New ion trap mass spectrometer boosts protein characterisation

1st April 2013

Anew ion trap liquid chromatograph and mass spectrometer (LC/MS) that allows scientists to study proteins in a manner that was previously achievable only on a million-dollar floor-standing instrument that requires a dedicated operator.

That’s the claim being made by Agilent Technologies for its new Agilent 6340 ion trap LC/MS (Fig.1).

A new instrument in the company’s 6000 Series portfolio of LC/MS systems, the 6340 fits on a bench top and is equipped with an electron transfer dissociation (ETD) unit – a new tool for the study of proteins and post-translational modifications.

“The 6340 ion trap MS makes the fragmentation power of ETD – formerly attainable only with Fourier-transform MS – affordable for the average laboratory and accessible to all scientists,” said Linda Lopez, product manager. “Our complete solution, which includes innovative separation technologies, the 6340 and data processing software designed expressly for ETD data, will bring unsurpassed performance, reliability and productivity to proteomics research,” she added.

Proteins regulate most biological processes, and their activity is often controlled by the attachment of molecules such as phosphate groups, also known as post-translational modifications. Scientists use various approaches to identify and characterise proteins – and chemical modifications – that may be involved in normal biological functions or diseases such as cancer.

Although ion trap mass spectrometers are a popular choice for protein studies, analysis of post-translational modifications can be challenging because standard ion fragmentation methods often cause labile phosphates, glycans and other chemical modifications to dissociate from peptides. This makes it difficult to determine the attachment point of these modifications and affords minimal peptide sequence information. Agilent says its new ETD provides a ‘softer’ mode of fragmentation that preserves these labile modifications.

When operated in ETD mode, the 6340 provides extensive and easy-to-interpret amino acid sequence information in the form of complementary c- and z-series ions. Other features that make the 6340 an ideal tool for the study of post-translational modifications include the ability to alternate between ETD and collision induced dissociation (CID) modes of fragmentation from scan to scan, which helps to pinpoint the precise identity and location of a chemical modification. In addition, neutral-loss triggered auto-MS3 and pseudo-MSn modes can be used to target specific families of modifications.

Unlike FT-MS devices, the 6340 supports rapid nano-scale chromatography, which facilitates

‘shot-gun’ proteomics studies involving the analysis of all the proteins extracted from whole cell lysates. These are the contents released during the decomposition of a cell. When used in concert with Agilent’s HPLC-Chip, the 6340 will enhance researchers’ ability to identify and characterise protein modifications in extremely complex samples.

Other new features and advances of the 6340 include: a high-speed data acquisition system that provides unsurpassed scan collection and transfer rates; ETD reagent anion monitoring; selective or automatic charge state data collection; and reproducible ETD spectra. The company offers an entire line of ion traps (6310, 6320 and 6330) to accommodate a wide range of budget and performance requirements.

For its part, Thermo Electron Corporation has concluded a licensing agreement with the University of Virginia for electron transfer dissociation (ETD), its innovative new ion fragmentation technology that provides sequence information not available from conventional methods currently in use on ion trap mass spectrometers.

Ken Miller, product marketing manager for proteomics at Thermo, says the power of ETD on the Finnigan LTQ has already been demonstrated for:

  • Mapping of post-translational modification (PTM) sites, particularly phosphorylation.

  • Allowing more comprehensive proteomic sample profiling than with collision-induced dissociation (CID) alone.

  • Fragmenting and analysing large peptide fragments as well as intact proteins.

The results of these studies have been shown in recent seminars, technical posters, and presentations at major scientific conferences.

“ETD will help shed new light on many important, unanswered questions in contemporary biology,” said Don Hunt, principal investigator at the University of Virginia. “ETD represents a landmark advance in the field of proteomics. This new methodology is a powerful and reliable analytical solution for protein characterisation.”





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