Application of ion trap-MS with H/D exchange and QqTOF-MS in the identification of microbial degradates of trimethoprim in nitrifying activated sludge

In this work, the identification of two microbial degradation products of the antimicrobial trimethoprim (290 Da) is described. The structural elucidation of the metabolites, which were produced by nitrifying activated sludge bacteria in a small-scale laboratory batch reactor, was accomplished by electrospray ionization-ion trap mass spectrometry conducting consecutive fragmentation steps (MS(n)) combined with H/D-exchange experiments. Although one metabolite corresponded to alpha-hydroxytrimethoprim (306 Da), oxidation of the aromatic ring within the diaminopyrimidine substructure was determined for the second degradate (324 Da). Accurate mass measurements of the two metabolites were provided by a hybrid quadrupole time-of-flight-mass spectrometer operated in MS/MS mode. With absolute mass errors of <5 mDa, it allowed us to confirm the proposed elemental composition for the protonated precursor ions as well as for a series of fragment ions that were previously identified by ion trap mass spectrometry. The study emphasized the potential of nitrifying activated sludge bacteria for breaking down an environmentally relevant pharmaceutical that is otherwise poorly degradable by a bacterial community encountered in conventional activated sludge.     

Structural characterization of protein tryptic peptides via liquid chromatography/mass spectrometry and collision-induced dissociation of their doubly charged molecular ions

The formation of multiply charged molecular ions via the field-assisted ion evaporation mechanism during electrospray ionization enables the use of an atmospheric pressure ionization quadrupole mass spectrometer system for characterizing biologically important peptides. The straightforward implementation of high-performance liquid chromatography (HPLC) into this new strategy to determine the molecular weight of tryptic peptides via the pneumatically assisted electrospray (ion spray) interface is presented. Examples utilizing both microbore (1.0 mm) and standard bore (4.6 mm) inside diameter columns are shown for the LC/MS molecular weight determination of tryptic peptides in methionyl-human growth hormone (met-hGH). Injected levels from 50 to 75 pmol of tryptic digest onto 1 mm i.d. HPLC columns provided full-scan LC/MS or LC/MS/MS results without postcolumn splitting of the effluent. When standard 4.6 mm i.d. HPLC columns were used, a 20:1 postcolumn split was utilized, which required from 1 to 5 nmol of injected tryptic digest for full-scan LC/MS or LC/MS/MS results. Collision-induced dissociation (CID) mass spectra resulting from either "infusion" or on-line LC/MS/MS analysis of the abundant doubly charged ions that predominate for tryptic peptides under electrospray conditions provided structurally useful sequence information for met-hGH and human hemoglobin tryptic digests. The slower mass spectrometer scan rate used during infusion of sample provides more accurate mass assignments than on-line LC/MS or LC/MS/MS, but the latter on-line experiments preclude ambiguities caused by matrix or component interferences. However, in some instances very weak CID product ions preclude complete tryptic peptide structural characterization based upon the CID data alone.(ABSTRACT TRUNCATED AT 250 WORDS)     

Measuring the mass of an electron by LC/TOF-MS: a study of "twin ions"

While investigating the in-source CID fragmentation of nonsteroidal antiinflammatory drugs (NSAIDs), it was noticed that the same fragment ion (nominal mass) formed in either positive or negative ion electrospray for a suite of NSAIDs. For example, ibuprofen with a molecular mass of 206, fragments to the m/z 161 ion in negative ion from its deprotonated molecule (m/z 205, [M - H]-) and fragments to the m/z 161 ion in positive ion from its protonated molecule (m/z 207, [M + H]+). This fragment ion was euphemistically called a "twin ion"because of the same nominal mass despite opposite charge. The CID fragmentation of the twin ions was confirmed also by LC/MS/MS ion trap. Accurate mass measurements in negative ion show that the loss was due to CO2 (measured loss of 43.9897 atomic mass units (u) versus calculated loss of 43.9898 u for N = 10) and in positive ion the loss is due to HCOOH (measured loss of 46.0048 u versus calculated loss of 46.0055 u, N = 10). It was realized that, in fact, the ions were not "identical mass twins of opposite charge" but separated in accurate mass by two electrons. The accurate mass measurement by liquid chromatography/time-of-flight-mass spectrometry (LC/TOF-MS) can distinguish between the two fragment ions of ibuprofen (161.13362 +/- 0.00019 and 161.13243 +/- 0.00014 for N = 20). This experiment was repeated for two other NSAIDs, and the mass of an electron was measured as the difference between the twin ions, which was 0.00062 u +/- 14.8% relative standard deviation (N = 20 analyses). Thus, the use of continuous calibration makes it possible to measure the mass of an electron within one significant figure using the NSAID solution. This result shows the importance of including electron mass in accurate mass measurements and the value of a benchmark test for LC/TOF-MS mass accuracy.     

Computing fragmentation trees from tandem mass spectrometry data

The structural elucidation of organic compounds in complex biofluids and tissues remains a significant analytical challenge. For mass spectrometry, the manual interpretation of collision-induced dissociation (CID) mass spectra is cumbersome and requires expert knowledge, as the fragmentation mechanisms of ions formed from small molecules are not completely understood. The automated identification of compounds is generally limited to searching in spectral libraries. Here, we present a method for interpreting the CID spectra of the organic compound's protonated ions by computing fragmentation trees that establish not only the molecular formula of the compound and all fragment ions but also the dependencies between fragment ions. This is an important step toward the automated identification of unknowns from the CID spectra of compounds that are not in any database.     

Collisionally induced dissociation in the study of A-ring hydroxylated vitamin D type compounds.

Collisionally induced dissociation (CID) is often used to determine the structure of ions based on comparison with the CID spectra of known ions. The latter are generated from judiciously selected compounds taking into account basic principles of ion chemistry. We report here on the use of this approach toward determination of the site of A-ring hydroxylation of vitamin D. Although not intrinsically an aromatic compound, vitamin D gives rise in its mass spectrum to an aromatic methylstyryl cation at m/z 118. A-ring hydroxylated metabolites of vitamin D would thus incorporate the extra OH group on the ion at m/z 118, shifting it to m/z 134. The position of substitution of the extra OH group on a metabolite could then be ascertained by comparing the CID spectrum of its m/z 134 fragment to those of the four possible (hydroxymethyl)styryl cations generated from synthesized authentic compounds. Because of their propensity to polymerize, these cations were generated in situ via the McLafferty rearrangement of the corresponding (hydroxyphenyl)ethanols. For optimum differentiation of isomeric ions, preparation of permethylated derivatives of vitamin D was necessary. The validity of the hypothesis was verified using 1,25-dihydroxy-vitamin D3 as a test compound. This method provides a viable approach for the characterization of A-ring hydroxylated metabolites of vitamin D as well as for related aromatic compounds.     

MALDI-FTICR imaging mass spectrometry of drugs and metabolites in tissue

A new approach is described for imaging mass spectrometry analysis of drugs and metabolites in tissue using matrix-assisted laser desorption ionization-Fourier transform ion cyclotron resonance (MALDI-FTICR). The technique utilizes the high resolving power to produce images from thousands of ions measured during a single mass spectrometry (MS)-mode experiment. Accurate mass measurement provides molecular specificity for the ion images on the basis of elemental composition. Final structural confirmation of the targeted compound is made from accurate mass fragment ions generated in an external quadrupole-collision cell. The ability to image many small molecules in a single measurement with high specificity is a significant improvement over existing MS/MS based technologies. Example images are shown for olanzapine in kidney and liver and imatinib in glioma.     

Study of the fragmentation mechanism of protonated 6-hydroxychlorzoxazone: application in simultaneous analysis of CYP2E1 activity with major human cytochrome P450s

The application of liquid chromatography tandem mass spectrometry for simultaneous analysis of major human cytochrome P450 activities via a single atmospheric pressure ionization (API) LC/MS/MS method has been hampered by the preferred detection of 6-hydroxychlorzoxazone (HCZ), the metabolite of the CYP2E1 probe, chlorzoxazone, under negative API. An initial simulation of the dissociation constants suggested the potential ionization of the enol form of HCZ at low pH, and the accurate mass measurements confirmed the presence of the protonated HCZ signal under (+) ESI at pH 3. However, the CID spectrum of the protonated HCZ resulted in a few intense, but uncommon, fragment ions that could be utilized for specific selected reaction monitoring (SRM) transitions. The deduced elemental compositions of these fragment ions indicated possible aromatic ring opening for the first two intense product ions at m/z 130 and 115, as well as chlorine radical loss for the third ion at m/z 151. Further precursor and product ion scan studies, along with the deuterium ion exchange in solution, revealed the involvement of three distinct pathways of fragmentation. The m/z 186-->130 transition, which was shown to be specific in human plasma and rat hepatic microsomes, was further combined with the SRM transition of reserpine (internal standard) and eight probe substrates for human cytochrome P450 isoforms. This led to the development of a full LC/MS/MS method capable of analyzing a total of nine human P450 activities within 3 min, including CYP2E1, using a single assay in the (+) ESI mode. The HCZ assay showed excellent linearity with a coefficient of determination (R2) greater than 0.98 at dynamic range of 0.05 (LOQ) to 40 microM. Preliminary data from the three-day validation of the HCZ assay indicated that the accuracy and precision for quality control samples was within +/- 15% of the spiked concentration at all levels.     

Polyphenol identification based on systematic and robust high-resolution accurate mass spectrometry fragmentation

High-mass resolution multi-stage mass spectrometry (MS(n)) fragmentation was tested for differentiation and identification of metabolites, using a series of 121 polyphenolic molecules. The MS(n) fragmentation approach is based on the systematic breakdown of compounds, forming a so-called spectral tree. A chip-based nanoelectrospray ionization source was used combined with an ion-trap, providing reproducible fragmentation, and accurate mass read-out in an Orbitrap Fourier transform (FT) MS enabling rapid assignment of elemental formulas to the molecular ions and all fragment ions derived thereof. The used protocol resulted in reproducible MS(n) fragmentation trees up to MS(5). Obtained results were stable over a 5 month time period, a concentration change of 100-fold, and small changes in normalized collision energy, which is key to metabolite annotation and helpful in structure and substructure elucidation. Differences in the hydroxylation and methoxylation patterns of polyphenolic core structures were found to be reflected by the differential fragmentation of the entire molecule, while variation in a glycosylation site displayed reproducible differences in the relative intensities of fragments originating from the same aglycone fragment ion. Accurate MS(n)-based spectral tree data are therefore a powerful tool to distinguish metabolites with similar elemental formula, thereby assisting compound identification in complex biological samples such as crude plant extracts.     

Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides

Collision-induced dissociation (CID) is a common ion activation technique used to energize mass-selected peptide ions during tandem mass spectrometry. Characteristic fragment ions form from the cleavage of amide bonds within a peptide undergoing CID, allowing the inference of its amino acid sequence. The statistical characterization of these fragment ions is essential for improving peptide identification algorithms and for understanding the complex reactions taking place during CID. An examination of 1465 ion trap spectra from doubly charged tryptic peptides reveals several trends important to understanding this fragmentation process. While less abundant than y ions, b ions are present in sufficient numbers to aid sequencing algorithms. Fragment ions exhibit a characteristic series-specific relationship between their masses and intensities. Each residue influences fragmentation at adjacent amide bonds, with Pro quantifiably enhancing cleavage at its N-terminal amide bond and His increasing the formation of b ions at its C-terminal amide bond. Fragment ions corresponding to a formal loss of ammonia appear preferentially in peptides containing Gln and Asn. These trends are partially responsible for the complexity of peptide tandem mass spectra.     

In vivo analysis and spatial profiling of phytochemicals in herbal tissue by matrix-assisted laser desorption/ionization mass spectrometry

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) was developed for spatial profiling of phytochemicals and secondary metabolites in integrated herbal tissue without solvent extraction. Abundant alkaloid ions, including (+)-menisperine (m/z 356), magnoflorine (m/z 342), stepharanine (m/z 324), protonated sinomenine (m/z 330), protonated sinomendine (m/z 338), and a metabolite at m/z 314, could be directly desorbed from alpha-cyano-4-hydroxycinnamic acid- (CHCA-) coated stem tissue of Sinomenium acutum upon N2 laser (337 nm) ablation, while the ion signals desorbed from sinapinic acid- (SA-) coated and 2,5-dihydroxybenzoic acid- (DHB-) coated stem tissue were at least 10 times weaker. Solvent composition in the matrix solution could have significant effects on the ion intensity of the metabolites. Under optimized conditions that maximize the ion intensity and form homogeneous matrix crystals on the tissue surface, spatial distributions of the metabolites localized in different tissue regions, including cortex, phloem, xylem, rim, and pith, and their relative abundances could be semiquantitatively determined. The three metabolites detected at m/z 356, 342, and 314 showed specific distributions in the herbal samples collected from different growing areas, while others were not. By applying principal component analysis (PCA), the characteristic metabolites in specific tissue regions could be easily determined, allowing unambiguous differentiation of the herbal samples from different geographic locations.     

Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges

A kinetic model, based on the "mobile proton" model of peptide fragmentation, has been reported previously for quantitative prediction of low-energy collision-induced dissociation (CID) spectra of singly or doubly charged peptides. For peptides with three or more charges, however, the simulation process is complex and time-consuming. This paper describes a simplified model for quantitative prediction of CID spectra of peptide ions with three or more charges. Improvements on other aspects of the model were also made to accommodate large peptides. The performance of the simplified model was evaluated by generating predictions for many known highly charged peptides that were not included in the training data set. It was shown that the model is able to predict peptide CID spectra with reasonable accuracy in fragment ion intensities for highly charged peptide ions up to 5000 u in mass.     

Mass spectral metabonomics beyond elemental formula: chemical database querying by matching experimental with computational fragmentation spectra

Despite recent advances in NMR and mass spectrometry, the structural identification of organic compounds in complex biofluids remains a significant analytical challenge. For mass spectroscopy applications, chemical identification is generally limited to determination of elemental formula. Here we test the hypothesis that unknown chemical structures can be determined by matching their experimental collision-induced dissociation (CID) fragmentation spectra with computational fragmentation spectra of compounds retrieved from chemical databases. The monoisotopic molecular weights (MIMW +/- 10 ppm) of 102 "test" compounds were used to download 102 "bins" from the PubChem database. Each bin contained the corresponding test compound and, on average, 272 other candidate compounds, including 158 compounds having the same elemental formula as the test compound. Commercially available software was used to generate fragmentation spectra for all compounds in each of the 102 bins. Experimental CID spectra for each of the 102 test compounds were then compared to the computational spectra in order to rank candidate compounds based on number of fragment MIMW matches. This method returned the test compound as the highest ranking (or tied with the highest ranking) compound for 65 of the 102 bins. The test compound was ranked within the top 20 candidate compounds for 87 bins. In addition, the correct elemental formula was ranked first for 98 of 102 bins. Thus, matching experimental with computational fragmentation spectra is a valid method for rapidly discriminating among compounds having the same elemental formula and provides a novel approach for querying chemical databases for structural information.     

Tandem parallel fragmentation of peptides for mass spectrometry

Parallel fragmentations of peptides in the source region and in the collision cell of tandem mass spectrometers are sequentially combined to develop parallel collision-induced-dissociation mass spectrometry (p2CID MS). Compared to MS/MS spectra, the p2CID mass spectra show increased signal intensities (2-400-fold) and number of sequence ions. This improvement is attributed to the fact that p2CID MS virtually samples all the ions generated by electrospray ionization, including intact and fragment ions of different charge states from a peptide. We implement the method using a quadrupole time-of-flight tandem mass spectrometer. The instrument is operated in TOF-MS mode that allows the ions from source region broadband-passing the first mass analyzer to enter the collision cell. Cone voltage and collision energy are investigated to optimize the outcome of the two parallel CID processes. In the in-source parallel CID, elevated cone voltage produces singly charged intact peptide ions and large fragment ions, as well as decreases the charge-state distribution of peptide ions mainly to double and single charges. The in-collision-cell parallel CID is optimized to dissociate the ions from the source region to produce small and medium fragment ions. The method of p2CID MS is especially useful for sequencing of large peptides with labile amide bonds and peptides with C-terminal arginine. It has unique potential for de novo sequencing of peptides and proteome analysis, especially for affinity-enriched subproteomes.     

Evaluation of coupling reversed phase, aqueous normal phase, and hydrophilic interaction liquid chromatography with Orbitrap mass spectrometry for metabolomic studies of human urine

In this study, we assessed three liquid chromatographic platforms: reversed phase (RP), aqueous normal phase (ANP), and hydrophilic interaction (HILIC) for the analysis of polar metabolite standard mixtures and for their coverage of urinary metabolites. The two zwitterionic HILIC columns showed high-quality chromatographic performance for metabolite standards, improved separation for isomers, and the greatest coverage of polar metabolites in urine. In contrast, on the reversed phase column, most metabolites eluted very rapidly with little or no separation. Using an Exactive Orbitrap mass spectrometer with a HILIC liquid chromatographic platform, approximately 970 metabolite signals with repeatable peak areas (relative standard deviation (RSD) ≤ 25%) could be putatively identified in human urine, by elemental composition assignment within a 3 ppm mass error. The ability of the methodology for the verification of nonmolecular ions, which arise from adduct formation, and the possibility of distinguishing isomers could also be demonstrated. Careful examination of the raw data and the use of masses for predicted metabolites produced an extension of the metabolite list for human urine.     

Applying in-silico retention index and mass spectra matching for identification of unknown metabolites in accurate mass GC-TOF mass spectrometry

One of the major obstacles in metabolomics is the identification of unknown metabolites. We tested constraints for reidentifying the correct structures of 29 known metabolite peaks from GCT premier accurate mass chemical ionization GC-TOF mass spectrometry data without any use of mass spectral libraries. Correct elemental formulas were retrieved within the top-3 hits for most molecular ion adducts using the "Seven Golden Rules" algorithm. An average of 514 potential structures per formula was downloaded from the PubChem chemical database and in-silico-derivatized using the ChemAxon software package. After chemical curation, Kovats retention indices (RI) were predicted for up to 747 potential structures per formula using the NIST MS group contribution algorithm and corrected for contribution of trimethylsilyl groups using the Fiehnlib RI library. When matching the range of predicted RI values against the experimentally determined peak retention, all but three incorrect formulas were excluded. For all remaining isomeric structures, accurate mass electron ionization spectra were predicted using the MassFrontier software and scored against experimental spectra. Using a mass error window of 10 ppm for fragment ions, 89% of all isomeric structures were removed and the correct structure was reported in 73% within the top-5 hits of the cases.     

Enabling MALDI-FTICR-MS/MS for high-performance proteomics through combination of infrared and collisional activation

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is a central tool for proteomic analysis, yet the singly protonated tryptic peptide ions produced by MALDI are significantly more difficult to dissociate for tandem mass spectrometry (MS/MS) than the corresponding multiply protonated ions. In order to overcome this limitation, current proteomic approaches using MALDI-MS/MS involve high-energy collision-induced dissociation (CID). Unfortunately, the use of high-energy CID complicates product ion spectra with a significant proportion of irrelevant fragments while also reducing mass accuracy and mass resolution. In order to address the lack of a high-resolution, high mass accuracy MALDI-MS/MS platform for proteomics, Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and a recently developed MS/MS technique termed CIRCA (for combination of infrared and collisional activation) have been applied to proteomic analysis. Here, CIRCA is shown to be suitable for dissociating singly protonated tryptic peptides, providing greater sequence coverage than either CID or infrared multiphoton dissociation (IRMPD) alone. Furthermore, the CIRCA fragmentation spectra are of sufficient quality to allow protein identification based on the MS/MS spectra alone or in concert with the peptide mass fingerprint (PMF). This is accomplished without compromising mass accuracy or mass resolution. As a result, CIRCA serves to enable MALDI-FTICR-MS/MS for high-performance proteomics experiments.     

Prediction of low-energy collision-induced dissociation spectra of peptides

A kinetic model, based on the "mobile proton" model of peptide fragmentation, was developed to quantitatively simulate the low-energy collision-induced dissociation (CID) spectra of peptides dissociated in a quadrupole ion trap mass spectrometer. The model includes most fragmentation pathways described in the literature, plus some additional pathways based on the author's observations. The model was trained by optimizing parameters within the model for predictions of CID spectra of known peptides. A best set of parameters was optimized to obtain best match between the simulated spectra and the experimental spectra in a training data set. The performance of the mathematical model and the associated optimized parameter set used in the CID spectra simulation was evaluated by generating predictions for a large number of known peptides, which were not included in the training data set. It was shown that the model is able to predict peptide CID spectra with reasonable accuracy in fragment ion intensities for both singly and doubly charged peptide parent ions up to 2000 u in mass. The optimized parameter set was evaluated to gain insight into the collision-induced peptide fragmentation process.     

Electrospray ionization tandem mass spectrometry for structural elucidation of protonated brevetoxins in red tide algae

Brevetoxins, the toxic components of "red tide" algae, all share one of two robust polycyclic ether backbone structures, but they are distinguished by differing side-chain substituents. Electrospray ionization mass spectrometry analyses of brevetoxins have shown that the polyether structure invariably has a very high affinity for sodium cations that results in the production of abundant (M + Na)+ ions even when sodium cations are only present as impurities. Because the ionic charge tends to remain localized on the sodium atom and because at least two bonds must be broken in order to produce polycyclic backbone fragmentation, it is extremely difficult to obtain abundant product ions (other than Na+) from (M + Na)+ brevetoxin precursor ions in low-energy collision-induced dissociation (CID) MS/MS experiments. This report establishes that acid additives (oxalic acid, trifluoroacetic acid, and particularly hydrochloric acid) in aqueous methanol solutions can promote high yields of protonated brevetoxin molecules (MH+ ions) for Btx-1, -2, and -9 brevetoxins. Most importantly, unlike their (M + Na)+ counterparts, MH+ precursor ions offer readily detectable product ions in CID MS/MS experiments, even under low-energy collisions. This direct structural characterization approach has provided decomposition information from brevetoxins that was previously inaccessible, including the identification of diagnostic product ions for "type A" brevetoxins (m/z 611) and "type B" brevetoxins (m/z 779, 473, 179) and characteristic ions for Btx-1 (m/z 221, 139), Btx-2 (m/z 153), and Btx-9 (m/z 157, 85). Precursor ion scans and constant neutral loss scans are proposed to enable screening of individual type A or type B brevetoxins present in naturally occurring mixtures.     

Implementation of ion/ion reactions in a quadrupole/time-of-flight tandem mass spectrometer

A commercial quadrupole/time-of-flight (QqTOF) tandem mass spectrometer has been adapted for ion/ion reaction studies. To enable mutual storage of oppositely charged ions in a linear ion trap, the oscillating quadrupole field of the second quadrupole of the system (Q2) serves to store ions in the radial dimension while auxiliary radio frequency is superposed on the end lenses of Q2 during the reaction period to create barriers in the axial dimension. A pulsed dual electrospray (ESI) source is directly coupled to the instrument interface for the purpose of proton transfer reactions. Singly and doubly charged protein ions as high in mass as 66 kDa are readily formed and observed after proton-transfer reactions. For the modified instrument, the mass resolving power is approximately 8000 for a wide m/z range, and the mass accuracy is approximately 20 ppm for external calibration and approximately 5 ppm for internal calibration after ion/ion reactions. Parallel ion parking is demonstrated with a six-component protein mixture, which shows the potential application of reducing spectral complexity and concentrating certain charge states. The current system has high flexibility with respect to defining MS(n) experiments involving collision-induced dissociation (CID) and ion/ion reactions. Protein precursor and CID product masses can be determined with good accuracy, providing an attractive platform for top-down proteomics. Electron transfer dissociation ion/ion reactions are implemented by using a pulsed nano-ESI/atmospheric pressure chemical ionization dual source for ionization. The reaction between protonated peptide ions and radical anions of 1,3-dinitrobenzene formed exclusively c- and z-type fragment ions.     

Effects of fragile ions on mass resolution and on isolation for tandem mass spectrometry in the quadrupole ion trap mass spectrometer.

In the quadrupole ion trap, it has been noted that factors other than an ion's mass and charge may affect its measured m/z, resulting in compound-dependent, or "chemical", mass shifts. We propose that ions can exhibit a chemical mass shift because they are "fragile" and may fragment during the application of resonance ejection during mass analysis; these effects were studied using ions that include protonated, deprotonated, and adduct ions of explosives, acylcarnitines, and macrolide antibiotics. Fragile ions affect mass resolution by causing broader peaks than nonfragile ions, especially at slower scan speeds, as the result of the application of resonance ejection. Fragile ions may also be fragmented by the application of the isolation waveform during selection of the parent ion for tandem mass spectrometry experiments, making it impossible to achieve unit isolation of a fragile ion. To obtain adequate isolation intensity, the isolation waveform notch width must be increased and the time period of isolation must be decreased. Fragile ions also require lower optimum collision energy to achieve efficient collision-induced dissociation. We have developed criteria for the determination of the degree of ion fragility based upon experimental results.