MS Citation Tips

Notes on citing MS instruments and mass spectra

In general, MS citations are divided into two parts for diploma theses, doctoral theses or publications. In the first part, the instruments and methods used are listed at the beginning of the experimental part (if necessary, common measurement parameters such as spray voltage or MALDI matrix used can also be listed there). The second part is given in the characterization of the substance by specifying the respective measurement together with the obtained result.

Citation of instruments and methods:

On the example of university MS instruments

  • ESI mass spectra acquired on the quadrupole ion trap mass spectrometer Finnigan LCQ Deca (ThermoQuest, San José, USA).
  • MALDI mass spectra were obtained with an UltraFlex ToF/ToF (Bruker Daltonics, Bremen, D). An N2 laser with 337 nm wavelength and 3 ns pulse duration was used. As matrix DCTB (2-[(2E)-3-(4-tert-Butylphenyl)-2-methylprop-2-enylidene]malononitrile) was used. The mass calibration was performed directly before the sample measurement on polystyrene (Ag adduct).
  • ESI and APCI mass spectra were measured on a Finnigan LCQ Deca (ThermoQuest, San José, USA). Data acquisition and control was performed on a personal computer running Windows 2000 (Microsoft Corp., USA) with the control and data analysis software Xcalibur (Version 1.3, ThermoQuest).
  • ESI exact mass measurements were performed on the time-of-flight mass spectrometer micrOTOF (Bruker Daltonics, Bremen, D) using an ApolloTM "Ion Funnel" ESI ion source. Mass calibration was performed directly before sample measurement on sodium formate clusters or using the ESI Tune-Mix standard (Agilent, Waldbronn, D). Data acquisition and analysis were carried out using a personal computer under Windows XP (Microsoft Corp., USA) with the Compass control software (Version 1.1).
  • LC-ESI mass spectra were recorded on the triple quadrupole mass spectrometer with linear ion trap Q-Trap 4000 (Applied Biosystems, MDS SCIEX, Darmstadt, Germany) using an on-line Nano-ESI source. For sample separation, the nanospray inlet was coupled to a Nano-LC UltiMate 2000 (LC Packings, Dionex, Frankfurt, D). Data acquisition and processing were performed on a personal computer running Windows XP (Microsoft Corp., USA) with the control software Analyst (version 1.4.1) and Chromeleon (version 6.6).

In case of doubt you can always ask the MS-Team!

Citation of chemical compounds in the experimental part:

MS/ESI (+):

m/z (%) = 365 (100) [M+H]+, 387 (54) [M+Na]+

m/z (%) = 365 (100) [C29H17]+, 387 (54) [C29H16Na]+


m/z = 311.1074 [M+H]+ calculated for [C22H15O2]+ = 311.1072

Note: for measurements of the exact mass, results with a deviation of < 5 ppm are accepted.

For complex isotope distributions, the center of the isotope pattern is given:
 (corresponds to the stoichiometric mass of the measured ion)

MS/APCI (+):
Isotope cluster at m/z = 638.2 [M+H]+ corresponds to the isotope distribution for [C29H18Br3O2]+

If the isotope pattern is not clearly separated (e.g. MALDI in the high mass range), the stoichiometric m/z value (center of the isotope pattern) is cited::


m/z (isotope center) (%) = 9202.2 (100) [C496H720N32O128Na]+