Mass Spectrometry

The CMA has three mass spectrometers available for general use:

Applied Biosystems Voyager DE-STR MALDI-TOF

Thermo LCQ ESI/APCI Ion Trap

Waters Q-TOF II ESI/APCI/Nanospray

• For users expecting to have fewer than 3 samples per month, please use our sample drop-off service.

• Users expecting to run samples frequently (more than 3/month for a year or longer) should contact Dr. Mark Bier to schedule training on the required instrument(s).

• CMA provides a sample preparation bench for general use with common resources such as pipettes, sample vials etc. but users must provide:

  • Solvents for dilution, instrument rinsing etc.

  • MALDI:  Calibrant, matrix, sample plate (Part # V700666 from Applied Biosystems).

  • LCQ/Q-TOF:  Square-tipped ("LC-style") gas-tight syringe.

• Users must reserve time on the instrument calendar prior to use.

• For more information about mass spectrometry, see our useful links.

Applied Biosystems Voyager DE-STR MALDI-TOF

Funded by NSF grant #CHE-9808188

The PerSeptive Voyager STR MS is a matrix assisted laser desorption ionization (MALDI) time of flight (TOF) mass spectrometer. Ions are formed in the gas phase from a laser focused onto a matrix/analyte solid sample. The matrix compound is typically a small organic molucule, chosen for its ability to absorb photons at 337 nm from the nitrogen laser. Gas phase ions (positive ions are typically protonated) are then accelerated down the 2 meter flight tube with 20-25 keV of kinetic energy (KE). Low m/z ions hit the detector first followed by the slower, higher m/z ions. To a first order, the ions follow the equation KE=1/2mv². Typical analyte molecules include polymers, peptides, proteins, and DNA.

See how MALDI works!

System Overview:

• Mass range 1-400,000 Da

• Positive and negative ion modes

• Linear (R=3000) and reflector (R=15000) modes

• Post-source decay (PSD) with CID

• 337nm nitrogen laser

• 100 well standard sample plate (user-supplied)

• Polymeric analysis tool (PDI, M_n, M_w, M_z calculation)

• 5ppm mass accuracy in reflectron mode with internal reference

• Femtomole-level detection with proper sample preparation

Calibration:

• Must be performed on a per-session basis by each individual user

Sample Preparation:

• Sample and matrix should be prepared in similar or miscible solvent systems.

• Preparation typically only requires 1µL of sample

• Selecting the proper matrix has a large effect on results.  This decision can be based on previous successful MALDI analyses of similar samples, the NIST polymer recipes page for polymer samples, or see the general guide found in the Voyager manual (section 3.1.1 - "Selecting a Matrix").

  • Sinapic acid is the most common protein (>10kDa) matrix used.

  • α-Cyano-4-hydroxycinnamic acid is the most common peptide (<10kDa) matrix used.

• Samples must be completely dry before loading into the instrument.

• For positive ion samples, a small amount of acetic acid or TFA (0.1% v/v) can be added to enhance the signal.

• Approximate recommended sample concentrations are as follow:

  • Small peptides: 1-10 pmol/µL

  • Proteins: 1-50 pmol/µL

  • Polymers: 1-10 mM

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Thermo-Fisher LCQ ESI/APCI Ion Trap

Funded by NSF grant #DBI-9729351

The Finnigan LCQ is a quadrupole field ion trap mass spectrometer with electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) sources. The LCQ has MSⁿ capabilities, which is a powerful analytical tool for use in structural analysis. This mass spectrometer can provide molecular weight and sequence information for small peptides (MW below 2000 Da) at the femtomole level with proper analyte introduction.

System Overview:

• Optimum mass range 50-2000 m/z, 4000 m/z in limited capacity

• Resolution of >1000 across optimum mass range on a full ms scan

• Zoom and turbo scan features

• Positive / negative ion modes

• ESI and APCI sources

• MSⁿ (i.e. MS-MS-MS-...) mode for structural analysis

• LC-MS capability

• Protein identification with SEQUEST software

• Deconvolution tool for protein mass measurement

Calibration:

• Done by CMA staff only

Sample Preparation:

• All samples should be in an ESI-friendly solvent system such as 50/50 Water/Acetonitrile, Water/Methanol, etc.

• For positive ion samples, a small amount of acetic acid (0.1% v/v) can be added to enhance the signal.  TFA is not recommended.

• For direct injection, prepare at least 100µL of sample.  For flow-injection analysis 20µL is typically sufficient.

• Recommended sample concentrations are as follow:

  • Small organics: 10-100µM

  • Small peptides: 5µM (pmol/µL)

  • Large proteins: 20-100µM (pmol/µL)

  • Polymers: 100-1000µM

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Waters Q-TOF II ESI/APCI Quadrupole-TOF

The Micromass Q-TOF II is a hybrid mass spectrometer designed specifically for high performance in the mass range 100-2000 m/z, especially with protein identification in mind.  Samples are introduced via ESI, APCI, or Nanospray ionization sources, analyzed (optionally) by the quadrupole, fragmented (optionally) in the hexapole collision cell, then accelerated orthogonally into the TOF tube for high-resolution mass analysis.  The Q-TOF II is capable of MS and MS-MS analysis and achieves resolution exceeding 10,000.  It can also be used to detect ions above 2000 m/z although not specifically optimized to do so.

System Overview:

• Optimum mass range 2-2000 m/z (theoretically 2-32,000 m/z)

• Quadrupole and orthogonal V-reflectron TOF analyzers

• Positive / negative ion modes

• ESI, APCI, and nanospray ion sources

• Auto-injector valve for flow-injection analysis

• Z-spray source inlet configuration for reduced noise & contamination

• MS and MS-MS (CID) modes

• Resolution exceeding 10,000 within optimum mass range

• Femtomole-level sensitivity within optimum mass range

• 5ppm mass accuracy with proper internal reference over 150-900 m/z

Calibration:

• Must be performed daily by individual users.

Sample Preparation:

• All samples should be in an ESI-friendly solvent system such as 50/50 water/acetonitrile, water/methanol, etc.

• For positive ion samples, a small amount of acetic acid (0.1% v/v) can be added to enhance the signal.  TFA is not recommended.

• For direct injection, prepare at least 100µL of sample.  For flow-injection analysis 20µL is typically sufficient.

• Approximate recommended sample concentrations are as follow:

  • Small organics: 1-100µM

  • Small peptides: 1-20µM (pmol/µL)

  • Large proteins: 2-100µM (pmol/µL)

  • Polymers: 100-1000µM

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