Introduction to Peptide Sequencing
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1 Introduction to Peptide equencing Quadrupole Ion Traps tructural Biophysics Course December 3, /8/14 Introduction to Peptide equencing - athan Yates 1
2 Why are ion traps used to sequence peptides? ensitive tandem mass spectrometers Improved ion statistics in MM mode compared to M due to the storage and isolation of a single parent m/z igh CID efficiency due to the continuous and mass selective excitation of the parent Rapid scan rate allows several full scan M/M spectra to be acquired each second Data-dependent acquisition of tandem M spectra Integration with automated sequencing tools EQUET, Mascot, Pepsea, GPM, Peptide Prophet, etc 12/8/14 Introduction to Peptide equencing - athan Yates 2
3 Example CAD / CID spectrum - LCQ sq3027 # RT: AV: 3 L: 4.53E7 T: + c EI RM ms @35.00 [ ] x2 x2 x2 x4 x Relative Abundance /8/14 Introduction to Peptide equencing m/z - athan Yates 3
4 Acknowledgment 12/8/14 Introduction to Peptide equencing - athan Yates 4
5 ample Peptide tructure and C Termini 2 C C C 3 -Terminus basic site of protonation blocked by acetyl group, cyclization, and pyroglutamic acid basicity in gas phase close to amide bond 2 C-Terminus carboxilic acid acetyl Pyroglutamic acid 12/8/14 Introduction to Peptide equencing - athan Yates 5
6 ample Peptide tructure Glycine Glycine GLY (G) 57 2 C C C /8/14 Introduction to Peptide equencing - athan Yates 6
7 ample Peptide tructure 2 C C C 3 Alanine ALA (A) /8/14 Introduction to Peptide equencing - athan Yates 7
8 ample Peptide tructure erine and Threonine erine ER () 87 2 C C C 3 Threonine TR (T) erine and Threonine alcohol loses 2 common site for phosphorylation 12/8/14 Introduction to Peptide equencing - athan Yates 8
9 ample Peptide tructure - Proline 2 C C C 3 Proline PR (P) 97 2 Proline 3 bonds to make it the most basic AA in gas phase preferential cleavage on the -terminal side 12/8/14 Introduction to Peptide equencing - athan Yates 9
10 ample Peptide tructure - Valine Valine VAL (V) 99 2 C C C /8/14 Introduction to Peptide equencing - athan Yates 10
11 ample Peptide tructure - Cysteine Cystiene CY (C) 103 C 2 2 C C C 3 Cystiene group can be oxidized during chromatography carboxymethylation of with iodoacetic acid forms disulfide bonds with other Cys reduce to brake - bonds 2 Caboxymethylcystiene CMC (C) /8/14 Introduction to Peptide equencing - athan Yates 11
12 ample Peptide tructure Leucine and Isoleucine Leucine LEU (L) Isoleucine ILE (I) Leucine and Isoleucine Identical residue mass Differentiated by high energy collisions Lxx (X) takes place of ILE and LEU 12/8/14 Introduction to Peptide equencing - athan Yates 12
13 ample Peptide tructure Asparagine and Glutamine Asparagine A () 114 Glutamine GL (Q) 128 Asparagine and Glutamine amide side chains lose ammonia -17 slightly basic 12/8/14 Introduction to Peptide equencing - athan Yates 13
14 ample Peptide tructure Lysine Lysine LY (K) Lysine 2 nd most basic site side chain free amino group acetylated with acetic anhydride C-terminal cleavage with trypsin o ammonia loss distinguishes from Gln (128) 12/8/14 Introduction to Peptide equencing - athan Yates 14
15 ample Peptide tructure Aspartic and Glutamic Acid Aspartic Acid AP (D) Aspartic and Glutamic Acid Carboxylic acids o ammonia loss distinguish Asp/Asn and Glu/Gln Glutamic Acid GLU (E) /8/14 Introduction to Peptide equencing - athan Yates 15
16 ample Peptide tructure Methionine and Met sulfoxide 2 Methionine Met (M) Methionine Readily oxidized with sample handeling Met sulfoxide and Phenylalanine = 147 Met sulfoxide can be reduced (-16) Met ulfoxide CMC (C) /8/14 Introduction to Peptide equencing - athan Yates 16
17 ample Peptide tructure istidine istidine I () istidine 3 rd most basic side chain characteristic low mass fragment = /8/14 Introduction to Peptide equencing - athan Yates 17
18 ample Peptide tructure Phenylalanine 2 2 Phenylalanine PE (F) 147 Phenylalanine Met sulfoxide and Phenylalanine = 147 Met sulfoxide can be reduced (-16) 12/8/14 Introduction to Peptide equencing - athan Yates 18
19 ample Peptide tructure Arginine Arginine ARG (R) Arginine most basic side chain c-terminal cleavage by trypsin proton held tight, blocks fragmentation in middle of molecule 12/8/14 Introduction to Peptide equencing - athan Yates 19
20 ample Peptide tructure Tyrosine and Tryptophan 2 Tryptophan TRP (W) Tyrosine less common site of phosphorylation Tyrosine TYR (Y) /8/14 Introduction to Peptide equencing - athan Yates 20
21 Table 1 - Amino Acid Gas Phase Proton Affinity Amino Acid R- PA (kcal/mol relative to 3 = 205 kcal/mol) Glycine Gly G Alanine Ala A C Cysteine Cys C -C erine er -C Valine Val V (C 3 ) 2 -C Aspartic acid Asp D C-C Leucine Leu L (C 3 ) 2 -C-C Threonine Thr T C 3 -C() Isoleucine Ile I C 3 -C 2 -C(C 3 ) Phenylalanine Phe F Ph-C Tyrosine Tyr Y -p-ph-c Methionine Met M C 3 --(C 2 ) Asparagine Asn 2 -C-C Glutamic acid Glu E C-(C 2 ) Proline Pro P -C 2 -C 3 -C Tryptophan Trp W Ph--C=C-C Glutamine Gln Q 2 -C-(C 2 ) Lysine Lys K 2 -(C 2 ) istidine is -C=-C=C-C Arginine Arg R =C( 2 )--(C 2 ) /8/14 Introduction to Peptide equencing - athan Yates 21
22 Table 2 - Amino Acid Residue Mass and Mass Increments Amino Acid R- Residue Mass Me Increment Glycine Gly G Alanine Ala A C erine er -C Proline Pro P -C 2 -C 3 -C Valine Val V (C 3 ) 2 -C Threonine Thr T C 3 -C() Cysteine Cys C -C Isoleucine Ile I C 3 -C 2 -C(C 3 ) Leucine Leu L (C 3 ) 2 -C-C Asparagine Asn 2 -C-C Aspartic acid Asp D C-C Glutamine Gln Q 2 -C-(C 2 ) Lysine Lys K 2-(C2) Glutamic acid Glu E C-(C 2 ) Methionine Met M C 3 --(C 2 ) istidine is -C=-C=C-C Phenylalanine Phe F Ph-C Arginine Arg R =C( 2 )--(C 2 ) Carboxymethyl Cystiene Cmc C CC 2 --C Tyrosine Tyr Y -p-ph-c Tryptophan Trp W Ph--C=C-C Residue masses have structure --C(-R)-C- 12/8/14 Introduction to Peptide equencing - athan Yates 22
23 Table 3 - Amino Acid eutral Loss and Low Mass Fragments Amino Acid R- eutral Loss Low Mass Fragment Glycine Gly G Alanine Ala A C erine er -C 2-18 (2) - Proline Pro P -C 2 -C 3 -C Valine Val V (C 3 ) 2 -C Threonine Thr T C 3 -C()- 18 (2) - Cysteine Cys C -C 2-34 (2) - Isoleucine Ile I C 3 -C 2 -C(C 3 ) Leucine Leu L (C 3 ) 2 -C-C Asparagine Asn 2 -C-C 2-17 (3) 70, 87 Aspartic acid Asp D C-C Glutamine Gln Q 2 -C-(C 2 ) 2-17 (3) 84, 101, 129 Lysine Lys K 2-(C2)4-84, 101, 129 Glutamic acid Glu E C-(C 2 ) 2-18 (2) 84, 102 Methionine Met M C 3 --(C 2 ) 2-48 (C2) 104 istidine is -C=-C=C-C Phenylalanine Phe F Ph-C Arginine Arg R =C( 2 )--(C 2 ) 3-17 (3) 70, 98, 129 Carboxymethyl Cystiene Cmc C CC 2 --C 2-92 (C2C) 134 Tyrosine Tyr Y -p-ph-c Tryptophan Trp W Ph--C=C-C Bold face indicates strong signals 12/8/14 Introduction to Peptide equencing - athan Yates 23
24 Table 4 - Combined Residue Mass for Two Amino Acids Gly Ala er Pro Val Thr Cys Lxx Asn Asp Gln Lys Glu Met is Phe Arg Cmc Tyr Trp AA Gly Ala er Pro Val Thr Cys Lxx Asn Asp Gln Lys Glu Met is Phe Arg Cmc Tyr Trp /8/14 Introduction to Peptide equencing - athan Yates 24
25 12/8/14 Introduction to Peptide equencing - athan Yates 25
26 12/8/14 Introduction to Peptide equencing - athan Yates 26
27 Fragment Ion omenclature Roepstorff, P and Fohlman, J, Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed Mass pectrom, 11(11) 601 (1984). 12/8/14 Introduction to Peptide equencing - athan Yates 27
28 Fragment Ion omenclature Immonium Ions An internal fragment with just a single side chain formed by a combination of a type and y type cleavage is called an immonium ion. These ions are labelled with the 1 letter code for the corresponding amino acid. Internal Cleavage Ions Double backbone cleavage gives rise to internal fragments. Usually, these are formed by a combination of b type and y type cleavage to produce the illustrated structure, an amino-acylium ion. ometimes, internal cleavage ions can be formed by a combination of a type and y type cleavage, an amino-immonium ion. Internal fragments are labeled with their 1 letter amino acid code. 12/8/14 Introduction to Peptide equencing - athan Yates 28
29 Fragmentation scheme for [M+2] 2+ ion of ATFYK b 2 -ion + 2 y 4 -ion 12/8/14 Introduction to Peptide equencing - athan Yates 29
30 Formation of b-ion eries Fragment Ions b-ions Ala - Thr - er - Phe - Tyr - Lys y-ions 2 + b 5 -ion + 2 [M+2] b 3 -ion b 4 -ion The ion of type b 1, --C(R)-C +, is at m/z = residue mass of amino acid #1 + + b 1 = (AA ). b 2 = (b 1 + AA 2 ) etc. [M+] + = b n-1 + AA n b 1 -ion b 2 -ion 12/8/14 Introduction to Peptide equencing - athan Yates 30
31 Formation of y-ion eries Fragment Ions b-ions Ala - Thr - er - Phe - Tyr - Lys y-ions y 5 -ion [M+2] y 4 -ion 2 y 3 -ion The ion of type y 1, C(R)-C-, is at m/z = AA n y 1 = (AAn ). y 2 = (y 1 + AA n-1 ) etc. [M+] + = y n-1 + AA y 2 -ion /8/14 Introduction to Peptide equencing y 1 -ion - athan Yates 31
32 Corresponding b and y ion pairs [M+2]=910 b-ions Tyr Gly Gly Thr Thr Val Ala Lxx Lys y-ions /8/14 Introduction to Peptide equencing - athan Yates 32
33 trategy for Interpreting CAD pectra Inspect the low-mass region for immonium ions Inspect the low-mass region for the b 2 and a 2 ions check dipeptide table for possibilities look for corresponding y-ions Inspect the low-mass region for the y 1 ion, Lys = 147, Arg = 175 Inspect the high-mass region to identify y n-1 ion Extend the y-ion series toward lower m/z calculate corresponding b-ions Extend the b-ion series toward higher m/z calculate corresponding y-ions Calculate the mass of the peptide Reconcile the amino acid content with spectrum data immonium ions, charge state Attempt to identify all ions in the spectrum doubly charged, internal cleavage, - 2, - 3, -C 3
34 Collision Activated Dissociation pectrum - Example 1 sq3027 # RT: AV: 3 L: 4.53E7 T: + c EI RM ms @35.00 [ ] x2 x2 x2 x4 x Relative Abundance /8/14 Introduction to Peptide equencing m/z - athan Yates 34
35 Calc [M+] + sq3027 # RT: AV: 3 L: 4.53E7 T: + c EI RM ms @35.00 [ ] x2 x2 x2 x4 x [M+] + = ([M+2] 2+ * 2) = (612.4*2)-1 = = Relative Abundance /8/14 Introduction to Peptide equencing m/z - athan Yates 35
36 Find b 2 + & a 2 + candidate ions sq3027 # RT: AV: 3 L: 4.53E7 T: + c EI RM ms @35.00 [ ] x2 x2 x2 x4 x [M+] + = ([M+2] 2+ * 2) = (612.4*2)-1 = = Relative Abundance b a /8/14 Introduction to Peptide equencing m/z - athan Yates 36
37 Look up possible amino acid combinations for b 2 + ion sq3027 # RT: AV: 3 L: 4.53E7 T: + c EI RM ms @35.00 [ ] x2 x2 x2 x4 x Relative Abundance EV? XD?? MP? b [M+] + = ([M+2] 2+ * 2) = (612.4*2)-1 = = a /8/14 Introduction to Peptide equencing m/z - athan Yates 37
38 Look for corresponding y n-1 ion sq3027 # RT: AV: 3 L: 4.53E7 T: + c EI RM ms @35.00 [ ] x2 x2 x2 x4 x [M+] + = ([M+2] 2+ * 2) = (612.4*2)-1 = = Relative Abundance b a /8/14 Introduction to Peptide equencing m/z - athan Yates 38 y n-1
39 Extend the y-ion series toward lower m/z sq3027 # RT: AV: 3 L: 4.53E7 T: + c EI RM ms @35.00 [ ] x2 x2 x2 x4 x [M+]+ = y n Relative Abundance b a y n /8/14 Introduction to Peptide equencing m/z - athan Yates 39 y n-1
40 Extend the y-ion series toward lower m/z sq3027 # RT: AV: 3 L: 4.53E7 T: + c EI RM ms @35.00 [ ] x2 x2 x2 x4 x [M+]+ = y n Relative Abundance VE b b y n a /8/14 Introduction to Peptide equencing m/z - athan Yates 40 y n-1
41 Extend the y-ion series toward lower m/z sq3027 # RT: AV: 3 L: 4.53E7 T: + c EI RM ms @35.00 [ ] x2 x2 x2 x4 x y n-4 [M+]+ = y n-2 70 y n Relative Abundance VE b b y n a y y n-6 n y n-1 y n /8/14 Introduction to Peptide equencing m/z - athan Yates 41
42 Extend the b-ion series toward higher m/z sq3027 # RT: AV: 3 L: 4.53E7 T: + c EI RM ms @35.00 [ ] x2 x2 x2 x4 x y n-4 [M+]+ = y n-2 70 y n Relative Abundance VE b b b b y n a y n /8/14 Introduction to Peptide equencing m/z - athan Yates y b n b 9 y n-7 b 7 b 6 y n
43 Reconcile amino acid content sq3027 # RT: AV: 3 L: 4.53E7 T: + c EI RM ms @35.00 [ ] x2 x2 x2 x4 x y n-4 [M+]+ = y n-2 70 y n Relative Abundance VE b b b b y n a y n /8/14 Introduction to Peptide equencing m/z - athan Yates y b n b 9 y b b n-7 o 6 7 o o y n
44 olution to CAD >643 trp causes some difficulty 767->643 = 124 not an AA b2 combinations = MP, VE, 12/8/14 Introduction to Peptide equencing - athan Yates 44
45 Collision Activated Dissociation pectrum - Example 2 sq3027 # RT: AV: 3 L: 1.85E8 T: + c EI RM ms @35.00 [ ] Relative Abundance /8/14 Introduction to Peptide equencing m/z - athan Yates 45
46 Collision Activated Dissociation pectrum - Example 3 sq3027 # RT: AV: 2 L: 5.21E6 T: + c EI RM ms @35.00 [ ] Relative Abundance /8/14 Introduction to Peptide equencing m/z - athan Yates
47 CAD Example 3 - Expanded sq3027 # RT: AV: 2 L: 5.21E6 T: + c EI RM ms @35.00 [ ] x m/z Relative Abundance /8/14 Introduction to Peptide equencing m/z - athan Yates 47
48 Collision Activated Dissociation pectrum - Example 4 sq3027 # RT: AV: 4 L: 2.47E7 T: + c EI RM ms @35.00 [ ] x4 x2 x4 x Relative Abundance m/z 12/8/14 Introduction to Peptide equencing - athan Yates
49 CAD Example 4 - Expanded sq3027 # RT: AV: 4 L: 2.47E7 T: + c EI RM ms @35.00 [ ] x4 x2 x m/z 100 x4 x20 x4 x50 x Relative Abundance /8/14 Introduction to Peptide equencing m/z - athan Yates 49
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