1

1

260.841 Protein Bioinformatics:Mass Spectrometry

Robert J. CotterMiddle Atlantic Mass Spectrometry Laboratory

Pharmacology and Molecular Sciences

Johns Hopkins University School of MedicineBaltimore, MD

2

What is a mass spectrometer?

ion source mass analyzer detector

Chemical TOF: time-of-flight multiplier

EI: electron impact ITMS: ion trap mass spectrometer channelplate

CI: chemical ionization FTMS: Fourier transform mass spectrometer

Biological …. and combinations of these (QTOF, TOF/TOF, IT/TOF)

MALDI: matrix-assisted laser desorption/ionization

ESI: electrospray ionization

AP/MALDI: atmospheric pressure MALDI a balance for weighing molecules

vacuum system

2

3

MALDI is one method for ionizing peptides and other biomolecules

Matrix-assisted laser desorption/ionization

MALDI mechanism

1. The matrix absorbs UV or IR energy from the pulsed laser

2. The matrix ionizes and dissociates; it undergoes a phase change to a supercompressed gas; charge is passed to some of the analyte molecules

3. Matrix expands at supersonic velocity; additional analyte ions are formed in the gas phase; ions are entrained in the expanding plume

laser

peptide

matrix

4

The MALDI “matrix”:In MALDI, samples are deposited in solutions of a UV-absorbing matrix, which absorbs the laser energy, ionizes and then protonatesthe sample molecules

3

5

DeVmt

2/1

2⎟⎠⎞

⎜⎝⎛=

Short source region (s) with a high field for extracting the ions

Longer field-free drift region (D)

Flight times follow a simple square root dependence on mass:

MALDI is most often used with a time-of-flight (TOF) mass spectrometer:

6

Time-of-flight mass spectrum.

Mass spectrum of a mixture of 11 peptides obtained with pulsed (delayed) extraction on a linear TOF.

160

180

200

220

240

0S 10uS 20uS 30uS

Substance P, 1348 Da

Methionine enkephalin-Arg-Gly Leu 900Da

Peptide sequencing standard, 1639 Da

Parathyroid hormone 28-48, 2148

Beta-melanocyte, 2660 Da

Hepatitus B virus pre-S region 120-145, 3008

Diabetes-associated peptide 8-37, 3200

ACTH 7-38, 3659 Da

ACTH 1-39, 4541 Da

Pancreatic polypeptide, 4182 Da

Biocytin beta-endorphin, 3819 Da

matrix ions

noise form extraction pulse

Raw data spectrum vs. time

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7

Mass resolution is improved using a “single-stage” reflectron mass analyzer

t = m

2eV [ L + L + 4d]

1/ 2

1 2⎛⎝⎜

⎞⎠⎟

Flight times are still proportional to the square root of the mass:

8

Reflectrons compensate for the initial kinetic energy spread of ions.

The “dual-stage” reflectron mass analyzer provides “second order” focusing.

Flight times are proportional to the square root of mass.

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9

160

180

200

220

240

0S 10uS 20uS 30uS

150

160

170

180

38.66uS 38.68uS 38.7uS 38.72uS 38.74uS

34000

36000

38000

40000

0S 20uS 40uS 60uS 80uS

34000

34500

35000

35500

36000

90.75uS 90.8uS 90.85uS 90.9uS

Comparison of linear and reflectron mass spectra

Mass spectrum of a mixture of 11 peptides obtained on a linear TOF

Mass spectrum of a mixture of 9 peptides obtained on a reflectron TOF

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Another way to improve mass resolution is using “delayed extraction*”:

*also known as “pulsed extraction” or “time-lag focusing”

During the delay period, ions with different energies array themselves in different locations.

When the extraction pulse is applied the slower ions will be accelerated the most, and will catch up with the faster ions when they reach the detector

s0 s1 dbefore delay

after delay

V0 V1 V2 (ground)

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11

Whittal, R.M.; Li, L., Anal. Chem. 67 (1995) 1950-1954Brown, R.S.; Lennon, J.J., Anal Chem. 67 (1995) 1998-2003.Vestal, M.L.; Juhasz, P.; Martin, S.A, Rapid Commun. Mass Spectrom. 9 (1995) 1044-1050.

V0

V1

V2

V0

V1

V2

20 kV (constant)

18 kV (constant)

Ground (constant) Ground (constant)

2 kV pulse20 kV18 kV

20 kVNegative pulse

0 V

delay delay

timetime

ABI, Kratos and others Bruker and others

A number of different methods are used to pulse the field in the first extraction region:

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Maximum mass resolution results from a combination of a reflectron and delayed extraction

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Introduced by John Fenn:

Yamashita, M.; Fenn, J.B., J. Phys. Chem. 88 (1984) 4451.Whitehouse, C.M.; Dreyer, R.N.; Yamashita, M.; Fenn, J.B., Anal. Chem. 57 (1985) 675.Fenn, J.B.; Mann, M.; Meng, C.K.; Wong, S.F.; Whitehouse, C.M., Science 246 (1989) 64.

Electrospray ionization (ESI)

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Based on an ion evaporation model:Iribarne, J.V.; Thomson, B.A., J. Chem. Phys. 64 (1976) 2287.Thomson, B.A.; Iribarne, J.V., J. Chem. Phys. 71 (1979) 4451.

Tip at high positive voltage

Evaporation (desolvation) of positively-charged droplets until the Rayleigh limit is reached.

Ejection of positively charged ions from droplet.

Favors ejection of multiply-charged ions

8

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ESI produces multiply-charged ions

Ions have the formula:

(M + nH)+n

From which one can determine M.

Average m/z are around 1000, which is compatible with quadrupole mass spectrometers and ion traps.

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ESI is commonly used on quadrupole ion trap mass spectrometers (ITMS)

• 1.1 MHz

• Used to trap the ions

• used to scan the mass range in either mass-selective instability or resonance ejection modes

• supplementary RF for resonance ejection mode and high mass

• mass selection

• excitation in MS/MS mode

9

17

20

20

20 )2(

8Ω+

=zrm

eVqz

20

20

20 )2(

16Ω+

−=

zrmeUaz

zqzrV

zm

20

20

20 )2(

8Ω+

=

Mathieu parameters:

Mass selective instability mode: if dc voltage on the endcaps is zero, then scan along the az line (by varying the rf voltage); ion ejection occurs at the stability boundary when az = 0.908

The mass ejected is then given by:

Where z is the number of charges and Ω0 is the angular drive frequency(Ω0/2π = 1.1 MHz)

Williams, J.D.; Cox, K.A.; Schwartz, J.C.; Cooks, R.G., in Practical Aspects of Ion Trap Mass Spectrometry, Volume II, Cairns, T., Ed., CRC Press, Boca Raton (1995), pp. 3-50

endc

apbi

as v

olta

ge U

1.1 MHz ring voltage V

V mass scan

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Resonance ejection mode:

A supplementary rf voltage is applied to the endcaps

The fundamental rf voltage on the ring electrode is scanned

Ions are ejected “through a hole in the stability region”

Extension of mass range through axial modulation

Supplementary rf = 69.9 kHzqeject = 0.182m/z = (0.91/0.182) x 650 = 5 x 650 = 3,250

Supplementary rf = 35.2 kHzqeject = 0.091m/z = (0.91/0.091) x 650 = 10 x 650 = 6,500

1.1 MHz ring voltage V

V

endc

apbi

as v

olta

ge U

U

mass scan

10

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The “LCQ” ion trap mass spectrometry uses a quadrupole or octapole inlet system to interface to the atmosphere

RF-only quadrupole or octapole filters that collimate ions from high pressure ESI source.

Ion trap mass spectrometer

Electrospray source at atmospheric pressure

Capillary needle (3.5 kV)

N2

Increasing vacuum

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Using mass spectrometry (MS) for peptide mapping and sequencing

Molecular weights obtained following the use of endoand exopeptidases

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Amino acid “residue” masses tableAmino acid Three

letter code

Single letter code

Nominal mass

Monoisotopic mass

Average mass

Alanine Ala A 71 71.037 71.079 Arginine Arg R 156 156.101 156.188 Asparagine Asn N 114 114.043 114.104 Aspartic acid Asp D 115 115.027 115.089 Cysteine Cys C 103 103.009 103.143 Glutamic acid Glu E 129 129.043 129.116 Glutamine Gln Q 128 128.059 128.131 Glycine Gly G 57 57.021 57.052 Histidine His H 137 137.059 137.141 Isoleucine Ile I 113 113.084 113.160 Leucine Leu L 113 113.084 113.160 Lysine Lys K 128 128.095 128.175 Methionine Met M 131 131.040 131.197 Phenylalanine Phe F 147 147.068 147.177 Proline Pro P 97 97.053 97.117 Serine Ser S 87 87.032 87.078 Threonine Thr T 101 101.048 101.105 Tryptophan Trp W 186 186.079 186.214 Tyrosine Tyr Y 163 163.063 163.176 Valine Val V 99 99.068 99.133

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Chemical reagents and proteolyticenzymes for “peptide mapping”

Chemical reagents

Cleavage sites Comments

Cyanogen bromide after M Homoserine –30.1 Da Homoserine lactone –48.1 Da

BNPS-skatole or DMSO + HCl after W Acid hydrolysis

D/P then random

Endopeptidases

Cleavage sites

Trypsin after K/R Endoproteinase Lys-C after K Endoproteinase Asp-N before D Endoproteinase Arg-C after R Chymotrypsin after F/W/Y/L Pepsin after F/W/Y/L Thermolysin before L/I/M/F/W

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Mass balancing: the sum of the molecular weights of n enzymatic fragments, minus n-1 water molecules, add up to the molecular weight of the intact protein.

Proteolytic enzymes for “peptide sequencing”

Exopeptidases

Selectivity

Carboxypeptidase A stops at R/PX, sometimes G/S/D/E Carboxypeptidase B cleaves at R/K Carboxypeptidase P cleaves PX/D/E, sometimes stops at S/G Carboxypeptidase Y

cleaves at PX/E, sometimes stops at K/R/S/G

Aminopeptidase M non-specific Leucine aminopeptidase

stops at or near K/R/P

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Example. β-amyloid peptide (βA1-40):DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMGGVV

tryptic digest:

DAEFR MW = 636.7 βA1-5 MH+ observed = 637.8HDSGYEVHHQK MW = 1336.5 βA6-16 MH+ observed = 1337.1LVFFAEDVGSNK MW = 1325.7 βA17-28 MH+ observed = 1326.7GAIIGLMVGGVV MW = 1085.5 βA29-40 MH+ observed = 1086.1

cyanogen bromide:

VGGVV MW = 429.6 βA36-40 MH+ observed = 431.1VGGVVIA MW = 613.8 βA36-42 MH+ observed = 614.2GAIIGLM MW = 673.9 βA29-35 MH+ observed = 626.0homoserine MW = 643.8homoserine lactone MW = 625.8

636.7 + 1336.5 + 1325.7 + 1085.5 – 3(18) = 4,329.9

Note that cyanogen bromide digestion revealed a longer amyloid peptide!

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Chemical cleavage: Cyanogen bromide (CNBr) cleaves the amide bond on the C-terminal side of a methionine residue:

forming a terminal homoserine (∆m = -30) or homoserine lactone (∆m = -48) residue

NH

HC C OH

H2C

O

CH2

OH

NH

HC C

H2C

O

CH2

O

homoserine

homoserine lactone

NH

HC C N

HCH

C

CH2

CH2

S

CH3

O R O

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Peptide mapping: tryptic digest of myoglobin

0

10

20

30

40

50

60

70

80

90

100

%Int.

1000 1200 1400 1600 1800 2000Mass/Charge

3[c].G

92 mV[sum= 27531 mV] Profiles 1-300 Smooth Av 1

AXIMA-QIT Data: myoglobin dig dhb0002.G7 19 Dec 2002 12:12 Cal: combined 19 Dec 2002 12:46 Kratos PC Axima QIT V2.3.1: Mode Positive, Mid 750+, Power: 59

1271.71 1606.92

1378.90

1854.01

1272.74

1379.88 1855.01 1982.111607.93

1268.591983.08

952.531192.70

1502.721273.73 1856.001608.90 1984.111380.91953.53 1096.56

1503.75996.52 1120.69 1856.991270.65902.471985.14997.53 1506.96 1609.881143.64 1393.83

MS obtained on a Kratos AXIMA Qit/TOF

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PMF: Peptide Mass FingerprintingTaxonomy : Mammalia (mammals) (246067 sequences)Timestamp : 19 Dec 2002 at 12:18:46 GMTTop Score : 158 for gi|2506462, Myoglobin

Probability Based Mowse Score

Protein Summary Report

Switch to Concise Protein Summary Report

To create a bookmark for this report, right click this link: Protein Summary Report (../data/20021219/FtTtonYe.dat)

Index

Accession Mass Score Description1. gi|2506462 16941 158 Myoglobin2. gi|70561 16940 138 myoglobin [validated] - horse3. gi|2554649 16942 137 Myoglobin (Horse Heart) Mutant With Leu 104 Replaced By Asn (L104n)4. gi|494711 16967 118 Myoglobin (Horse Heart) Mutant With His 64 Replaced By Tyr (H64y)5. gi|2914321 16905 118 H64t Variant Of Myoglobin (Horse Heart) Recombinant Wild-Type

Complexed With Azide6. gi|999870 16967 117 Myoglobin Mutant With His 93 Replaced By Tyr (H93y)7. gi|1942750 16969 117 Myoglobin (Horse Heart) Mutant With Ser 92 Replaced By Asp (S92d)8. gi|25029635 33033 88 similar to pORF2 [Mus musculus domesticus]9. gi|127664 17226 66 Myoglobin

10. gi|127671 17034 65 MYOGLOBIN

Results List

1. gi|2506462 Mass: 16941 Score: 158MyoglobinObserved Mr(expt) Mr(calc) Delta Start End Miss Peptide941.48 940.47 940.47 0.01 146 - 153 1 YKELGFQG1271.67 1270.66 1270.66 0.01 32 - 42 0 LFTGHPETLEK1378.83 1377.82 1377.83 -0.01 64 - 77 0 HGTVVLTALGGILK1502.68 1501.67 1501.66 0.01 119 - 133 0 HPGDFGADAQGAMTK1506.94 1505.93 1505.93 0.00 64 - 78 1 HGTVVLTALGGILKK1606.85 1605.84 1605.85 -0.01 17 - 31 0 VEADIAGHGQEVLIR1815.88 1814.87 1814.90 -0.02 1 - 16 0 GLSDGEWQQVLNVWGK1853.94 1852.93 1852.95 -0.02 80 - 96 0 GHHEAELKPLAQSHATK1885.00 1883.99 1884.01 -0.02 103 - 118 0 YLEFISDAIIHVLHSK1982.02 1981.01 1981.05 -0.04 79 - 96 1 KGHHEAELKPLAQSHATK

No match to: 931.53, 934.49, 949.50, 951.50, 952.52, 968.46, 978.46, 988.49, 1006.54

The masses of the tryptic peptides from the mass spectrum can be used to identify the parent protein

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Post-translational modifications will produce changes in the masses of tryptic fragments

Name

Site Modification ∆m

N-terminal acetylation terminal NH2- replaced by CH3CONH- +42 N-terminal formylation terminal NH2- replaced by HCONH- +28 N-terminal myristylation terminal NH2- replaced by CH3(CH2)12CONH- +210 N-terminal palmitoylation terminal NH2- replaced by CH3(CH2)14CONH- +238 C-terminal amidation terminal –COOH replaced by –CONH2 -1 disulfide bonds 2 Cys –SH replaced by –S-S- -2 glycosylation (N-linked) N-X-S/T addition of sugar glycosylation (O-linked) S/T addition of sugar sulfation -OH of Y replaced by –OSO3H +80 phosphorylation -OH of Y/S/T replaced by –OPO3H2 +80 N-methylation -NH2 of K/R/H/Q relaced by –NHCH3 +14 O-methylesterification -COOH of E/D replaced by –COOCH3 +14 carboxylation -NH2 of E/D replaced by –NHOCH3 +30 Hydroxylation

-NH2 of P/K/D replaced by –NHOH +16

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Protein phosphorylation by kinasesEnzyme

Consensus sequence

protein kinase C (R/K1-3,X2-0)-S/T-(X2-0, R/K1-3)cAMP-dependent PK R-R-X-S/T cGMP-dependent PK R/K2-3-X-S/T casein kinase I S[P]-X1-3-S/T casein kinase II

S/T-(D/E/S[P])1-3,X2-0

X = unspecified peptide; S[P] = phosphorylated serine

30

Carboxypeptidase ladder sequencing 1 115.1 71.1 129.1 147.2 156.2 17 1 H - Asp - Ala - Glu - Phe - Arg - OH - H+ 637.7

1 115.1 71.1 129.1 147.2 17 1 H - Asp - Ala - Glu - Phe - OH - H+ 481.5

1 115.1 71.1 129.1 17 1 H - Asp - Ala - Glu - OH - H+ 334.3

1 115.1 71.1 17 1 H - Asp - Ala - OH - H+ 205.2

1 115.1 17 1 H - Asp - OH - H+ 134.1

Digestion of the tryptic peptide DAEFR from βAmyloid with carboxypeptidase followed by mass spectral analysis of the ladder mixture

All masses are molecular masses

16

31

1 115.1 71.1 129.1 147.2 156.2 17 1 H - Asp - Ala - Glu - Phe - Arg - OH - H+ 637.7

1 71.1 129.1 147.2 156.2 17 1 H - Ala - Glu - Phe - Arg - OH - H+ 522.6

1 129.1 147.2 156.2 17 1 H - Glu - Phe - Arg - OH - H+ 451.5

1 147.2 156.2 17 1 H - Phe - Arg - OH - H+ 322.4

1 156.2 17 1 H - Arg - OH - H+ 175.2

Aminopeptidase ladder sequencing

Digestion of the tryptic peptide DAEFR from βAmyloid with aminopeptidasefollowed by mass spectral analysis of the ladder mixture

All masses are molecular masses

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In situ digestion: several aliquots of the intact peptide are place on different locations on the sample probe or slide. Enzyme (in excess) is added to each spot and quenched after a predetermined time by addition of the matrix solution.

Timed-course digests provide a means to maximize amino acid sequence information.

Patterson, D.H.; Tarr, G/E.; Regnier, F.E., Martin, S.A.; Anal. Chem. 67 (1995) 3971-3978.

Example of “timed”carboxypeptidase ladder sequencing

17

33

1 87.1 156.2 167.1 57.1 71.1 113.2 128.2 17 1H Ser Arg Ser Gly Ala Leu Lys OH H+ MW = 799.0

PO3H

1 156.2 167.1 57.1 71.1 113.2 128.2 17 1H Arg Ser Gly Ala Leu Lys OH H+ MW = 711.9

PO3H

1 167.1 57.1 71.1 113.2 128.2 17 1H Ser Gly Ala Leu Lys OH H+ MW = 555.7

PO3H

1 57.1 71.1 113.2 128.2 17 1H Gly Ala Leu Lys OH H+ MW = 388.6

1 71.1 113.2 128.2 17 1H Ala Leu Lys OH H+ MW = 331.5

1 113.2 128.2 17 1H Leu Lys OH H+ MW = 260.4

1 128.2 17 1H Lys OH H+ MW = 47.2

For phosphopeptides, amino and carboxypeptidase ladder sequencing is carried out in the same manner, but the sequence includes a phosphoserinewhich has a residue mass of:

87 + 80 = 167

Ladder sequencing of a phospho-peptide:

34

Sequencing by fragmentation: tandem and hybrid mass spectrometers

The tandem mass spectrometer:

• two or more mass analyzers (or mass analysis steps: “tandem in time”)

• the ability to select a ions of a particular mass observed in a mass spectrum and to observe its fragments in a subsequent spectrum

• a means for activating the ions to induce fragmentation

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C-terminal ions: the “y” ions

NH

HC C N

H

HC C

R1

O

R2

O

NH

HC C N

H

HC C

R1

O

R2

O

NH

HC C N

H

HC C

R1

O

R2

O

H3NHC C

O

HC C

R2

O

H

H- NH3

+ H H

R2 y-ion

z-ion

36

N-terminal ions: the “a” and “b” ions

NH

HC C N

H

HC C

R1

O

R2

O

NH

HC C N

H

HC C

R1

O

R2

O

NH

HC C N

HC C

R1

O

R2

O

NH

HC C

R1

O

NH

HC C

R1

+ H

O

H

H

NH

CH

R1

H

- COb-ion

a-ion

19

37

y-ion masses can be determined for a known sequence:

b-ion masses can also be determined:

a-ion masses are determined by subtracting 28 from the masses of the b-ions

Sequence fragment nomenclature

Use these schemes to verify the masses in the next figure

38

Amino acid sequencing by fragmentation.

De novo sequencing of an unknown is complicated by the fact that one does not know a priori which type of fragmentation will occur.

Approaches include the location of peaks 28 mass units apart (a and b series) and noting that the molecular ion is a yion).

20

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Tandem Mass SpectrometryMass filters vs. mass analyzersMass selectionCollision-induced dissociation (CID)

MS1 Collision chamber

MS2S D

In a normal configuration:

Mass filter:passes a single mass

Collision gas: He or Xe

Collision-induced dissociation

High energy (1-20 Kev) single collisions, or

Low energy (10-50 ev multiple collisions.

Mass analyzer:records a mass spectrum

Normal mode = product ion scan

40

Some examples of tandem (and hybrid) instruments

Tandem in time:Ion trap mass spectrometer (ITMS)Fourier transform mass spectrometer (FTMS)Linear ion trap/FTMS (LTQ-FT)

Tandem in space:Triple quadrupolesQuadrupole/time-of-flight (QTOF)Time-of-flight/time-of-flight (TOF/TOF)Ion trap/time-of-flight (trapTOF, Qit/TOF)

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S D

Scan modes of the triple quadrupole:

Product ion (normal) scan:mass filter:single precursor mass

RF-only mode:

mass analyzer:Scan product masses for selected precursor

Precursor ion scan:

Constant neutral loss (CNL) scan (reaction ion monitoring):

mass analyzer:Scan precursor masses for selected product

RF-only mode:

RF-only mode:

mass filter:single product mass

mass analyzer:scan precursor masses

mass analyzer:scan product masses differing by constant mass difference

42

The ion trap mass spectrometer is a “tandem” mass spectrometer

Fundamental rf applied to ring electrode (1.1 MHz)

dc and excitation voltages applied to the end caps

Trapping cycle: fixed amplitude of the fundamental rf voltage

Ion ejection cycle: remove unwanted ions by symmetric or asymetric pulses on endcaps; stored waveform inverse Fourier transform (SWIFT) or filtered noise field techniques

Mass analysis cycle:mass selective instability mode: scan fundamental rfvoltage; mass range approx. 650resonance ejection mode: set supplemental rf voltage on endcaps and then scan fundamental rf voltage

MS/MS mode: low amplitude supplemental rf voltage applied to endcaps

22

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Tandem-in-timeI, II and III: trapping cycle: fundamental (1.1 MHz) RF voltage on ring electrode

IV: mass isolation cycle (MS1): resonant ejection of all but selected ion, using high amplitude supplementary RF on ring electrode

V: excitation cycle (low energy CID): low amplitude supplementary RF voltage on endcaps

VII: mass analysis cycle (MS2): resonance ejection mode, high amplitude supplementary RF voltage on endcaps while scanning the amplitude of the fundamental RF voltage on the ring electrode

44

IR AP MALDI from 0.1 % TFA solution

800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 m/z0

100

Rel

ativ

e A

bund

ance

1420.4

1274.1

1079.5

2117.3

1296.6787.1

2101.1

[M+Na]+

[M+Na]+

[M+Na]+

MAN6

A1F

M3N2F

800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 m/z0

100

Rel

ativ

e A

bund

ance

1420.4

1274.1

1079.5

2117.3

1296.6787.1

2101.1

800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 m/z0

100

Rel

ativ

e A

bund

ance

1420.4

1274.1

1079.5

2117.3

1296.6787.1

2101.1

[M+Na]+

[M+Na]+

[M+Na]+

MAN6

A1F

M3N2F

650 700 750 800 850 900 950 1000 1050 m/z0

100

Rel

ativ

e A

bund

ance

1061.4

933.3712.2

1062.3

978.4979.5

714.4 917.4 1063.5980.4916.2 969.2 1049.7730.0 1077.5686.7 1009.6899.9832.1 959.3629.1 772.0 801.8

MS/MS 1079Da

M3N2F -Fuc

-Fuc

-GlcNAc

-GlcNAc

650 700 750 800 850 900 950 1000 1050 m/z0

100

Rel

ativ

e A

bund

ance

1061.4

933.3712.2

1062.3

978.4979.5

714.4 917.4 1063.5980.4916.2 969.2 1049.7730.0 1077.5686.7 1009.6899.9832.1 959.3629.1 772.0 801.8

650 700 750 800 850 900 950 1000 1050 m/z0

100

Rel

ativ

e A

bund

ance

1061.4

933.3712.2

1062.3

978.4979.5

714.4 917.4 1063.5980.4916.2 969.2 1049.7730.0 1077.5686.7 1009.6899.9832.1 959.3629.1 772.0 801.8

MS/MS 1079Da

M3N2F -Fuc

-Fuc

-GlcNAc

-GlcNAc

MS/MS 1079Da

M3N2F -Fuc

-Fuc

-GlcNAc

-GlcNAc

650 700 750 800 850 900 950 1000 1050 1100 1150 1200 1250 1300 1350 1400 m/z0

100

Rel

ativ

e A

bund

ance

1198.5

1401.4

1318.41216.5

995.2 1036.51257.4

1095.5875.3 1115.3 1321.3723.1 833.2772.2 1157.3

MS/MS 1420Da

MAN6-Man

-Man-Man

-GlcNAc-GlcNAc-GlcNAc

-Man

650 700 750 800 850 900 950 1000 1050 1100 1150 1200 1250 1300 1350 1400 m/z0

100

Rel

ativ

e A

bund

ance

1198.5

1401.4

1318.41216.5

995.2 1036.51257.4

1095.5875.3 1115.3 1321.3723.1 833.2772.2 1157.3

650 700 750 800 850 900 950 1000 1050 1100 1150 1200 1250 1300 1350 1400 m/z0

100

Rel

ativ

e A

bund

ance

1198.5

1401.4

1318.41216.5

995.2 1036.51257.4

1095.5875.3 1115.3 1321.3723.1 833.2772.2 1157.3

MS/MS 1420Da

MAN6-Man

-Man-Man

-GlcNAc-GlcNAc-GlcNAc

-Man

AP/IRIS MS spectrum of 3-oligosaccharide mixture(8 pmol of each oligosaccharide)

Taranenko N.I., Atmospheric Pressure Infrared Ionization from Solutions (AP/IRIS), Proceedings of the 51st

ASMS Conference on Mass Spectrometry and Allied Topics, Montreal, 2003.

23

45

S D

q1 is an RF-only quadrupole filter that collimates ions from high pressure source.

q3 is an RF-only quadrupole filter used as a collision chamber.

Collisions are low energy.

Q2 is a quadrupole mass filter that selects the precursor mass

The TOF makes it possible to analyze product ions with higher m/z than their precursors

Combined quadrupole and time-of-flight mass spectrometers (QTOF)

46

MS/MS spectrum of doubly charged ion on a QTOF mass spectrometerFigure 2. Fragment ion spectra of doubly-charged Bradykinin 2–9 (m/z 452.74) obtained on a hybrid quadrupole-time of flight instrument at (a) 20 V, (b) 25 V, (c) 35 V, and (d) 45 V potential difference.

Rogalski, J.C.; Lin, M.S.; Sniatynski, M.J.; Taylor, R.J.; Youhnovski, N.; Przybylski, M.; Kast, J. Statistical evaluation of electrospray tandem mass spectra for optimized peptide fragmentation, J. Am. Soc. Mass Spectrom. 16 (2005) 505-514.

24

47

Combined ion trap and time-of-flight mass spectrometer (trapTOF)

MSn-1 MSn

Kratos AXIMA Qit/TOF

MSn-1 MSn

Kratos AXIMA Qit/TOF

Compared with QTOF: can carry out MSn-1 steps in the ion trap

Compared with ion trap alone: obtain high resolution MSn spectrum

48

• Mass selection from an ion trap provides high accuracy, narrow mass range

• Full kinetic energy of product ions provides high mass resolution in MSn modes

0

10

20

30

40

50

60

70

80

90

100

%Int.

700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000 2100 2200 2300 2400 2500Mass/Charge

4[c].N

705 mV[sum= 100100 mV] Profiles 1-142 Unsmoothed

Data: sample HM40001.N1 19 Aug 2002 15:59 Cal: Oklahoma 19 Aug 2002 16:10 Kratos PC Kompact MALDI 7 V2.3.0a: Mode PosMidMass, Power: 110

1014.57

921.50

1015.56

1260.63

922.481055.60

1261.65

997.54 1242.691147.591016.59

923.53 1535.731243.671026.61741.42 1148.61858.47 1438.831283.77 1611.87956.52742.43 1439.83 1847.941612.842348.101469.76 2166.071587.77 2041.061851.02

0

10

20

30

40

50

60

70

80

90

100

%Int.

200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600Mass/Charge

1[c].P

18 mV[sum= 5546 mV] Profiles 1-300 Smooth Av 5 -Baseline 100X5 X5 X5

Data: sample HM4 1611 ms20001.N1 19 Aug 2002 16:35 Cal: Oklahoma 19 Aug 2002 16:10 Kratos PC Kompact MALDI 7 V2.3.0a: Mode PosMidMass, Power: 120

1054.63

587.031055.64

955.59458.04

588.07 1056.65

1036.64

570.051037.64858.53368.95 956.56 1592.92759.45702.21

587.40

1452.89

1053.77

1567.95895.56459.08 799.46 1169.67 1269.73343.15 682.14215.48 1455.881361.83 1568.73

0

10

20

30

40

50

60

70

80

90

100

%Int.

300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 1050 1100 1150 1200 1250Mass/Charge

1[c].N

3.7 mV[sum= 1114 mV] Prof iles 1-300 Smooth Av 5 -Baseline 100

Data: sample HM4 1260ms20001.N1 19 Aug 2002 17:04 Cal: Oklahoma 19 Aug 2002 16:10 Kratos PC Kompact MALDI 7 V2.3.0a: Mode PosMidMass, Power: 120

973.63

303.97

1243.71

566.94 715.27659.11 974.60314.96469.98 539.01400.95 756.43652.09355.97 955.56 1244.69697.15 842.51442.95 555.99 1102.65296.98 781.45

MALDI MS and MS/MS spectra obtained on a trapTOF

25

49

Mascot Search ResultsSearch title : digestMS data file : C:\Program Files\Kompact\data\Customers\Oklahoma\mass lists\HM4 1611 ms2.txtDatabase : NCBInr 20020814 (1030915 sequences; 326041867 residues)Taxonomy : Drosophila (fruit flies) (28122 sequences)Timestamp : 19 Aug 2002 at 16:03:04 GMTSignificant hits: gi|5921205 ATP synthase alpha chain, mitochondrial precursor (Protein bellwether)

1. gi|5921205 Mass: 59384 Total score: 48 Peptides matched: 1 1 1611.15 1610.14 1609.87 0.27 0 48 1 TGAIVDVPVGDELLGR

Mascot Search ResultsSearch title : digestMS data file : C:\Program Files\Kompact\data\Customers\Oklahoma\mass lists\HM4 1260 ms2.txtDatabase : NCBInr 20020814 (1030915 sequences; 326041867 residues)Taxonomy : Drosophila (fruit flies) (28122 sequences)Timestamp : 19 Aug 2002 at 16:17:32 GMTSignificant hits: gi|5921205 ATP synthase alpha chain, mitochondrial precursor (Protein bellwether)1. gi|5921205 Mass: 59384 Total score: 38 Peptides matched: 1 1 1260.70 1259.69 1259.64 0.06 0 38 1 SAEISNILEER

Both MS/MS spectra give the same IDMS/MS of 1611

MS/MS of 1260

50

Tandem time-of-flight (TOF/TOF) mass spectrometers

ion source

mass selection gate

retarding lens

collision cell

2nd source pulsed extraction

Applied BioSystems• 20 keV ions decelerated to 1-2 keV• product ions are reaccelerated by 18 keV• does not record metastable products formed in MS1• can be operated with (CID) or without (PSD) gas

CID = collision-induced disssociationPSD = post-source decay (metastable decomposition)

26

51

ion source

mass selection gate

collision cell “lift” cell

ion source mass selection gate

Bruker Daltonics• 8 keV collisions with products accelerated by lift cell• records metastables (PSD) and collision (CID) products

Kratos AXIMA• PSD with curved-field reflectron

52

MS/MS or sequence spectrum of 2-17 from HAT

Y-ions

GS

Y+H2O

SHHHHH

H H H H H S S G E N L

B-ions

27

53

b25

b23

b20

b18

b17

b15

b12

b9b8b4

b27

b26b29

b28

c31

y23

y9b5

c24

c19

c16

c7

c11

KREENTSNESTDVTKAcGDSKAcNAKAcKAcKAcNNKAcKAcTSKAcN

b25

b23

b20

b18

b17

b15

b12

b9b8b4

b27

b26b29

b28

c31

y23

y9b5

c24

c19

c16

c7

c11

KREENTSNESTDVTKAcGDSKAcNAKAcKAcKAcNNKAcKAcTSKAcN

MS/MS analysis of acetylated peptides from histone acetyl transferaseThompson, P.; Wang, D.; Wang, L.; Fulco, M.; Pediconi, N.; Zhang, D.; An W.; Ge Q.; Roeder, R.G.; Wong, J.; Levrero, M.; Sartorelli, V.; Cotter, R.J. and Cole, P.A., Regulation of the p300 HAT Domain via a Novel Activation Loop. Nature: Struct. Mol. Biol. 11(2004) 308-15.

54

Sequence tagsFor identification we need only a partial sequence …

FTMS/MS of a bacterial agent biomarker with a mass of 6710.5

28

55

… which can be combined with a molecular weight to obtain an identification with very high specificity

Here two peptides are found with the same sequence segment, but only one has the correct molecular weight

56

High energy and low energy collisionsHigh energy collisions• precursor ion kinetic energy: E1 = 1-20 keV

• single collision conditions

• product ion energy:

• used in instruments in which mass measurement depends upon kinetic energy, i.e. TOF/TOF mass spectrometers

• collision energy (Erel) in the center-of-mass frame

where M is the molecular ion and n is the collision gas

11

22 E

mmE =

MMn

nrel E

mmmE+

=

29

57

Protein MW 1 keV 8 keV 20 keV Substance P 1,348 2.97 ev 23.7 ev 59.4 ev Ubiquitin 8,566 0.47 ev 3.7 ev 9.3 ev Cytochrome C 12,328 0.32 ev 2.6 ev 2.5 ev C fragment of tetanus toxin 51,819 0.08 ev 0.6 ev 1.5 ev Bovine serum albumin 66,430 0.06 ev 0.5 ev 1.2 ev

High energy and low energy collisions

Low energy collisions• precursor ion kinetic energy = 10-50 ev

• activation through multiple collisions

• used in instruments in which the ion residence time is long

quadrupole ion traps (ITMS)linear ion traps (LTQ)Fourier transform mass spectrometers (FTMS)

58

High energy and low energy collisionsSome observations:• both high energy and low energy CID are less effective for high

mass because of the relativistic effect

• CID generally produces more internal fragment ions and single residue ions for amino acid composition

• low energy CID raises the internal energy slowly and has a tendency to break the weakest bonds: at proline and glutamic acid residues, losses of phosphate and other charged PTMs

• high energy CID produces more “remote site” fragmentation

What is needed…..

• Ability to fragment higher masses

• Ability to fragment without losing PTMs

Use something other than collisions

30

59

New methods of ion activation

On an FTMS:

• IRMPD• ECD

on an ion trap:

• ETD

Method

Characteristics

Metastable fragmentation Post-source decay

- Primarily b, y ions

Low energy collision induced dissociation (Low energy CID)

- Multiple low energy (20 – 200 ev) collisions - Used primarily for instruments with long ion residence times, i.e. quadrupole, ion trap or FTMS

High energy collision induced dissociation (High energy CID)

- Single high energy (1 keV to 20 keV) collisions - Primarily b, y ions (amide bond cleavage) - Some side chain losses for distinguishing residues of the same mass - Additional acyl and immonium internal ions

Infrared multiphoton dissociation (IRMPI)

- Similar to CID, but activation energy does not depend upon relative kinetic energy - Better for high mass - Requires high ion residence times for good cross section

Electron capture dissociation (ECD)

- Fewer neutral losses than CID, such as phosphate and sugar - More c and z ions (C-N bond cleavage) - Activation does not depend upon relative kinetic energy - Better for high mass - Used for “top down” proteomics - Requires high ion residence times for good cross section

60

Fourier transform mass spectrometer

frequency

frequency

time

FT

7 Tesla superconducting magnet field

8 MHz 100 KHz

31

61

Fourier transform mass spectrometer

What are the advantages?

• High mass accuracy:

• 2 ppm (external calibration)

• 1 ppm (internal calibration)

• Therefore, better protein identifications from mass fingerprinting

• Very high mass resolution

• Ability to carry out IRMPD and ECD, as well as CID

• Therefore, able to do “top-down” proteomics

62

Fourier transform mass spectrometer

Monoisotopic MH2+2 peaks for the peptides DRVYVHPF (m/z 516.76671) and

KRPPGFSPF (m/z 516.78490) at resolving powers of 15,000 and 56,700 , where thedifference in mass between these two peptides is 18.2 mmu or 35 ppm.

Courtesy: ThermoFinnegan

Inte

nsity

(%)

0

20

40

60

80

100

Mass [Th]516.65 516.70 516.75 516.80 516.85 516.90

516.77581 (observed)

516.76671(correct)

516.78490(correct) In

tens

ity (%

)

0

20

40

60

80

100

Mass [Th]516.65 516.70 516.75 516.80 516.85 516.90

516.78490516.76671

Inte

nsity

(%)

0

20

40

60

80

100

Mass [Th]516.65 516.70 516.75 516.80 516.85 516.90

516.77581 (observed)

516.76671(correct)

516.78490(correct)In

tens

ity (%

)

0

20

40

60

80

100

Mass [Th]516.65 516.70 516.75 516.80 516.85 516.90

Inte

nsity

(%)

0

20

40

60

80

100

0

20

40

60

80

100

Mass [Th]516.65 516.70 516.75 516.80 516.85 516.90516.65 516.70 516.75 516.80 516.85 516.90

516.77581 (observed)

516.76671(correct)

516.78490(correct) In

tens

ity (%

)

0

20

40

60

80

100

Mass [Th]516.65 516.70 516.75 516.80 516.85 516.90

516.78490516.76671

Inte

nsity

(%)

0

20

40

60

80

100

Mass [Th]516.65 516.70 516.75 516.80 516.85 516.90

Inte

nsity

(%)

0

20

40

60

80

100

0

20

40

60

80

100

Mass [Th]516.65 516.70 516.75 516.80 516.85 516.90516.65 516.70 516.75 516.80 516.85 516.90

516.78490516.76671

Salmonella GroEl (GMQFDRGYL) m/z 543.75575Mouse hsp (GMKFDRGYI) m/z 543.77390; 33 ppm,

32

63

Håkansson, Chalmers, M.J.; Quinn, J.P.; McFarland, M.A.; Hendrickson, C.L.; Marshall, A.G., Combined Electron Capture and Infrared MultiphotonDissociation for Multistage MS/MS in a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer, Anal. Chem. 75 (2003) 3256-3262.

ECD on a Fourier transform mass spectrometer

64

Håkansson, Chalmers, M.J.; Quinn, J.P.; McFarland, M.A.; Hendrickson, C.L.; Marshall, A.G., Combined Electron Capture and Infrared Multiphoton Dissociation for Multistage MS/MS in a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer, Anal. Chem. 75 (2003) 3256-3262.

Comparison of IRMPD and ECD on a Fourier transform mass spectrometerIRMPD fragmentation is similar to CID

33

65

60 m3/hr 300 L/s 400 L/sec 210 L/sec 210 L/sec

Actively Shielded7 Tesla Magnet

Cold ECD< 2 eV

IRMPD Laser

15 L/s

ESI source

Transfer capillary and skimmer

Octapoleion guide

Quadrupole lenses

Octapole ion transfer lens

Linear ion trap

Linear ion trap/FTMS

low energy CID

IRMPD and ECD

66

Syka, John E. P. et al. (2004) Proc. Natl. Acad. Sci. USA 101, 9528-9533

Fig. 4. Schematic of steps involved in the operation of the LTQ mass spectrometer for peptide sequence analysis by ETD. (A) Injection of multiply protonated peptide molecules (precursor ions) generated by ESI. (B) Application of a dc offset to move the precursor ions to the front section of the linear trap. (C) Injection of negatively charged reagent ions from the CI source into the center section of the linear trap. (D) Application of a supplementary dipolar broadband ac field to eject all ions except those within 3 mass-unit windows centered around the positively charged precursor ions and the negatively charged electron-donor reagent ions. (E) Removal of the dc potential well and application of a secondary RF voltage (100 V zero to peak, 600 kHz) to the end lens plates of the linear trap to allow positive and negative ion populations to mix and react. (F) Termination of ion/ion reactions by axial ejection of negativelycharged reagent ions while retaining positive ions in the centersection of the trap. This is followed by mass-selective, radial ejection of positively charged fragment ions to record the resulting MS/MS spectrum.

Electron transfer dissociation (ETD) on a linear ion trap (LTQ)

34

67

Low energy CID

Multiple collisions

High energy CID

Single collisions

IRMPD

ECD

Less dependent on mass

More thermal; breaks weakest bond

More random fragmentation

Summary of activation methods

ETD

Requires long residence times

LTQ

TOF/TOF only

68

McCloskey, J.A., ed.; Methods in Enzymology 193 (1990).

Packer, N.H.; Harrison, M.J., Glycobiology and Proteomics: Is Mass Spectrometry the Holy Grail? Electrophoresis 19 (1998) 1872-1882.

Vestling, M.M.; Fenselau, C., Surfaces for Interfacing Protein Gel Electrophoresis Directly with Mass Spectrometry, Mass Spectrom. Rev. 14 (1995) 169-178.

Siuzdak, G., Mass Spectrometry for Biotechnology, Academic Press, NY (1996)

Willoughby, R.; Sheehan, E., Mitrovich, S., A Global View of LC/MS, Global View Publishing, Pittsburgh (1998).

Cotter, R.J., Time-of-Flight Mass Spectrometry: Instrumentation and Applications in Biological Research, American Chemical Society, Washington DC (1997).

Handout available electronically on the Middle Atlantic Mass Spectrometry Laboratory website: http://www.hopkinsmedicine.org/mams

References