Using accurate mass electrospray ionization–time-of-flight mass spectrometry with in-source collision-induced dissociation to sequence peptide mixtures

Williams, Jon D.; Flanagan, Michael; Lopez, Linda; Fischer, Steven H.; Miller, Luke A. D.

doi:10.1016/j.chroma.2003.07.019

Cited by 35 publications

(32 citation statements)

References 40 publications

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“…This implies that [I 3 ] Ϫ might play an important role in CsI cluster ion formation. However, it was found that not all triiodides could give analyte cluster ions because no corresponding cluster ions were observed when another triiodide compound (tetrabutylammonium triiodide (N(Bu) 4 I 3 )) was used instead of CsI 3 .…”

Section: ]mentioning

confidence: 99%

“…The degree of mass accuracy largely depends on the instrument type and mass calibration method employed. Nowadays, accurate mass measurements with mass error of only a few parts per million (ppm) can be made using a variety of instrument types [1][2][3][4][5]. High mass accuracy is extremely important in the MS application of molecular formula determination and can significantly improve the level of confidence for compound identification, such as protein/peptide confirmation, through database searching [6 -10].…”

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confidence: 99%

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Generation of CsI cluster ions for mass calibration in matrix-assisted laser desorption/ionization mass spectrometry

Lou

Dongen

Meijer

2010

J. Am. Soc. Mass Spectrom.

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A simple method was developed for the generation of cesium iodide (CsI) cluster ions up to m/z over 20,000 in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). Calibration ions in both positive and negative ion modes can readily be generated from a single MALDI spot of CsI 3 with 2-[(2E)-3-(4-tert-butylphenyl)-2-methylprop-2-enylidene] malononitrile (DCTB) matrix. The major cluster ion series observed in the positive ion mode is [(CsI) (MS) analysis is to provide molecular weight information of analytes. The degree of mass accuracy largely depends on the instrument type and mass calibration method employed. Nowadays, accurate mass measurements with mass error of only a few parts per million (ppm) can be made using a variety of instrument types [1][2][3][4][5]. High mass accuracy is extremely important in the MS application of molecular formula determination and can significantly improve the level of confidence for compound identification, such as protein/peptide confirmation, through database searching [6 -10].For accurate mass measurements, a MS system must be precisely calibrated. Calibration constants are usually determined by measuring several reference ions covering the mass range of interest. Different calibration methods have been developed in matrix-assisted laser desorption/ionization (MALDI) MS aiming to improve the mass accuracy [11][12][13][14][15][16][17][18]. Nevertheless, a crucial step in calibration remains to be the generation of suitable ions. In principle, any compounds that can yield ions with known masses and do not interfere with the MS analysis might be applied as calibration standards. In MALDI MS, widely used standards include peptides, proteins, and synthetic polymers/oligomers. To establish a precise calibration, a number of standards spreading over the mass range of interest should be included. Because of the analyte suppression effect (ASE) in MALDI [19,20], some analyte/calibrant ions of interest might substantially or even completely be suppressed. As a consequence, the preparation of suitable calibrants in MALDI, even for external calibration, is not a simple task and may involve an extensive trial and error procedure. Furthermore, different calibration standards are generally required for different modes of ionization (positive or negative ion modes) and for different mass ranges of interest. In fact, MALDI MS still suffers from the lack of truly convenient mass standard calibrants.In this contribution, we described a convenient method of generating cesium iodide (CsI) cluster ions for MALDI MS calibration. CsI cluster ions, together with a number of other cluster ions, have frequently been used in electrospray ionization (ESI) MS calibration. Under suitable ESI conditions, cluster ions evenly covering a broad m/z range can be recorded. Calibration curves thus made have many data points and will generally provide a very precise calibration [21][22][23][24]. Compared with other types of cluster ions, the CsI cluster ions are quite unique because both C...

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Section: ]mentioning

confidence: 99%

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confidence: 99%

Generation of CsI cluster ions for mass calibration in matrix-assisted laser desorption/ionization mass spectrometry

Lou

Dongen

Meijer

2010

J. Am. Soc. Mass Spectrom.

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“…These bioanalytical demands were addressed by such hybrid instruments as the quadrupole/time-of-flight (QqTOF, where Q refers to a mass-resolving quadrupole, q to a radio frequency (RF)-only quadrupole or hexapole collision cell and TOF to a time-of-flight mass spectrometer) (Morris et al, 1996) and the linear quadrupole ion trap/Fourier transform ion cyclotron resonance (LIT/FT-ICR) (Syka et al, 2004b) that perform in the high resolution (>10,000) and high mass accuracy (<5 ppm) regimes (Marshall, Hendrickson, & Jackson, 1998;McLuckey & Wells, 2001;Williams et al, 2003). The QqTOF, which can be regarded as a triple quadrupole (QqQ) instrument where the third quadrupole is replaced by an orthogonal TOF, was originally used for rapid de novo peptide sequencing (Shevchenko et al, 1997) but has found application in many areas of research including metabolite (Levsen et al, 2005), nucleic acid (Oberacher, Niederstatter, & Parson, 2005) and glycoprotein (Morris et al, 2007) analysis.…”

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confidence: 99%

Orbitrap mass spectrometry: Instrumentation, ion motion and applications

Perry

Cooks

Noll

2008

Mass Spectrometry Reviews

402

290

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Since its introduction, the orbitrap has proven to be a robust mass analyzer that can routinely deliver high resolving power and mass accuracy. Unlike conventional ion traps such as the Paul and Penning traps, the orbitrap uses only electrostatic fields to confine and to analyze injected ion populations. In addition, its relatively low cost, simple design and high space‐charge capacity make it suitable for tackling complex scientific problems in which high performance is required. This review begins with a brief account of the set of inventions that led to the orbitrap, followed by a qualitative description of ion capture, ion motion in the trap and modes of detection. Various orbitrap instruments, including the commercially available linear ion trap–orbitrap hybrid mass spectrometers, are also discussed with emphasis on the different methods used to inject ions into the trap. Figures of merit such as resolving power, mass accuracy, dynamic range and sensitivity of each type of instrument are compared. In addition, experimental techniques that allow mass‐selective manipulation of the motion of confined ions and their potential application in tandem mass spectrometry in the orbitrap are described. Finally, some specific applications are reviewed to illustrate the performance and versatility of the orbitrap mass spectrometers. © 2008 Wiley Periodicals, Inc., Mass Spec Rev 27: 661–699, 2008

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“…This approach has its roots in precursor ion scanning techniques in which all precursors were fragmented simultaneously either in the source region or in the collision cell, and the appearance of specific “reporter ions” for a modification of interest was recorded (6–8). Several groups reported the identification of peptides from MS scans in conjunction with MS/MS scans without precursor ion selection (9–12). Yates and co-workers (13) pursued an intermediate strategy by cycling through the mass range in 10 m/z fragmentation windows.…”

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Proteomics on an Orbitrap Benchtop Mass Spectrometer Using All-ion Fragmentation

Geiger¹,

Cox²,

Mann³

2010

Molecular & Cellular Proteomics

229

201

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The orbitrap mass analyzer combines high sensitivity, high resolution, and high mass accuracy in a compact format. In proteomics applications, it is used in a hybrid configuration with a linear ion trap (LTQ-Orbitrap) where the linear trap quadrupole (LTQ) accumulates, isolates, and fragments peptide ions. Alternatively, isolated ions can be fragmented by higher energy collisional dissociation. A recently introduced stand-alone orbitrap analyzer (Exactive) also features a higher energy collisional dissociation cell but cannot isolate ions. Here we report that this instrument can efficiently characterize protein mixtures by alternating MS and "all-ion fragmentation" (AIF) MS/MS scans in a manner similar to that previously described for quadrupole time-of-flight instruments. We applied the peak recognition algorithms of the MaxQuant software at both the precursor and product ion levels. Assignment of fragment ions to co-eluting precursor ions was facilitated by high resolution (100,000 at m/z 200) and high mass accuracy. For efficient fragmentation of different mass precursors, we implemented a stepped collision energy procedure with cumulative MS readout. AIF on the Exactive identified 45 of 48 proteins in an equimolar protein standard mixture and all of them when using a small database. The technique also identified proteins with more than 100-fold abundance differences in a high dynamic range standard. When applied to protein identification in gel slices, AIF unambiguously characterized an immunoprecipitated protein that was barely visible by Coomassie staining and quantified it relative to contaminating proteins. AIF on a benchtop orbitrap instrument is therefore an attractive technology for a wide range of proteomics analyses.

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Using accurate mass electrospray ionization–time-of-flight mass spectrometry with in-source collision-induced dissociation to sequence peptide mixtures

Cited by 35 publications

References 40 publications

Generation of CsI cluster ions for mass calibration in matrix-assisted laser desorption/ionization mass spectrometry

Generation of CsI cluster ions for mass calibration in matrix-assisted laser desorption/ionization mass spectrometry

Orbitrap mass spectrometry: Instrumentation, ion motion and applications

Proteomics on an Orbitrap Benchtop Mass Spectrometer Using All-ion Fragmentation

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