Mass spectrometry

The Mass Spectrometry of Biomolecules Service Unit at LMU (MSBioLMU) is part of the faculty. This service is available to both internal research groups and external research institutions. Low-molecular-weight substances/metabolites (metabolomics) and high-molecular-weight polypeptides/proteins (proteomics) are routinely measured and quantified in a wide variety of matrices. Various mass spectrometers and chromatographs are available for this purpose.

Mass spectronomy tubes

Devices

Metabolomics

The MSBioLMU Metabolomics Service Unit routinely performs GC-MS and LC-MS analyses of small molecules. Several instruments are available for analysis: two GC-TOF-MS and a UPLC-ESI-QTOF combination. The existing equipment allows a wide range of metabolites to be identified and quantified. These include amino acids, organic acids, sugars, fatty acids, glucosinolates, indoles, phenylpropanoids, flavonoids, lipids, and porphyrins.

The service offering includes sample measurements, consulting on experimental design, and data analysis. Analysis is performed using various programs and compound libraries.

Sample Preparation

Before sending any samples, establish contacts to the service unit to check the machine run time capacity and confirm the correct receipt of your samples. To ensure the degree of purity required for all consumables the sample preparation will be done exclusively in our laboratories. Methods of extraction will be adapted to the customer needs.

  • Ask the service unit for help in experimental design, if necessary.
  • Prepare at least 5 biological replicates (5 mg dry weight or 50 mg fresh weight, some extra material for testing is welcome)
  • Always use the highest grade reagents and consumables available.
  • Wear clean and powder-free gloves and avoid skin contact.
  • Harvest fast as possible! The metabolism needs to be stopped immediately by freezing in liquid nitrogen (solid sample) or adding ice cold methanol (liquid sample). Ask the MSBioLMU support in advance. If necessary lyophilise the sample. Ask in advance!
  • Store the sample at -80°C.
  • Send the samples on dry ice or lyophilised only.
  • Contact the MSBioLMU before sending any samples to ensure correct receipt.
  • Fill out the Sample Submission Form (PDF, 102 KB) and submit it together with your sample (rooms F02.17 or F02.021)
  • Please consider the MSBioLMU in acknowledgements.

Data Exploration

GC-MS data sets are evaluated using device-specific programs, as well as, the TagFinder software tool. The TagFinder employs spectra and retention time indices (RI) of the Golm Metabolom Database (GMD) for metabolite identification. LC-ESI-QTOF-MS data sets are evaluated by MassLynx V4.1 and further freeware tools.

Technical Equipment

GC-MS
The service unit has two Pegasus HT GC-TOF-MS (Leco) equiped with an autosampler (automated derivatisation/injection) to perform gas chromatography. This ensures a high comparability of the derivatisation process combined with minimised time offset between sample preparation and measurement. Furthermore, both GC machines have two different injection ports to enable hot and cold injection. A 30 m VF-5 ms column + 10 m guard column (Agilent Technologies) is routinely used.

LC-MS
LC analyses are performend on a UPLC-QTOF combination (Premier, Waters). The QTOF has an ESI source and different types of columns are available.

Costs

Information on pricing and user conditions is provided here (PDF, 152 KB).

Contact:
Organisation Martin Lehmann
Technische Assistenz Beate Minov
Räume: F02.017 und F02.021

Proteomics

What we offer

The service unit MSBioLMU subject routinely identifies proteins from distinct gel bands, gel spots, precipitates, complex mixtures or cell lysates.
Samples are analysed with a QTOF (Bruker timsTOF HT or Bruker Impact II) combined with a nano LC system. Typically, a RP C18 capillary column is used for peptide analysis.
The service includes sample measurements, advisory service in experimental design and data exploration. To analyse the data, several software tools (e.g. MaxQuant, DIA-NN) and mass spectral libraries are used.

Sample preparation guidelines

You are free to use protein preparation methods of your choice but we ask you to follow the rules
below to avoid sample contamination and to get best results. We accept gel pieces as well as solutions. Trypsin digest and sample clean-up will be performed by us.

General

  • All equipment should be as clean as possible
  • Use the highest grade reagents available
  • All glass- and plasticware including glass plates should be cleaned first with 70% ethanol, then with H2O
  • Do not autoclave pipet tips and reaction tubes
  • Wear clean and powder-free gloves and avoid skin contact.

For gel pieces

  • If you use home-made gels, don’t cast and run them on the same day
  • Do not heat gels in the microwave
  • Silver staining methods have to be MS compatible for e.g. see
  • Attachment of annotated gel image (including a molecular weight marker) to the sample submission form is required
  • Use fresh and clean blades on a clean surface for excision of gel pieces (store pieces at 4°C)
For samples in solution
    • Avoid detergents (especially polymeric ones like Triton, NP-40 etc.) and PEG!
    • Minimize salt concentrations

  • Sample submission

  • Before sending samples, please contact the service unit in advance to inquire about the device capacity and to ensure safe sample acceptance.

  • Pricing

Contact:

Organisation: Dr. Martin Lehmann, PD Dr. Serena Schwenkert, PD Dr. Jörg Meurer Technische Assistenz: Julia Davydova

Räume: F02.017 und F02.021 E-mail: ms@bio.lmu.de

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