Thermo Fisher Scientific Introduces New High-Field Orbitrap Mass Spectrometer at ASMS 2011

Novel high-field Orbitrap technology provides exceptional resolving power of >240,000 creating new possibilities in research and discovery

DENVER, CO. June 2, 2011.

Thermo Fisher Scientific Inc., the world leader in serving science, today introduced a new milestone in Orbitrap technology, the Thermo Scientific Orbitrap Elite. The Orbitrap Elite hybrid mass spectrometer integrates Thermo Scientific's faster, more sensitive ion trap - the Thermo Scientific Velos Pro - with the company's new high-field Orbitrap and advanced signal processing technologies. The system offers outstanding resolving power of 240,000, previously available only on Fourier transform ion cyclotron resonance (FTICR) mass spectrometers, as well as a range of fragmentation techniques, helping customers explore and address the most complex challenges in proteomics, metabolomics, lipidomics and metabolism applications. The new mass spectrometer can be seen in the Thermo Scientific hospitality suite at the Hyatt Regency in Centennial Ballroom D during the 59th Annual ASMS Conference on Mass Spectrometry and Allied Topics, from June 5-9 in Denver.

"Thermo Scientific Orbitrap technology is the recognized standard for accurate mass and high-resolution measurement," said Thomas Moehring, product manager, Thermo Fisher Scientific. "With the introduction of the high-field Orbitrap and advanced signal processing technology, we created a new standard in ultrahigh resolution and accurate mass for laboratories performing comprehensive proteomics and metabolism studies."

The Orbitrap Elite embodies multiple advanced technologies including its mass analyzer geometry, unique signal processing, new ion-transfer optics that improve ion beam transmission into the Orbitrap mass analyzer and a new image current pre-amplifier. These capabilities are coupled with new Velos Pro ion trap technology - linear detection electronics, fast scanning and neutral-blocking front-end ion optics - to enhance overall system quantitative performance, speed and uptime. The sum of these unique innovations offers:

• Maximum resolving power of greater than 240,000 FWHM at m/z 400
• An amazing four-fold increase in scan speed for increased precision and confidence in quantitative results, and enhanced compatibility with UHPLC.
• More high-quality, higher-energy collisional induced dissociation (HCD) spectra and FTMSn spectral fragmentation trees for confident structural elucidation.
• Exceptional sensitivity for the detection of very low abundance proteins, peptides and metabolites

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Comparison of Different Signal Thresholds on Data Dependent Sampling in Orbitrap and LTQ Mass Spectrometry for the Identification of Peptides and Proteins in Complex Mixtures

We evaluate the effect of ion-abundance threshold settings for data dependent acquisition on a hybrid LTQ-Orbitrap mass spectrometer, analyzing features such as the total number of spectra collected, the signal to noise ratio of the full MS scans, the spectral quality of the tandem mass spectra acquired, and the number of peptides and proteins identified from a complex mixture. We find that increasing the threshold for data dependent acquisition generally decreases the quantity but increases the quality of the spectra acquired. This is especially true when the threshold setting is set above the noise level of the full MS scan. We compare two distinct experimental configurations: one where full MS scans are acquired in the Orbitrap analyzer, while tandem MS scans are acquired in the LTQ analyzer and one where both full MS and tandem MS scans are acquired in the LTQ analyzer. We examine the number of spectra, peptides, and proteins identified under various threshold conditions, and we find that the optimal threshold setting is at or below the respective noise level of the instrument regardless of whether the full MS scan is performed in the Orbitrap or in the LTQ analyzer. When comparing the high-throughput identification performance of the two analyzers, we conclude that, used at optimal threshold levels, the LTQ and the Orbitrap identify similar numbers of peptides and proteins. The higher scan speed of the LTQ, which results in more spectra being collected, is roughly compensated by the higher mass accuracy of the Orbitrap, which results in improved database searching and peptide validation software performance.
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Orbitrap/LTQ signal threshold

We evaluate the effect of ion-abundance threshold settings for data dependent acquisition on a hybrid
LTQ-Orbitrap mass spectrometer, analyzing features such as the total number of spectra collected,
the signal to noise ratio of the full MS scans, the spectral quality of the tandem mass spectra acquired,
and the number of peptides and proteins identified from a complex mixture. We find that increasing
the threshold for data dependent acquisition generally decreases the quantity but increases the quality
of the spectra acquired. This is especially true when the threshold setting is set above the noise level
of the full MS scan. We compare two distinct experimental configurations: one where full MS scans
are acquired in the Orbitrap analyzer, while tandem MS scans are acquired in the LTQ analyzer and
one where both full MS and tandem MS scans are acquired in the LTQ analyzer. We examine the
number of spectra, peptides, and proteins identified under various threshold conditions, and we find
that the optimal threshold setting is at or below the respective noise level of the instrument regardless
of whether the full MS scan is performed in the Orbitrap or in the LTQ analyzer. When comparing
the high-throughput identification performance of the two analyzers, we conclude that, used at
optimal threshold levels, the LTQ and the Orbitrap identify similar numbers of peptides and proteins.
The higher scan speed of the LTQ, which results in more spectra being collected, is roughly
compensated by the higher mass accuracy of the Orbitrap, which results in improved database
searching and peptide validation software performance.

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mass accuracy of Orbitrap: internal communications

From communications with one colleague.


It was mentioned during the training course last month that, while performing DDA, the Orbitrap performs a "pre-scan" of the ions entering the mass spectrometer. This pre-scan is really just a part of the full scan. Rather than waiting for the completion of the full scan at a high resolution, instead, part way through, it registers the pre-scan (at a resolution of about 15,000) for the purpose of selecting ions for MS/MS. The full scan continues to completion, but the MS/MS scans on the linear ion trap already are underway by the time this happens.

The point here is that the precursor masses reported for the MS/MS spectra are from the pre-scan, not the higher resolution (if one was specified in the methods file) full scan.

At my request, he installed a utility named extractMSn on the computer associated with OT1. This utility takes a .RAW data file and extracts all of the MS and MS/MS spectra, creating a set of .dta files. The first line of each .dta file representing a MS/MS file contains the m/z value of the precursor as determined by the full scan, not the pre-scan.


The purpose of the pre-scan is to speed up the process of data-dependent acquisition (DDA). Instead of waiting for an entire full scan to be completed before doing the first MS/MS, it collects data when the full scan is partially complete. This doesn't mean it only has covered a part of the scan range. The full range of ions are present in both the pre-scan and the full scan; they are just better resolved in the full scan (and a little more accurate).

The pre-scan is not inherently more useful than the full scan. In fact, the peaks of the full scan should be better resolved. The problem is that the precursor m/z values reported for the MS/MS spectra (i.e. the values that appear in the .dtas) are the less-resolved pre-scan values. So something is needed to go back to the full scan and pick out the better resolved values if those are what one wants.

I decided to have a look at whether it makes any signficant difference. So, for 63 MS/MS spectra representing BSA peptides, I calculated the ppm error for precursor m/z values taken from the pre-scan and the full scan. This data is attached as a spreadsheet.

For the pre-scan precursor m/z values, the ppm error ranged from -2.1 ppm to as high as 10.9 ppm in what seems to be a uniform distribution.

For the full scan precursor values, most fell into the range -2.8 ppm to 3.4 ppm, with an average of -0.8. This matches what I've observed for y ions of MS/MS spectra. However, there was a second range or errors, from -31.9 ppm to -22.1 ppm, for the precursors of 11 peptides.

Possibly, the second range arises from the utility selecting an interfering peak rather than the proper one in certain instances. I'll look into it further.

That is what ExtractMSn does (generates peak lists with the full scan m/z value for the precursor included instead of the pre-scan value), but it apparently doesn't always do it well. If it did it with 100% success, I would recommend using it for applications where resolution greater than 15,000 is important. But it doesn't.

In any case, it seems the extractMSn utility isn't very helpful and should not be used.