This review offers an introduction to the principles and generic applications of FT-ICR mass spectrometry, directed to readers with no prior experience with the technique. We are able to explain the fundamental FT-ICR phenomena from a simplified theoretical treatment of ion behavior in idealized magnetic and electric fields. The effects of trapping voltage, trap size and shape, and other nonidealities are manifested mainly as perturbations that preserve the idealized ion behavior modified by appropriate numerical correction factors. Topics include: effect of ion mass, charge, magnetic field, and trapping voltage on ion cyclotron frequency; excitation and detection of ICR signals; mass calibration; mass resolving power and mass accuracy; upper mass limit(s); dynamic range; detection limit, strategies for mass and energy selection for MSn; ion axialization, cooling, and remeasurement; and means for guiding externally formed ions into the ion trap. The relation of FT-ICR MS to other types of Fourier transform spectroscopy and to the Paul (quadrupole) ion trap is described. The article concludes with selected applications, an appendix listing accurate fundamental constants needed for ultrahigh-precision analysis, and an annotated list of selected reviews and primary source publications that describe in further detail various FT-ICR MS techniques and applications. © 1998 John Wiley & Sons, Inc., Mass Spec Rev 17, 1–35, 1998

Fourier transform ion cyclotron resonance mass spectrometry: A primer

Characterization and verification of the structures of large biomolecules with high-resolution tandem Fourier transform mass spectrometry with electrospray ionization is critically dependent on the technique used to fragment the multiply charged ions produced. Infrared multiphoton dissociation (IRMPD) of ionized proteins as large as carbonic anhydrase (29 kDa) yields fragment information similar to, but with valuable additions to, that of other dissociation techniques. IRMPD yields product ions on-axis, providing efficient dissociation in further stages; MS3 of ubiquitin (8.6 kDa) yields 11 new sequence ions. Optimum irradiation times for protein ion dissociation vary by more than a factor of 6, with times for oligonucleotides far lower, possibly due to photon resonance with a P-O stretching frequency. IRMPD provides far greater selectivity than collisionally activated dissociation and also appears to yield much less mass discrimination and to dissociate much more stable ions. A technique to remove product ions on formation from the laser beam should improve the present efficiencies of 30-80%.

Infrared Multiphoton Dissociation of Large Multiply Charged Ions for Biomolecule Sequencing

Disulfide bonds in gaseous multiply-protonated proteins are preferentially cleaved in the mass spectrometer by low-energy electrons, in sharp contrast to excitation of the ions by photons or low-energy collisions. For S−S cyclized proteins, capture of one electron can break both an S−S bond and a backbone bond in the same ring, or even both disulfide bonds holding two peptide chains together (e.g., insulin), enhancing the sequence information obtainable by tandem mass spectrometry on proteins in trace amounts. Electron capture at uncharged S−S is unlikely; cleavage appears to be due to the high S−S affinity for H• atoms, consistent with a similar favorability found for tryptophan residues. RRKM calculations indicate that H• capture dissociation of backbone bonds in multiply-charged proteins represents nonergodic behavior, as proposed for the original direct mechanism of electron capture dissociation.

Electron Capture Dissociation of Gaseous Multiply-Charged Proteins Is Favored at Disulfide Bonds and Other Sites of High Hydrogen Atom Affinity

The detection, correlation, and comparison of peptide and product ions from a data independent LC-MS acquisition strategy with data dependent LC-MS/MS is described. The data independent mode of acquisition differs from an LC-MS/MS data acquisition since no ion transmission window is applied with the first mass analyzer prior to collision induced disassociation. Alternating the energy applied to the collision cell, between low and elevated energy, on a scan-to-scan basis, provides accurate mass precursor and associated product ion spectra from every ion above the LOD of the mass spectrometer. The method therefore provides a near 100% duty cycle, with an inherent increase in signal intensity due to the fact that both precursor and product ion data are collected on all isotopes of every charge-state across the entire chromatographic peak width. The correlation of product to precursor ions, after deconvolution, is achieved by using reconstructed retention time apices and chromatographic peak shapes. Presented are the results from the comparison of a simple four protein mixture, in the presence and absence of an enzymatically digested protein extract from Escherichia coli. The samples were run in triplicate by both data dependant analysis (DDA) LC-MS/MS and data-independent, alternate scanning LC-MS. The detection and identification of precursor and product ions from the combined DDA search results of the four protein mixture were used for comparison to all other data. Each individual set of data-independent LC-MS data provides a more comprehensive set of detected ions than the combined peptide identifications from the DDA LC-MS/MS experiments. In the presence of the complex E. coli background, over 90% of the monoisotopic masses from the combined LC-MS/MS identifications were detected at the appropriate retention time. Moreover, the fragmentation pattern and number of associated elevated energy product ions in each replicate experiment was found to be very similar to the DDA identifications. In the case of the corresponding individual DDA LC-MS/MS experiment, 43% of the possible detectable peptides of interest were identified. The presented data illustrates that the time-aligned data from data-independent alternate scanning LC-MS experiments is highly comparable to the data obtained via DDA. The obtained information can therefore be effectively and correctly deconvolved to correlate product ions with parent precursor ions. The ability to generate precursor-product ion tables from this information and subsequently identify the correct parent precursor peptide will be illustrated in a companion manuscript.

The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS.

This tutorial presents the most common ion activation techniques employed in tandem mass spectrometry. In-source fragmentation and metastable ion decompositions, as well as the general theory of unimolecular dissociations of ions, are initially discussed. This is followed by tandem mass spectrometry, which implies that the activation of ions is distinct from the ionization step, and that the precursor and product ions are both characterized independently by their mass/charge ratios. In collision-induced dissociation (CID), activation of the selected ions occurs by collision(s) with neutral gas molecules in a collision cell. This experiment can be done at high (keV) collision energies, using tandem sector and time-of-flight instruments, or at low (eV range) energies, in tandem quadrupole and ion trapping instruments. It can be performed using either single or multiple collisions with a selected gas and each of these factors influences the distribution of internal energy that the activated ion will possess. While CID remains the most common ion activation technique employed in analytical laboratories today, several new methods have become increasingly useful for specific applications. More recent techniques are examined and their differences, advantages and disadvantages are described in comparison with CID. Collisional activation upon impact of precursor ions on solid surfaces, surface-induced dissociation (SID), is gaining importance as an alternative to gas targets and has been implemented in several different types of mass spectrometers. Furthermore, unique fragmentation mechanisms of multiply-charged species can be studied by electron-capture dissociation (ECD). The ECD technique has been recognized as an efficient means to study non-covalent interactions and to gain sequence information in proteomics applications. Trapping instruments, such as quadrupole ion traps and Fourier transform ion cyclotron resonance instruments, are particularly useful for the photoactivation of ions, specifically for fragmentation of precursor ions by infrared multiphoton dissociation (IRMPD). IRMPD is a non-selective activation method and usually yields rich fragmentation spectra. Lastly, blackbody infrared radiative dissociation is presented with a focus on determining activation energies and other important parameters for the characterization of fragmentation pathways. The individual methods are presented so as to facilitate the understanding of each mechanism of activation and their particular advantages and representative applications.

http://aether.cmi.ua.ac.be/artikels/MB_31643.pdf

Ion activation methods for tandem mass spectrometry.

https://link.springer.com/content/pdf/10.1016/1044-0305(90)85022-E.pdf

Surface-induced dissociation of peptide ions in Fourier-transform mass spectrometry.

https://link.springer.com/content/pdf/10.1016/1044-0305(90)85003-5.pdf

Efficiency of collisionally-activated dissociation and 193-nm photodissociation of peptide ions in fourier transform mass spectrometry.

The simultaneous collection of multiple spectra using tandem and multidimensional mass spectrometry from multiple precursors yields correspondingly enhanced sensitivity through Hadamard transform deconvolution. For MS n spectra, the product relationships are coded by a Hadamard differences method wherein the combined daughter spectrum of a selected half of the precursors is subtracted from the combined daughter spectrum of the remaining precursors, so that no ions are lost.

Hadamard transform measurement of MSN Fourier-transform mass spectra

The neutralization-reionization mass spectra of alkane radical ions indicate significant differences between the structures and geometries of alkane molecules and their molecular ions, confirming recent ab initio predictions. Ionic isomers that are indistinguishable by collisionally-activated dissociation because of easy interconversion can be characterized by neutralization-reionization if the corresponding neutrals show different reactivities, as is demonstrated for the [C2H5]+/C2H5˙ system and for [C2H4O2]+˙ isomers. For identification of mixtures of more than one neutral species, the relative efficiency for reionizing each neutral must be determined; e.g. the O2 reionization efficiency of ˙CH2OH radicals is ∼4 times greater than that of CH3O˙. This information and reference reionization spectra of CH3O˙ and ˙CH2OH show that metastable or collisionally activated methyl acetate cations lose CH3O˙, not ˙CH2OH as previously reported; the newly-formed CH3O˙ undergoes partial (∼20%) isomerization to ˙CH2OH in the ∼10−6s before reionization. Similar results are obtained for [B(OCH3)3]+˙.

Neutralization‐reionization mass spectrometry (NRMS). Structural information from vertical neutralization and reionization efficiencies

https://link.springer.com/content/pdf/10.1016/1044-0305(90)85015-E.pdf

Evan R. Williams

Papers

Surface-induced dissociation of peptide ions in Fourier-transform mass spectrometry.

Efficiency of collisionally-activated dissociation and 193-nm photodissociation of peptide ions in fourier transform mass spectrometry.

Hadamard transform measurement of MSN Fourier-transform mass spectra

Neutralization‐reionization mass spectrometry (NRMS). Structural information from vertical neutralization and reionization efficiencies

193 nm Laser photoionization and photodissociation for isomer differentiation in Fourier-transform mass spectrometry.