Automated deconvolution and deisotoping of electrospray mass spectra

Electrospray ionization (ESI) of peptides and proteins produces a series of multiply charged ions with a mass/charge (m/z) ratio between 500 and 2000. The resulting mass spectra are crowded by these multiple charge values for each molecular mass and an isotopic cluster for each nominal m/z value. Here, we report a new algorithm simultaneously to deconvolute and deisotope ESI mass spectra from complex peptide samples based on their mass-dependent isotopic mean pattern. All signals corresponding to one peptide in the sample were reduced to one singly charged monoisotopic peak, thereby significantly reducing the number of signals, increasing the signal intensity and improving the signal-to-noise ratio. The mass list produced could be used directly for database searching. The developed algorithm also simplified interpretation of fragment ion spectra of multiply charged parent ions.     

Ultrasonication-assisted spray ionization mass spectrometry for the analysis of biomolecules in solution

In this paper, we describe a novel technique—ultrasonication-assisted spray ionization (UASI)—for the generation of singly charged and multiply charged gas-phase ions of biomolecules (e.g., amino acids, peptides, and proteins) from solution; this method employs a low-frequency ultrasonicator (ca. 40 kHz) in place of the high electric field required for electrospray ionization. When a capillary inlet is immersed into a sample solution within a vial subjected to ultrasonication, the solution is continually directed to the capillary outlet as a result of ultrasonication-assisted capillary action; an ultrasonic spray of the sample solution is emitted at the outlet of the tapered capillary, leading to the ready generation of gas-phase ions. Using an ion trap mass spectrometer, we found that singly charged amino acid and multiply charged peptides/proteins ions were generated through this single-step operation, which is both straightforward and extremely simple to perform. The setup is uncomplicated: only a low-frequency ultrasonicator and a tapered capillary are required to perform UASI. The mass spectra of the multiply charged peptides and proteins obtained from sample solutions subjected to UASI resemble those observed in ESI mass spectra.     

The nature of collision-induced dissociation processes of doubly protonated peptides: comparative study for the future use of matrix-assisted laser desorption/ionization on a hybrid quadrupole time-of-flight mass spectrometer in proteomics.

Comparative MS/MS studies of singly and doubly charged electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) precursor peptide ions are described. The spectra from these experiments have been evaluated with particular emphasis on the data quality for subsequent data processing and protein/amino acid sequence identification. It is shown that, once peptide ions are formed by ESI or MALDI, their charge state, as well as the collision energy, is the main parameter determining the quality of collision-induced dissociation (CID) MS/MS fragmentation spectra of a given peptide. CID-MS/MS spectra of singly charged peptides obtained on a hybrid quadrupole orthogonal time-of-flight mass spectrometer resemble very closely spectra obtained by matrix-assisted laser desorption/ionization post-source decay time-of-flight mass spectrometry (MALDI-PSD-TOFMS). On the other hand, comparison of CID-MS/MS spectra of either singly or doubly charged ion species shows no dependence on whether ions have been formed by ESI or MALDI. This observation confirms that, at the time of precursor ion selection, further mass analysis is effectively decoupled from the desorption/ionization event. Since MALDI ions are predominantly formed as singly charged species and ESI ions as doubly charged, the associated difference in the spectral quality of MS/MS spectra as described here imposes direct consequences on data processing, database searching using ion fragmentation data, and de novo sequencing when ionization techniques are changed.     

Size exclusion chromatography/mass spectrometry applied to the analysis of polysaccharides.

A novel method for analysing polysaccharide materials is described which employs size-exclusion chromatography (SEC) followed by detection by on-line electrospray ionisation mass spectrometry (ESI-MS) and off-line matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS). It is demonstrated through SEC/ESI ion trap mass spectrometry that the formation of multiply charged oligomer ions, which bind up to five sodium cations, allows the rapid analysis of polysaccharide ions with molecular weights in excess of 9 kDa. MALDI spectra generated from fractionation of the effluent collected from the same SEC separation are shown to be in good agreement with the ESI spectra with respect to molecular weight distributions and types of ions generated. ESI and MALDI mass spectra of samples obtained from sequential graded ethanol precipitation and SEC fractionation of acid and enzymatically digested arabinoxylan polysaccharides show important structural differences between polysaccharide fragments. In addition, a comparison is made between the mass spectra of native and permethylated SEC-separated fragments of acid and enzymatically treated arabinogalactan. Linkage information of the permethylated arabinogalactan oligomers can be rapidly established through the use of on-line SEC/ESI-MS( n) experiments.     

Rapidly switchable matrix-assisted laser desorption/ionization and electrospray quadrupole-time-of-flight mass spectrometry for protein identification

We describe a new interface for a prototype quadrupole-quadrupole-time-of-flight (TOF) mass spectrometer (Centaur, Sciex) that allows rapid switching between electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) modes of operation. Instrument performance in both modes is comparable (i.e., resolution approximately 10,000 FWHM, mass accuracy <10 ppm, sensitivity approximately 1 fmol) because the ion source is decoupled from the TOF mass analyzer by extensive gas collisions in the quadrupole stages of the instrument. The capacity to obtain side-by-side high quality ESI and MALDI mass spectra from a single proteolytic mixture greatly facilitates the identification of proteins and elucidation of their primary structures. Improved strategies for protein identification result from this ability to measure spectra using both ionization modes in the same instrument and to perform MS/MS on singly charged as well as multiply charged ions. Examples are provided to demonstrate the utility and performance of the modified instrument.     

Self-esterification of fulvic acid model compounds in methanolic solvents as observed by electrospray ionization mass spectrometry

The self-esterification of two fulvic acid model compounds in methanolic solvents was studied by electrospray ionization mass spectrometry (ESI-MS). The strongly acidic tetrahydrofurantetracarboxylic acid rapidly self-esterified to form mono- and dimethyl esters when stored in methanol, even at reduced temperatures. The weakly acidic analogue, cyclopentanetetracarboxylic acid, reacted minimally under the same conditions. The use of 50:50 methanol/water as a solvent reduced self-esterification of the strong acid. However, the presence of water promoted the formation of multiply charged ions in the ESI mass spectra. The use of water and 50:50 acetonitrile/water as solvents eliminated self-esterification but the mass spectra still contained multiply charged ions. This study implies that the use of methanolic solvents with humic substances may compromise analytical data through the formation of methyl esters.     

Positive ion electrospray ionization mass spectrometry of oligonucleotides

Positive ion electrospray ionization mass spectra have been obtained of deoxyribonucleic acids (DNA) and ribonucleic acids (RNA), including transfer RNAs (77-mer, ～ 25 kDa). For several different solution conditions, the charge state distributions of DNA and RNA molecules were determined. It is postulated that the production of the multiply charged positive ions results from gas phase dissociation of complexes between nitrogen-containing bases and oligonucleotides.     

Analysis of carrageenans by matrix-assisted laser desorption/ionization and electrospray ionization mass spectrometry. I. kappa-Carrageenans.

Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) mass spectra of small kappa-carrageenans are reported and discussed. MALDI spectra can be obtained in both positive and negative ion mode. In the absence of extraneous metal ions, positive ions are formed by the attachment of one Na(+) ion to the carrageenan, whereas for negative ions one Na(+) ion is detached from the sulfate group. Multiply charged species are not observed in MALDI. Intense ESI spectra can be obtained in negative ion mode and now multiply charged species are seen. Alkali exchange experiments show that in these small carrageenan anions one, but only one, alkali metal ion is bound in a bidentate coordination with two ionic sulfate groups. G2-type ab initio calculations on model ions HO(-) [M(+)] (-)OH (M = Li, Na, K, Cs), as well as arguments based on a simple Coulombic interaction model, show that the bidentate stabilization energy drops rapidly as the size of the alkali cation increases. Exchange of Na(+) with Li(+) leads to expulsion of the Na(+) ion generating, in ESI, intense multiply charged anions. An attempt is made to rationalize this behavior in terms of hydration effects.     

Capillary electrophoresis-electrospray mass spectra of the herbicides paraquat and diquat

The positive ion electrospray mass spectra of the quaternary ammonium salt herbicides paraquat and diquat are examined by on-line separation with capillary electrophoresis (CE) and by direct infusion of the analytes. The analytes are separated by CE in 7–10 min at pH 3.9 in 50% methanol-water by using several different separation buffer electrolytes. The capillary electrophoresis-electrospray ionization (CE-ES) mass spectra of paraquat and diquat consist primarily of doubly charged molecular ions, singly charged molecular ions, and singly charged deprotonated ions. The direct infusion spectra consist primarily of doubly charged molecular ions and singly charged deprotonated ions. The relative abundances of the doubly charged and deprotonated ions depend strongly on the presence or absence of ammonium ion in the CE separation buffer or the direct infusion solution. A deprotonation mechanism is proposed in which the free base ammonia is the deprotonating agent in the desolvating charged droplets or in the gas phase. The analytical potential of the CE-ES electrospray approach for environmental analyses is evaluated in terms of the precision of replicate injections, linear concentration range, and estimated detection limit.     

Charge state separation for protein applications using a quadrupole time-of-flight mass spectrometer

A novel method for separating ions according to their charge state using a quadrupole time-of-flight mass spectrometer is presented. The benefits of charge state separation are particularly apparent in protein identification applications at low femtomole concentration levels, where in conventional TOF MS spectra peptide ions are often lost in a sea of chemical noise. When doubly and triply charged tryptic peptide ions need to be filtered from singly charged background ions, the latter are suppressed by two to three orders of magnitude, while from 10-50% of multiply charged ions remain. The suppression of chemical noise reduces the need for chromatography and can make this experimental approach the electrospray equivalent of conventional MALDI peptide maps. If unambiguous identification cannot be achieved, MS/MS experiments are performed on the precursor ions identified through charge separation, while the previously described Q2-trapping duty cycle enhancement is tuned for approximately 1.4 of the precursor m/z to enhance intensities of ions with m/z values above that of the precursor. The resulting product ion spectra contain few fragments of impurities and provide quick and unambiguous identification through database search. The multiple charge separation technique requires minimal tuning and may become a useful tool for analysis of complex mixtures.     

Effect of electrospray ionization conditions on low-energy tandem mass spectra of peptides

The effect of electrospray ionization (ESI) conditions on low-energy tandem mass spectra of peptides in the relative molecular mass range 400–1200 was examined. For singly charged peptide ions the source skimmer potential (which determines the degree of acceleration of the ions through the intermediate pressure region in the source) can strongly influence the extent of fragmentation observed in tandem mass spectra, especially at low collision energies. For each peptide there is an optimum skimmer potential which represents a balance between generating ions with sufficient internal energy for subsequent tandem mass spectrometric experiments and inducing the onset of other processes such as source fragmentation. The fragmentation which can be achieved in tandem mass spectra with high skimmer potentials differs from ESI source fragmentation for the same peptides. We have found that fragmentation in ESI mass spectra depends both on skimmer potential and on solvent pH, presumably because the latter determines the proportion of doubly charged species generated from a given peptide. Low-energy tandem mass spectra of peptides following ESI are equally as sensitive to peptide structure and the type of adduct studied (e.g. [M + H]⁺ vs. [M + NH₄]⁺) as tandem mass spectra obtained following older ionization methods such as fast atom bombardment.     

Liquid chromatographic/electrospray ionization mass spectrometric studies of proanthocyanidins in foods

The proanthocyanidins in three foods (pinto beans, plums and cinnamon) were studied with electrospray ionization (ESI) mass spectrometry (MS) in the negative mode following separation by normal-phase high-performance liquid chromatography. The MS/MS analysis demonstrated that the major ions derived from heterocyclic ring fission and retro-Diels-Alder reaction of flavan-3-ol provided information about the hydroxylation pattern and type of interflavan bond. The connection sequence of the oligomers was identified through diagnostic ions derived from quinone methide (QM) cleavage of the interflavan bond. Novel heterogeneous B-type proanthocyanidins containing (epi)afzelechin as subunits were identified in pinto beans. Proanthocyanidins with interestingly different A-type linkages were identified in plums and cinnamon. In efforts aimed at extending the identification capacity of ESI-MS to polymers, we found that the polymeric procyanidins fragmented readily instead of forming multiply charged ions in the negative ESI mode. Fragmentation patterns were proposed based on our data obtained by ESI-MS/MS and ESI time-of-flight MS.     

New example of proline-induced fragmentation in electrospray ionization mass spectrometry of peptides

The positive ion electrospray ionization (ESI+) mass spectra of peptides usually display only protonated molecules provided that soft ionization conditions are applied (low cone voltage to prevent in-source dissociations). Such ions can be multiply charged depending on the molecular weight of the studied compounds. We have experienced an unexpected behavior during the ESI analysis of a modified peptide of relatively high mass (3079 Da). A specific fragmentation occurred even under soft energetic conditions, leading to a mass spectrum containing multiply charged molecular and fragment ions. The selective rupture involved the amide bond between the glutamic acid and proline residues (E-P sequence). The successive replacement of each amino acid by an alanine residue (positional scanning study) was undertaken to assess which part of the sequence induced such selective and abundant fragmentation on multiply charged species. The succession P-P was evidenced as the minimum unit giving rise to the first peptide bond rupture in the sequence X-P-P. Any acidic amino acid at the X position (X = D, E) favored the fragmentation by an intramolecular interaction. Such proline-induced fragmentation occurring readily in the source differed from the literature data on the specific behavior of proline-containing peptides where bond ruptures occur solely in dissociation conditions.     

Mass spectra of doubly charged ions

The mass spectra of biological molecules, whose molecular mass exceeds 10 kDa, invariably contain multiply charged ions. For example, a survey scan of a small protein will produce singly, doubly and triply protonated molecules, the intensity of the doubly charged species often being greater than that of the singly charged entity. Although the spectra resulting from doubly charged peptides have not previously been studied, collisional activation of such doubly charged species may result in significant additional information pertaining to molecular structure. The techniques employed to study ions originating from multiply charged species were linked scanning of constant B/E and tandem mass spectrometry, namely low collision energy spectra acquired on a BEQQ hybrid instrument. The methodology was applied to model compounds whose tandem mass spectrometry characteristics are well known, e.g. gramicidin S and angiotensin I. The results for the product ions of the [M + 2H]²⁺ species of the models were obtained which highlight the methodology required for high-mass materials.     

A new liquid chromatography/electrospray ionization mass spectrometry method for the analysis of underivatized aliphatic long-chain polyamines: application to diatom-rich sediments

Natural polyamines are found in all three domains of life and long-chain polyamines (LCPAs) play a special role in silicifying organisms such as diatoms and sponges where they are actively involved in the complex formation and nanopatterning of siliceous structures. With chain lengths extending up to 20 N-methylated propylamine repeat units, diatom LCPAs constitute the longest natural polyamines. Mixtures of natural LCPAs are typically purified in bulk using ion-exchange, size-exclusion and dialysis and then analyzed either by direct infusion mass spectrometry or by MALDI-TOF. Here, we describe a novel ion-pairing liquid chromatographic method that allows baseline separation, detection and structural elucidation of underivatized aliphatic methylated and non-methylated LCPAs with a wide range of chain lengths. Complete separation of synthetic mixtures of LCPA species differing by either a propylamine or an N-methylpropylamine unit is achievable using this method and chromatographic separation of natural, diatom frustule bound LCPAs extracted from sediment core samples is greatly improved. Using electrospray ionization mass spectrometry (ESI-MS), we detected singly [M+H](+) and multiply [M+nH](n+) charged protonated ions. The abundance of multiply charged LCPA species increased linearly as a function of LCPA chain length (N) and multiprotonated ions [M+nH](n+) were more abundant for longer chain polyamines. The abundance of multiply charged LCPAs along with the concomitant disappearance of the singly charged protonated molecular ion significantly increases the complexity of the MS spectra, justifying the need for good chromatographic separation of complex LCPA mixtures. This analytical procedure will likely constitute a powerful tool for the characterization, quantification, as well as the purification of individual LCPAs in natural and synthetic samples for studies of silica precipitation as well as nitrogen and carbon isotopic analysis used in paleoceanographic studies.     

Kinetic energy release distributions in mass spectrometry

Kinetic energy releases (KERs) in unimolecular fragmentations of singly and multiply charged ions provide information concerning ion structures, reaction energetics and dynamics. This topic is reviewed covering both early and more recent developments. The subtopics discussed are as follows: (1) introduction and historical background; (2) ion dissociation and kinetic energy release: kinematics; potential energy surfaces; (3) the kinetic energy release distribution (KERD); (4) metastable peak observations: measurements on magnetic sector and time-of-flight instruments; energy selected results by photoelectron photoion coincidence (PEPICO); (5) extracting KERDs from metastable peak shapes; (6) ion structure determination and reaction mechanisms: singly and multiply charged ions; biomolecules and fullerenes; (7) theoretical approaches: phase space theory (PST), orbiting transition state (OTS)/PST, finite heat bath theory (FHBT) and the maximum entropy method; (8) exit channel interactions; (9) general trends: time and energy dependences; (10) thermochemistry: organometallic reactions, proton-bound clusters, fullerenes; and (11) the efficiency of phase space sampling.     

Fundamentals of the application of matrix-assisted laser desorption-ionization mass spectrometry to low mass poly(methylmethacrylate) polymers

Matrix-assisted laser desorption-ionization (MALDI) time of flight is shown to give a molar peak area response for isolated methylmethacrylate oligomers that have 25 and 50 repeat units when run on three different instruments in reflectron or linear mode and using three different matrix materials. In addition, fragmentation was not observed in any of the three different matrices or at higher laser power. No spectral differences were observed for syndiotactic and isotactic methylmethacrylate oligomers. These results suggest that the low most probable peak values observed for narrow distribution poly(methylmethacrylate) standards by MALDI mass spectrometry are not the result of mass discrimination or fragmentation.     

Detection of fragment ions produced by collisional activation of multiply charged ions in a floated collision cell

A scan law is derived for the detection of fragment ions formed by collisional activation (CA) of a multiply charged precursor in a floated collision cell of a tandem mass spectrometer. Comparisons of the CA spectra of multiply charged ions obtained in either a floated or a grounded collision cell demonstrate the benefits associated with raising the collision cell above ground potential. In addition to the advantages observed for singly charged ions, floating the collision cell increases the transmission of multiply charged ions through the first mass spectrometer by permitting higher source potentials to be used. This technique also increases the detection efficiency for products of charge separation reactions, which may prove useful in the charge state assignment of the fragment ions.     

Effect of varying counterions on the sensitivity of electrohydrodynamic and fast atom bombardment mass spectrometry

The abundance of ion pairs (CA⁺) relative to that of doubly charged ions (C²⁺) in electrohydrodynamic (EH) mass spectra of a series of anions with a common dication in glycerol was found to increase in the order acetate < nitrite < chloride < bromide ≈ nitrate < iodide < perchlorate. Correlation with enthalpies of hydration for the anions suggests that this trend reflects the solution chemistry of ion association. These spectra also reveal that solvation rather than interactions with the extracting field is more important in determining the overall EH mass spectrometric sensitivity to doubly charged ions. Therefore, the use of anions that promote more extensive ion pairing enhances the overall sensitivity to multiply charged ions that otherwise interact strongly with the solvent, but reduces sensitivity to singly charged ions. These observations hold in fast atom bombardment mass spectrometry, surviving the invasive effects of the primary beam.