new variant of β-globin, called Hb Montreal-Chori,
in which a threonine residue has been substituted by isoleucine at
position-87 in the β-chain. The substitution caused a mass change
from 15837.2 Da to 15879.3 Da.
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On-Line HPLC of Peptide Mix
Angiotensin 11
Unknown peptide 1010
Melanocyte stimulating
hormone
100
TIC
Bradykinin
Bombesin
Total Ion Current
Luteinising hormone
releasing hormone
Methionine enkephalin
Oxytocin
Time (min.)
Min
26.0
28.0
30.0
32.0
34.0
36.0
38.0
40.0
Figure 8(a) A mixture of peptides was separated by LC and the eluent was
passed into an electrospray source. The total ion current trace (a)
reveals the individual component peptides, each of which was
identified through its measured accurate mass, an illustration of
which is shown in (b) for luteinising hormone releasing hormone.
357 (30.345)
591.7
100
M+2H
Luteinising Hormone Releasing Hormone
592.4
0
m/z 300
568.3
329.6 464.7
363.3
509.4
400
500
599.3
742.5
602.6 709.3
808.2
600
700
800
956.2 1030.5
900
1000
M+H
1183.2
1133.1
1100
1200
Figure 8(b)
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Analysis of
Peptide Mixtures
The electrospray source can be coupled directly to a liquid
chromatographic column so that, as components of a mixture emerge
from the column, they are passed through the source to give accurate
mass data. As an example, a mixture of the peptides shown in
Figure 8(a) was separated by LC and accurately mass analysed by ES.
Figure 8(b) is the mass spectrum of one of these peptides (luteinising
hormone releasing hormone) which gave an abundant ion,
representing a doubly-protonated molecule [M+2H]+ at m/z 592.4
and therefore, a true relative molecular mass (M) of 1182.8.
Conclusion
Intact peptides and proteins can be examined by a variety of new
techniques, including MS-MS, dynamic-FAB and electrospray. Large
masses of tens of thousands of Daltons can be accurately measured
with unprecedented accuracy by electrospray.
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