Actual Instrumentation

Mass Spectrometry Actual Instrumentation November 2009 See also http://www.uni-bielefeld.de/chemie/analytik/ms for additional information 1. MALDI TOF MASS SPECTROMETRY ON THE VOYAGER DE 2 2. ELECTROSPRAY MASS SPECTROMETRY ON THE ESQUIRE 3000 3 3. EI AND CI MASS SPECTROMETRY ON THE AUTOSPEC X 4 4. ESI AND MALDI SPECTRA ON THE APEX III (FT-ICR MS) 5 5. GC/MS ON THE SHIMADZU GC17A/GCMS-QP 5050A 6 6. GC/MS ON THE VARIAN SATURN II 7

- 2-1. MALDI TOF Mass spectrometry on the Voyager DE MALDI TOF mass spectra were recorded with a Voyager DE Instrument (PE Biosystems GmbH, Weiterstadt, Germany) mounted with a 1.2m flight tube. Ionisation was achieved using a LSI nitrogen laser (337 nm beam wavelength, 3ns pulse width, 3 Hz repetition rate). Depending on the mass range the ions were accelerated at 15 to 25 kv with the option of detecting positive or negative ions. The Instrument Default Calibration was used for calibrating the mass axis. or The mass axis was externally calibrated with... as calibration standard on the same target. or The mass axis was internally calibrated with... as internal calibration standard. The spectra are recorded with the Voyager Instrument Control Software (V 5.10) by accumulation and averaging of... single laser shots. PE Data Explorer software V4.0.0.0 was used for processing the spectra. specify (example): MS (MALDI TOF, positive ions, Matrix, AcceleratingVoltage, Nr.of summed Spectra) m/z = Mass 1 [M 1 +H] +, Mass 1 [M 1 +Na] +, Mass 1 [M 1 +K] +, Mass 2 [M 2 +H] +,... MS (MALDI TOF, negative ions, Matrix, AcceleratingVoltage, Nr.of summed Spectra) m/z = Mass 1 [M 1 -H] -, Mass 2 [M 2 -H] -,... For soft ionisation techniques relative (!) intensities in the spectra should not be cited because they are not reproducible in substance mixtures and on different MS instruments. If the isotopic cluster of a compound shall be cited as a proof for the elemental composition of a special compound, relative ion abundances have to be given as values or (better) the cluster may be depicted in comparison with the calculated isotopic distribution. example: C26H47NO 8 13 CHNOLi 26 46 8 13 Mass x : m/z of the pseudomolecular ion

- 3-2. Electrospray Mass spectrometry on the Esquire 3000 ESI/APCI mass spectra were recorded using an Esquire 3000 ion trap mass spectrometer (Bruker Daltonik GmbH, Bremen, Germany) equipped with a standard ESI/APCI source. Samples were introduced by direct infusion with a syringe pump. Nitrogen served both as the nebulizer gas and the dry gas. Nitrogen was generated by a Bruker nitrogen generator NGM 11. Helium served as cooling gas for the ion trap and collision gas for MS n experiments. The spectra shown here are recorded with the Bruker Daltonik esquirent 5.2 esquirecontrol software by the accumulation and averaging of several single spectra (as cited). DataAnalysis software 3.4 was used for processing the spectra. MS (ESI, positive ions) m/z = Mass 1 [M 1 +H] +, Mass 1 [M 1 +Na] +, Mass 1 [M 1 +K] +, Mass 2 [M 2 +H] +,... MS (ESI, negative ions) m/z = Mass 1 [M 1 -H] -, Mass 2 [M 2 -H] -,... MS/MS (ESI, P 1 (m/z XXX), positive ions) m/z (%) = P 1 [precursor] +, D 1 (int) [daughter 1] +, D 2 (int) [daughter 2] +,... MS 3 (ESI, P 1 (m/z XXX) P 2 (m/z YYY), positive ions) m/z (%) = P 2 [precursor] +, D 1 (int) [daughter 1] +, D 2 (int) [daughter 2] +,... For soft ionisation techniques relative (!) intensities in the spectra should not be cited (exception: MS n spectra) because they are not reproducible in substance mixtures and on different MS instruments. If the isotopic cluster of a compound shall be cited as a proof for the elemental composition of a special compound, relative ion abundances have to be given as values or (better) the cluster may be depicted in comparison with the calculated isotopic distribution. example: Intens. x104 1.25 2219.53 [2M + H] + = 2218.6 1.00 0.75 2218.57 2220.46 C 136 H 216 N 8 O 16 + H + 0.50 2221.46 0.25 2222.49 2223.51 0.00 2216 2218 2220 2222 2224 2226 2228 m/z Mass x : m/z of the pseudomolecular ion P x : m/z of the precursor ion D x : m/z of the daughter ion

- 4-3. EI and CI Mass spectrometry on the Autospec X EI and CI mass spectra were recorded using an Autospec X magnetic sector mass spectrometer with EBE geometry (Vacuum Generators, Manchester, UK) equipped with a standard EI or CI source. Samples were introduced by push rod in aluminium crucibles if not otherwise noted. Ions were accelerated by 8 kv in EI mode and 6 kv in CI mode. The spectra shown here are recorded and processed with the OPUS software (V3.6, Micromass 1998) by the accumulation and averaging of several single spectra. MS (EI, 70eV) m/z (%) = P (int) [Parent] +, F 1 (int) [Fragment 1] +, F 2 (int) [Fragment 2] +,... MS (CI, ammonia) m/z (%) = P 1 (int) [M 1 +H] +, P 2 (int) [M 2 +H] + (more seldom in good 1 CI spectra: F 1 (int) [Fragment 1] +, F 2 (int) [Fragment 2] +,...) P x : m/z of the parent ion F x : m/z of the fragment ion 1 As the Chemical Ionisation (i.e. protonation of the analyte) is not the only process taking place, also some direct Electron Ionisation of the anylate takes place. Therefore (depending also on the analytes properties, i.e. basicisity etc.) the CI spectrum may also contain fragmentation patterns resulting from the fragmentation of Molekular Ions formed by EI (e.g. M -CH 3 ). A typical fragment ions of a CI pseudomolecular ions are formed by secession of neutrals like H 2 O or CH 3 COOH if chemically reasonable, e.g. [M +H -H 2 O] +, [M +H -CH 3 COOH] +.

- 5-4. ESI and MALDI spectra on the APEX III (FT-ICR MS) ESI and MALDI (or EI/CI) experiments were performed using a Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometer APEX III (Bruker Daltonik GmbH, Bremen, Germany) equipped with a 7.0 T, 160 mm bore superconducting magnet (Bruker Analytik GmbH Magnetics, Karlsruhe, Germany), infinity cell, and interfaced to an external (nano)esi or MALDI ion source. Nitrogen served both as the nebulizer gas and the dry gas for ESI. Nitrogen was generated by a Bruker nitrogen generator NGM 11. Argon served as cooling gas in the infinity cell and collision gas for MS n experiments. Scan accumulation and fourier transformation were performed with XMASS NT (7.08) on a PC Workstation, for further data processing DataAnalysis 3.4 was used. MS (ESI, positive ions) m/z = Mass 1 [M 1 +H] +, Mass 1 [M 1 +Na] +, Mass 1 [M 1 +K] +, Mass 2 [M 2 +H] +,... MS (ESI, negative ions) m/z = Mass 1 [M 1 -H] -, Mass 2 [M 2 -H] -,... MS/MS (ESI, P 1 (m/z XXX), positive ions) m/z (%) = P 1 [precursor] +, D 1 (int) [daughter 1] +, D 2 (int) [daughter 2] +,... MS 3 (ESI, P 1 (m/z XXX) P 2 (m/z YYY), positive ions) m/z (%) = P 2 [precursor] +, D 1 (int) [daughter 1] +, D 2 (int) [daughter 2] +,... For soft ionisation techniques relative (!) intensities in the spectra should not be cited (exception: MS n spectra) because they are not reproducible in substance mixtures and on different MS instruments. If the isotopic cluster of a compound shall be cited as a proof for the elemental composition of a special compound, relative ion abundances have to be given as values or (better) the cluster may be depicted in comparison with the calculated isotopic distribution.

- 6-5. GC/MS on the Shimadzu GC17A/GCMS-QP 5050A EI/CI GC/MS spectra were recorded using an Shimadzu GC17A/GCMS-QP 5050A mass spectrometer equipped with a standard EI or CI source. The spectra shown here are recorded and processed with the LabSolutions software GCMSsolution (V1.02, Shimadzu) by the accumulation and averaging of several single spectra for each GC peak using background subtraction. The GC used a 25 m silica capillary column HP 5 (0.2 mm ID, 0.33 µm film) 2. MS (EI, 70eV) m/z (%) = P (int) [Parent] +, F 1 (int) [Fragment 1] +, F 2 (int) [Fragment 2] +,... MS (CI, ammonia) m/z (%) = P 1 (int) [M 1 +H] +, P 2 (int) [M 2 +H] + (more seldom in good CI spectra: F 1 (int) [Fragment 1] +, F 2 (int) [Fragment 2] +,...) P x : m/z of the parent ion F x : m/z of the fragment ion 2 Please ask a GCMS operator for the actual column your samples have been separated with!

- 7-6. GC/MS on the Varian Saturn II EI/CI GC/MS spectra were recorded using an Varian Saturn II GS/MS mass spectrometer equipped with an ion trap used with EI (70 ev) or CI with internal ionization. The spectra shown here are recorded and processed with the Varian Saturn II Software Version 5.2 by the accumulation and averaging of several single spectra for each GC peak using background subtraction. The GC used a 25 m silica capillary column HP 5 MS (0.2 mm ID, 0.33 µm film) 3. MS (EI, 70eV) m/z (%) = P (int) [Parent] +, F 1 (int) [Fragment 1] +, F 2 (int) [Fragment 2] +,... MS (CI, methane) m/z (%) = P 1 (int) [M 1 +H] +, P 2 (int) [M 2 +H] + (more seldom in good CI spectra: F 1 (int) [Fragment 1] +, F 2 (int) [Fragment 2] +,...) P x : m/z of the parent ion F x : m/z of the fragment ion 3 Please ask a GCMS operator for the actual column your samples have been separated with!