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Although only a few years old, the combination of a linear ion trap with an Orbitrap analyzer has become one of the standard mass spectrometers to characterize proteins and proteomes. Here we describe a novel version of this instrument family, the Orbitrap Elite, which is improved in three main areas. The ion transfer optics has an ion path that blocks the line of sight to achieve more robust operation. The tandem MS acquisition speed of the dual cell linear ion trap now exceeds 12 Hz. Most importantly, the resolving power of the Orbitrap analyzer has been increased twofold for the same transient length by employing a compact, high-field Orbitrap analyzer that almost doubles the observed frequencies. An enhanced Fourier Transform algorithm—incorporating phase information—further doubles the resolving power to 240,000 at m/z 400 for a 768 ms transient. For top-down experiments, we combine a survey scan with a selected ion monitoring scan of the charge state of the protein to be fragmented and with several HCD microscans. Despite the 120,000 resolving power for SIM and HCD scans, the total cycle time is within several seconds and therefore suitable for liquid chromatography tandem MS. For bottom-up proteomics, we combined survey scans at 240,000 resolving power with data-dependent collision-induced dissociation of the 20 most abundant precursors in a total cycle time of 2.5 s—increasing protein identifications in complex mixtures by about 30%. The speed of the Orbitrap Elite furthermore allows scan modes in which complementary dissociation mechanisms are routinely obtained of all fragmented peptides. Although only a few years old, the combination of a linear ion trap with an Orbitrap analyzer has become one of the standard mass spectrometers to characterize proteins and proteomes. Here we describe a novel version of this instrument family, the Orbitrap Elite, which is improved in three main areas. The ion transfer optics has an ion path that blocks the line of sight to achieve more robust operation. The tandem MS acquisition speed of the dual cell linear ion trap now exceeds 12 Hz. Most importantly, the resolving power of the Orbitrap analyzer has been increased twofold for the same transient length by employing a compact, high-field Orbitrap analyzer that almost doubles the observed frequencies. An enhanced Fourier Transform algorithm—incorporating phase information—further doubles the resolving power to 240,000 at m/z 400 for a 768 ms transient. For top-down experiments, we combine a survey scan with a selected ion monitoring scan of the charge state of the protein to be fragmented and with several HCD microscans. Despite the 120,000 resolving power for SIM and HCD scans, the total cycle time is within several seconds and therefore suitable for liquid chromatography tandem MS. For bottom-up proteomics, we combined survey scans at 240,000 resolving power with data-dependent collision-induced dissociation of the 20 most abundant precursors in a total cycle time of 2.5 s—increasing protein identifications in complex mixtures by about 30%. The speed of the Orbitrap Elite furthermore allows scan modes in which complementary dissociation mechanisms are routinely obtained of all fragmented peptides. In many mass spectrometric applications, the resolving power of the instrument is of pivotal importance. Ultimate resolution has so far been obtained by Fourier Transform Mass Spectrometry (1Scigelova M. Hornshaw M. Giannakopulos A. Makarov A. Fourier transform mass spectrometry.Mol. Cell. Proteomics. 2011; 10 (M111.009431)Abstract Full Text Full Text PDF PubMed Scopus (153) Google Scholar) and in a recent example, Marshall and co-workers detected more than 26,000 components in a single spectrum of a crude oil mixture (2Kaiser N.K. Savory J.J. McKenna A.M. Quinn J.P. Hendrickson C.L. Marshall A.G. Electrically compensated fourier transform ion cyclotron resonance cell for complex mixture mass analysis.Anal. Chem. 2011; 83: 6907-6910Crossref PubMed Scopus (94) Google Scholar). In ion cyclotron resonance (ICR) 1The abbreviations used are:AGCautomatic gain controlCIDcollision induced dissociationETDelectron transfer dissociationFDRfalse discovery rateFTFourier transformHCDhigher energy collisional dissociationHPLChigh performance liquid chromatographyICRion cyclotron resonanceIPIInternational Protein IndexMS/MStandem mass spectrometrySIMselected ion monitoring. 1The abbreviations used are:AGCautomatic gain controlCIDcollision induced dissociationETDelectron transfer dissociationFDRfalse discovery rateFTFourier transformHCDhigher energy collisional dissociationHPLChigh performance liquid chromatographyICRion cyclotron resonanceIPIInternational Protein IndexMS/MStandem mass spectrometrySIMselected ion monitoring. Fourier transform mass spectrometry, resolution is determined by the length of the transient and by the strength of the magnetic field. Increasingly larger magnets have allowed resolution in excess of one million for small molecules. The relatively recently introduced OrbitrapTM analyzer utilizes a different physical principle to obtain high resolution (3Makarov A. Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis.Anal. Chem. 2000; 72: 1156-1162Crossref PubMed Scopus (641) Google Scholar, 4Scigelova M. Makarov A. Orbitrap mass analyzer—overview and applications in proteomics.Proteomics. 2006; 6: 16-21Crossref PubMed Scopus (174) Google Scholar, 5Makarov A. Denisov E. Kholomeev A. Balschun W. Lange O. Strupat K. Horning S. Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer.Anal. Chem. 2006; 78: 2113-2120Crossref PubMed Scopus (590) Google Scholar, 6Hu Q. Noll R.J. Li H. Makarov A. Hardman M. Graham Cooks R. The Orbitrap: a new mass spectrometer.J. Mass Spectrom. 2005; 40: 430-443Crossref PubMed Scopus (982) Google Scholar). The signal is recorded from the image current produced by ion packets which oscillate around and along the spindle-shaped inner electrode of the trap: the higher the electric field, the larger the number of oscillations per unit time and the higher the resolving power. To increase field strength, several design options can be pursued, including increasing the radius of the inner electrode of the device (7Makarov A. Denisov E. Lange O. Performance evaluation of a high-field Orbitrap mass analyzer.J. Am. Soc. Mass Spectrom. 2009; 20: 1391-1396Crossref PubMed Scopus (134) Google Scholar). Here we describe an Orbitrap analyzer that achieves higher resolving power through reduced trap dimensions. Resolution is further increased by making use of the phase information during Fourier Transformation (8Vining B.A. Bossio R.E. Marshall A.G. Phase correction for collision model analysis and enhanced resolving power of fourier transform ion cyclotron resonance mass spectra.Anal. Chem. 1999; 71: 460-467Crossref PubMed Scopus (29) Google Scholar, 9Beu S.C. Blakney G.T. Quinn J.P. Hendrickson C.L. Marshall A.G. Broadband phase correction of FT-ICR mass spectra via simultaneous excitation and detection.Anal. Chem. 2004; 76: 5756-5761Crossref PubMed Scopus (51) Google Scholar, 10Lange O. Damoc E. Wieghaus A. Makarov A. Enhanced Fourier Transform for Orbitrap Mass Spectrometry.Proc. 59th Conf. Amer. Soc. Mass Spectrom. 2011; (Denver, June 5 9, 2011)Google Scholar, 11Michalski A. Damoc E. Hauschild J.P. Lange O. Wieghaus A. Makarov A. Nagaraj N. Cox J. Mann M. Horning S. Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer.Mol. Cell. Proteomics. 2011; 10 (9, M111.011015. Epub 2011 Jun 3)Abstract Full Text Full Text PDF PubMed Scopus (626) Google Scholar). This ultra high resolution Orbitrap analyzer was combined with other instrumental improvements to construct a novel linear ion trap Orbitrap hybrid mass spectrometer termed the Orbitrap Elite. automatic gain control collision induced dissociation electron transfer dissociation false discovery rate Fourier transform higher energy collisional dissociation high performance liquid chromatography ion cyclotron resonance International Protein Index tandem mass spectrometry selected ion monitoring. automatic gain control collision induced dissociation electron transfer dissociation false discovery rate Fourier transform higher energy collisional dissociation high performance liquid chromatography ion cyclotron resonance International Protein Index tandem mass spectrometry selected ion monitoring. We describe principles of this instrument and characterize its operation for both intact protein analysis and for bottom up peptide mixture analysis. Top protein analysis has been with Fourier transform of high resolving power Chem. 2004; 76: PubMed Google Scholar, of in mass Chem. 2011; PubMed Scopus (51) Google Scholar, K. M. H. and of by mass Am. Soc. Mass Spectrom. PubMed Scopus Google Scholar). of the in using in proteomics has been to obtain cycle with liquid chromatography tandem MS time B.A. proteomics a time using linear ion trap fourier transform hybrid mass Chem. PubMed Scopus Google Scholar). The linear ion trap Orbitrap has been for proteomics Mann M. protein and a hybrid linear quadrupole ion mass spectrometer.Mol. Cell. Proteomics. 2006; Full Text Full Text PDF PubMed Scopus Google Scholar, S. Mann M. and of Am. Soc. Mass Spectrom. PubMed Scopus Google Scholar, Makarov Mass and top-down analysis of intact a hybrid linear quadrupole ion mass spectrometer.J. Am. Soc. Mass Spectrom. 2009; 20: PubMed Scopus Google Scholar, R. W. of an for Mass for and J. Mass Spectrom. 2011; PubMed Scopus Google Scholar). Here we of the ultra high resolution of the Orbitrap Elite to top-down scan In bottom-up proteomics complex peptide mixtures are The of PubMed Scopus Google Scholar, J. Mann M. proteomics for 2011; PubMed Scopus Google Scholar, M. M. R. 2011; PubMed Scopus Google Scholar). MS for of of R. K. to an a linear and number of Chem. 2011; 83: PubMed Scopus Google Scholar, A. Cox J. Mann M. than peptide in single proteomics the is to data-dependent 2011; PubMed Scopus Google Scholar) and this a the resolution of the survey proteomics the linear ion trap Orbitrap Orbitrap Orbitrap is a survey scan with resolution at m/z 400 ms and ion trap collision-induced dissociation scans of the most abundant Here we with higher resolution survey scans an increased number of per cycle by resolution MS M. the for high resolution and high mass S. A. PubMed Scopus Google has been routinely Orbitrap by higher energy collisional dissociation with the of the J. Damoc E. Denisov E. Lange O. M. M. Makarov A. Mann M. Horning S. dual linear ion trap Orbitrap instrument with high Cell. Proteomics. 2009; Full Text Full Text PDF PubMed Scopus Google Scholar). We that this from the and higher resolving power the Orbitrap Elite. has been that a combination of can information in peptide 2005; PubMed Scopus Google Scholar, M. a of spectra of 6: PubMed Scopus Google Scholar, J.J. tandem mass spectrometry for PubMed Scopus Google Scholar) and we this dual with and HCD of the same The Orbitrap Elite is a further of the Orbitrap J. Damoc E. Denisov E. Lange O. M. M. Makarov A. Mann M. Horning S. dual linear ion trap Orbitrap instrument with high Cell. Proteomics. 2009; Full Text Full Text PDF PubMed Scopus Google Scholar). This hybrid instrument a dual cell linear ion trap mass spectrometer with a high field Orbitrap mass analyzer The the J.J. linear ion trap mass spectrometer the analysis of complex protein Chem. 2009; PubMed Scopus Google Scholar) and its a new of ion optics of a quadrupole a and an ion transfer ion trap mass analysis scan speed of and a higher for improved and the of collisional dissociation for the ion trap The of a of to which an is This device is used in a high to the ion from a transfer through a M. M. J.J. of a ion a linear ion trap mass Amer. Soc. Mass Spectrom. Conf. Mass Spectrometry 2009; 5 Scholar). and the transfer are from the ion optics by a quadrupole ion The ion has been with to the in the so that and can through the the quadrupole than the This the for of the quadrupole ion The new allows for a to be in the of of the quadrupole ion a The combination of the quadrupole ion and the the rate of and the of the ion optics length at the and has been and the quadrupole device in this in the This to be more robust to and is used a dissociation device in the J. J.J. dissociation a collision Cell. Proteomics. 2011; 10 Full Text Full Text PDF PubMed Scopus Google Scholar). The dual cell linear ion trap allows for scan and higher resolution to the in the mass cell of the ion trap J.J. linear ion trap mass spectrometer the analysis of complex protein Chem. 2009; PubMed Scopus Google Scholar). The scan rate the is which achieves of at m/z and is to of the resonance and the phase the resonance and a small in resolution can a in scan In the the scan rate has been to than unit an at of at m/z this scan rate up to scans can be per of the scan the ion mass analysis are a higher is electron have been that the electron in the new electron have linear up to of is in the which the performance of the The linear of this the and for analysis enhanced of The Orbitrap mass analyzer of an electrode of radius and a electrode along the of radius with the electrode at the of the the electrode is at a for (3Makarov A. Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis.Anal. Chem. 2000; 72: 1156-1162Crossref PubMed Scopus (641) Google Scholar). In a standard Orbitrap and A. Denisov E. Kholomeev A. Balschun W. Lange O. Strupat K. Horning S. Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer.Anal. Chem. 2006; 78: 2113-2120Crossref PubMed Scopus (590) Google the high-field analyzer is more with 5 and 10 the electrode is by a of to an analyzer recently (7Makarov A. Denisov E. Lange O. Performance evaluation of a high-field Orbitrap mass analyzer.J. Am. Soc. Mass Spectrom. 2009; 20: 1391-1396Crossref PubMed Scopus (134) Google a of the from 2.5 to allows an increase in the in to the the total gain of to This is by an increase of the ion energy of Despite the increase in charge in the analyzer by a of the by the relatively electrode induced in the standard the was by the same the electrode to the of the field the an of the ion This was by a in the of a with a at a of up to which was at and by of This was the same the at the to the Orbitrap of the to to and to which in allowed the use of in the image current The increase of about in the same for the same number of in the standard analyzer for We that of the the and the an almost of of the This was by of the and of a transient is a relatively to achieve high resolving is to further increase the resolving power for a acquisition We a enhanced version of the Fourier Transformation which is in novel the Q A. Damoc E. Hauschild J.P. Lange O. Wieghaus A. Makarov A. Nagaraj N. Cox J. Mann M. Horning S. Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer.Mol. Cell. Proteomics. 2011; 10 (9, M111.011015. Epub 2011 Jun 3)Abstract Full Text Full Text PDF PubMed Scopus (626) Google Scholar). of the technique can be in O. Damoc E. Wieghaus A. Makarov A. Enhanced Fourier Transform for Orbitrap Mass Spectrometry.Proc. 59th Conf. Amer. Soc. Mass Spectrom. 2011; (Denver, June 5 9, 2011)Google Scholar). both and use of complex which can be by and the phase of the ion of the in a (8Vining B.A. Bossio R.E. Marshall A.G. Phase correction for collision model analysis and enhanced resolving power of fourier transform ion cyclotron resonance mass spectra.Anal. Chem. 1999; 71: 460-467Crossref PubMed Scopus (29) Google spectra have to be in the which to the phase in Orbitrap mass spectrometers the A. of Mass R.E. and Scholar) an phase of ion oscillations that is almost of This allows spectra in a that to phase for all m/z and In a combination of and spectra along with and to mass and of spectra is ion the of the and Orbitrap analyzer have that used for of the during of the Orbitrap that the is for the at the to the Orbitrap analyzer and of was by the the of and was reduced and by with by the of the Orbitrap The at the to the Orbitrap analyzer and of was by this a allowed the ion and of transient from almost 10 ms to a of a In to improved this of allows to the of the transient A. Denisov E. of of intact proteins in the Orbitrap mass analyzer.J. Am. Soc. Mass Spectrom. 2009; 20: PubMed Scopus Google for proteins intact and therefore of Orbitrap for analysis. The of the achieves up to twofold increase of resolving power for the same transient. For for from this gain is reduced to about of (8Vining B.A. Bossio R.E. Marshall A.G. Phase correction for collision model analysis and enhanced resolving power of fourier transform ion cyclotron resonance mass spectra.Anal. Chem. 1999; 71: 460-467Crossref PubMed Scopus (29) Google Scholar). The is to be in the MS time cycle time is determined by transient acquisition and ion and by of the The is to of the instrument and so that mass is to that of in spectra are to in proteins from in to MS analysis. For experiments, protein in in and The protein mixture was reduced with for at and with for 20 The proteins with for at The was with 12 with at was to the mixture to The peptide mixture was phase J. Mann M. and for and in Chem. 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N. A. Mann M. the 2011; PubMed Scopus Google Scholar). 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An of the different resolution a of transient length can be in the transient in a resolving power of that of the ms scan used for the Orbitrap In resolution for we scan modes the of transient time with and ion become and transient length of Orbitrap hybrid The resolution Orbitrap Elite by an can only be using the ms in a new resolution is an for resolving the different charge of intact proteins in top-down We selected a used standard in top-down proteomics, to the of the increased resolving power and speed of the We a that a survey scan with resolution by a high resolution SIM scan of a charge state in a This same m/z is fragmented by HCD and at a high resolving power of 120,000 We that the Orbitrap Elite is of resolving and this protein with a mass for to of the HCD spectra than in the Orbitrap with of a HCD in which charge state was and For and 20 of the charge state by For both of model proteins the increasing the collision energy of up to increased the number of to and for and and for The of the Orbitrap analyzer and signal allows the Orbitrap Elite to a high resolution a at m/z 400 and with standard signal In to the linear of resolving power the Orbitrap resolving power is to the of m/z (1Scigelova M. Hornshaw M. Giannakopulos A. Makarov A. Fourier transform mass spectrometry.Mol. Cell. Proteomics. 2011; 10 (M111.009431)Abstract Full Text Full Text PDF PubMed Scopus (153) Google Scholar). for acquisition an time its resolving power at m/z to a FT-ICR and be suitable for of larger proteins and we that charge state of intact be at a resolution of 240,000 to 768 ms To this a than was the resolution of intact be observed For the analysis of complex peptide a standard of operation is the acquisition of a survey spectrum in the Orbitrap analyzer the linear ion trap and scans the For this we the of the higher resolution in the survey spectra and of the Orbitrap precursors for the of a ms of the MS which time the scans are in the the resolution is increased resolution for all charge and the m/z at higher We that this increased the of ion To the instrument for the analysis of complex peptide mixtures cell we with a standard of 400 that was using different of the and scan modes that produced more and therefore this was for all The in the of MS and scans at different MS transient For a ms survey resolution is and is operation MS and to an with peptide ms resolution is 120,000 and a few scans are in with the survey the 768 ms transient about spectra are in total cycle time is the to be the increased resolution We use of the cycle time to the of high resolving power complex peptide mixture analysis. using and 240,000 resolution for the survey scan the peptide mixture with we that the number of peptide detected by from at resolution to at 240,000 resolution a the MS of the 240,000 resolution the resolution and the in complex peptide mixtures with of survey scan resolution at cycle in a new Fourier transform mass spectrometry of small can the in the of small with the same S. Marshall A.G. and of and in by mass Chem. PubMed Scopus Google to this has been in proteomics We the and and that the and from other the high resolution the of a in the the we selected a 240,000 resolution survey scan and scan the standard of the of the 400 peptide and proteins an increase of the analysis of the same the Orbitrap Although was observed to increase to the higher The Orbitrap Elite HCD and of the is in in resolution in the linear ion trap and in in the Orbitrap analyzer and In all modes can be and to the 5 three of scan In a HCD a survey scan is and is by HCD spectra that are recorded in the Orbitrap ms survey scan resolution of which is for most applications and which to the cycle time in this HCD spectra are at the resolution ms resolution at m/z about the same time for a with the resolution in MS and in in the We the 400 cell with this and obtained improved of peptide identifications with Orbitrap This HCD high speed and high mass spectra and is therefore to the analysis of complex In to the achieves of peptide is than in the linear ion trap have operation. for are higher in HCD and peptide from analysis of a HCD in a new The high scan of this instrument more complex scan modes For the resolution scan can be by high HCD Orbitrap analyzer scans To this we selected up to 10 precursors for by and of the same by can be in the this use of the hybrid The operation with allows time to a survey scan with 240,000 resolution total cycle In in spectra for of the peptides. The are in the of which the spectrum of the peptide the the HCD spectrum in the same The spectrum has the mixture of and the HCD spectrum a of few spectra for all a of all of this this dual information at an in cycle time and This HCD a total cycle time of to the HCD the same speed in complementary be in applications relatively high speed is peptide is for in the analysis of at a The in is a further in the same modes are all scans are in the Orbitrap this is and use the linear ion trap a mass 120,000 resolution survey scan by HCD scans about the same with the high resolution spectra are obtained by different information of the the HCD scan be for applications with peptide high peptide This be the in single protein applications, in proteomics is are Here we have the Orbitrap Elite, a mass spectrometer that achieves improved resolving power by increasing the electric field strength in the Orbitrap analyzer and by enhanced Fourier The high resolving power resolution of proteins in the mass of in a time In bottom-up proteomics, the instrument allows ultra high resolution survey scans and a number of in the linear ion For we the combination of a survey scan of 240,000 resolution with 20 scans all within a cycle this high resolution routinely resolving of peptides. We the acquisition of and HCD spectra of the same with analysis of the Although and HCD be to different peptide can be the of one be by the same other example, be by HCD and be recorded in the Orbitrap at a time are in principle and be to for a of and other
Michalski et al. (Fri,) studied this question.
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