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What Is a Mass Spectrum? 1265.6038 100 Outline EMBnet course 28.1.-1.2.2008 Day 1 Mass spectrometry in proteomics Mass spectrometry, general introduction What is a mass spectrum What are the constituents of a mass spectrometer How the instruments look like Pierre-Alain Binz Swiss Institute of Bioinformatics, proteome informatics group Geneva Bioinformatics SA (GeneBio) EMBnet course Basle, 28 Jan, 2008 What is a mass spectrum? 1265.6038 100 MALDI-DE-RE-TOF MS 80 1394.7169 tryptic digest of BSA 60 1252.6472 1757.8374 870.4042 1299.6103 * % Intensity 40 * 1930.0053 1742.8780 * 1410.7018 * 1787.7116 2062.0077 950.4584 2523.2021 20 * 1083.5082 1778.0565 2848.3 2285.1 2467.1695 848.2 1099.5 1859.9261 2065.0 2266.1 1364.7 1555.7 2501.3228 2016.0 2222.2043 2734.2 0 828.0 1263.2 1698.4 2133.6 2568.8 3004.0 Mass (m/z) Protein Identification using Mass Spectrometry Outline protein from gel/ tryptic digestion & Mass spectrometry, general introduction 1-DE, 2-DE, PVDF/LC fraction peptide extraction LC TYGGAAR EHICLLGK GANK PSTTGVEMFR unmodified and What is a mass spectrum Mass spectrometry, modified peptides peptide mass fingerprints What are the constituents of a mass spectrometer PMF identification How the instruments look like MS Fragmentation Mass spectrometry, MS/MS identification peptide MS fragments 1 What is a mass spectrum? How does a peptide signal looks like? 1265.6038 100 MALDI-DE-RE-TOF MS 80 1394.7169 tryptic digest of BSA Low resolution 60 1252.6472 1757.8374 870.4042 1299.6103 * % Intensity 40 * 1930.0053 1742.8780 * 1410.7018 * 1787.7116 2062.0077 High resolution 950.4584 2523.2021 20 * 1083.5082 1778.0565 2848.3 2285.1 2467.1695 848.2 1099.5 1859.9261 2065.0 2266.1 1364.7 1555.7 2501.3228 2016.0 2222.2043 2734.2 0 828.0 1263.2 1698.4 2133.6 2568.8 3004.0 Mass (m/z) Isotopic distribution Isotopic distribution Mass resolution 0.1% vs. 1 ppm Symbol Mass Abund. Symbol Mass Abund ------ ---------- ------ ------ ----------- ------- C(12) 12.000000 98.90 C(13) 13.003355 1.10 N(14) 14.003074 99.63 N(15) 15.000109 0.37 O(16) 15.994915 99.76 O(17) 16.999131 0.038 H(1) 1.007825 99.99 H(2) 2.014102 0.015 S(32) 31.972072 95.02 S(33) 32.971459 0.75 Mass resolution Mass resolution 1.0 FWHM 0.7 FWHM 0.5 FWHM 2000 Full width 1000 0.3 FWHM 0.2 FWHM 0.1 FWHM Half mass 2 524.3 262.6 100 100 95 95 90 90 85 85 80 80 75 Singly charged Ion: 75 Doubly charged Ion: 70 70 65 Distance between Peak 65 Distance between Peak and 60 and Isotop 1 amu 60 Isotop 0.5 amu 55 55 50 50 45 45 ∆ = 1.0 amu ∆ = 0.5 amu Relative Abundance Relative Abundance 40 40 35 35 30 30 525.3 25 25 ∆ = 1.0 amu 263.1 20 20 ∆ 15 15 = 0.5 amu 10 10 526.2 263.6 5 5 0 0 520 521 522 523 524 525 526 527 528 529 258 259 260 261 262 263 264 265 266 267 m/z m/z Resolution: Example Peptide Mw 2129.64, Ion 4+ M ultiply charged myoglobin ions from ES I Intens. (M2-1.008) /M1-M2 = Z1 x105 1060.5 533.46 100 M1 (Z1 * M1)-(Z*1.008) = Mwt 90 1131.1 Resolution 998.2 1211.9 4 M2 942.9 0.6 m/z 80 1305.0 2 70 893.3 60 848.6 1413.5 0 531 532 533 534 m/z 50 40 808.2 Intens. 1541.9 x105 532.62 532.85 30 771.5 20 1696.0 533.09 Resolution 616.2 738.1 1.0 10 707.3 1310.9 1884.2 1428.7 1563.0 1820.8 1888.9 533.33 0.2 m/z 0 0.5 600 800 1000 1200 1400 1600 1800 2000 533.61 m/z 0.0 531 532 533 534 m/z 9.9E+3 MALDI-DE-RE-TOF MS 100 90 tryptic digest of BSA 80 1265.6038 100 Deconvoluted myoglobin spectrum 70 60 50 16951.0 100 80 1394.7169 Intensity % 40 90 30 80 20 70 60 60 1252.6472 10 1757.8374 50 0 0 870.4042 1299.6103 1910.0* 1918.8 1927.6 1936.4 1945.2 1954.0 40 % Intensity 40 * Mass (m/z) 30 1930.0053 1742.8780 * 1410.7018 * 20 1787.7116 2062.0077 10 950.4584 2523.2021 15931.0 16104.0 16392.0 16582.0 16784.0 17088.0 17280.0 17562.0 17830.0 17995.0 20 * 1083.5082 2848.3 0 1778.0565 2285.1 16000 16200 16400 16600 16800 17000 17200 17400 17600 17800 18000 2467.1695 848.2 1099.5 1859.9261 2065.0 2266.1 mass 1364.7 1555.7 2501.3228 2016.0 2222.2043 2734.2 0 828.0 1263.2 1698.4 2133.6 2568.8 3004.0 Mass (m/z) 3 HPLC-ESI-autoMS/MS Ion fragmentation with Mass Spectrometry Int. H I 7 x10 TIC O O 4 H 2 I N O Tandem MS or MS/MS 0 4.0 5.0 Time [min] HO Ab. MS, Time=4.420min 100 634 m/z 634 One set of ions (one m/z value) is selected from a mixture of ions; 50 MS/MS These ions are fragmented; the fragments are measured. 545 0 100 200 300 400 500 600 m/z H I O Ab. MS/MS(634), Time=4.458min 545 OH 100 373 I 50 249 376 563 O HO 0 m/z 563 100 200 300 400 500 600 m/z Peptide fragmentation with MS/MS Outline Mass spectrometry, general introduction What is a mass spectrum What are the constituents of a mass spectrometer K C S C N P D M MAPNCSCK 2+ y3 [M+2H] MAPNCSC K y1 How the instruments look like MAPNCS CK y7 y4 y5 MAPNC SCK y2 y6 MAPN CSCK y8 ... How are mass spectra produced ? Generic description of a mass spectrometer • Ions are produced in the source and are transferred into the mass analyser Atmosphere Vacuum System Sample Ionisation Mass Data • They are separated according to their mass/charge Detector Inlet Method Analyser System ratio in the mass analyser (e.g. Quadrupole, Ion Trap, Time of Flight) • Ions of the various m/z values exit the analyser and are ‘counted’ by the detector 4 EI electron impact ionisation: beam of electrons through the gas-phase sample. Produces Ionization methods molecular ions or fragment ions. Typically 70eV. Sample heated. Ionization methods + Reproducible, structural information Analytes are ionized to be driven in the mass analyzer - sample must be volatile and stable, molecular ion often abscent mass range: < 1000Da Electron impact (EI) CI: chemical ionisation: reagent gaz (methane, isobutane, or ammonia) ionized with electrons. High gaz pressure: (R = reagent, S = sample, e = electron, . = radical electron , H = hydrogen) Chemical Ionisation (CI) R + e ---> R+. + 2e Fast atom bombardment (FAB) R+. + RH ---> RH+ + R. RH+ + S ---> SH+ + R Field desorption (FD) Heated sample. Atmospheric Pressure Chemical Ionisation (APCI) + [M+H]+ often visible, less fragmentation than EI - sample must be volatile and stable, less structural info than EI mass range: < 1000Da ESI Electro-Spray Ionization DCI: Desorption CI : CI on a heated filament MALDI Matrix Assisted Laser Desorption Ionization + rapid, simple - reproducibility mass range <1500Da NCI: negative-ion CI: electron capture; use of Methane to slow down electrons + efficient, sensitive; less fragmentation that EI, CI - not all molecule compatible, reproducibility mass range <1000Da FD: Field Desorption: sample deposited on filament gradually heated by electric field. ESI: electrospray ionisation: The sample solution is sprayed across a high potential Sample ionise by electron tunneling. Ions are M+ and [M+Na]+ difference (a few kilovolts) from a needle into an orifice in the interface. + simple spectra, almost no background Heat and gas flows are used to desolvate the ions existing in the sample solution. - sensitive to alkali, slow, volatile to desorb ESI often produces multiply charged ions with the number of charges tending to increase mass range <2000-3000Da as the molecular weight increases. High to low flow rates 1 ml/min to nl/min. FI: Field ionisation: sample introduced in gas phase (heaten or not), ionised by electron + good for charged, polar or basic compounds, m/z ok for most MS, best for multiply tunneling near the emitter. charged ions, low background, controlled fragmentation, MS/MS compatible + simple spectra, almost no background - complementary to APCI: not good for uncharged, non-basic, low-polarity compounds, - sample must be volatile low ion currents mass range <1000Da mass range <200’000Da FAB: fast atom bombardment: analyte in a liquid matrix (glycerol, etc.). Bombardment with APCI: atmospheric pressure CI: as in ESI, sample introduced in a high potential fast atom beam (xenon at 6keV). Desorbtion of molecular ions, fragments and matrix difference field. Uses a corona discharge for better ionisation of less polar molecules than clusters in ESI. APCI and ESI are complementary sample introduced liquid, or LC/MS + rapid, simple, good for variety of compounds, strong currents, high resolution MALDI: Matrix-Assisted Laser Desorption Ionization: analyte co-crystallised in matrix. - background, sample must be soluble in matrix The matrix chromophore absorbs and distribute the energy of a laser, produced a plasma, mass range ~300-6000Da vaporates and ionize the sample. + rapid, convenient for molecular weight (singly charged ions mostly) SIMS: soft ionisation: similar to FAB but with ion beam as gas (Ce+), allowing higher - MS/MS difficult, almost not compatible with LC coupling acceleration (energy) <500’000Da + idem FAB - idem FAB, target can get hotter, more maintenance mass range 300-13000Da Matrix Assisted Laser Desorption/Ionization Electrospray Ionization (ESI) MALDI UV or IR laser pump sample S S + + S S SH + + + + + + MH + S + + + + S MH SH MH target +++ + 2+ Membrane, gel or metal + + S + + 2+ S + S SnH MH2 MH2 S + Matrix Smaller Coulomb explosion: Ions grid droplet droplet Clusters and Analytes ionic species Modif.
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