Discrimination of isomers and isobars by varying the reduced-field across drift tube in proton-transfer-reaction mass spectrometry (PTR-MS)

Proton-transfer-reaction mass spectrometry (PTR-MS) is a powerful technique for the real time trace gas analysis of volatile organic compounds (VOCs). However, quadrupole mass spectrometer (MS) used in PTR-MS has a relatively low mass resolution and is therefore not suitable for differentiating isobars. Furthermore, because of the lack of chemical separation before analysis, isomers can not be identified, either. In the present study, by varying the reduced-field E/N in the reaction chamber with a range of 50–180 Td in PTR-MS, we studied the product ion distribution (PID) of three sets of isobars/isomers, i.e. n-propanol/iso-propanol/acetic acid, propanal/acetone and four structural isomers of butyl alcohol. The profiles of the reduced-field dependence (PFD) of the PID under the chosen E/N-values show obvious differences which can be used to discriminate between these isobars/isomers thus enabling the titled method. Noticeably, we have observed that even the isomers, in the case of four structural isomers of butyl alcohol, which show little difference with each other at high reduced-field, can be discriminated easily at low reduced-field. Finally, two examples for the application of this method are discussed: (1) cyclohexanone was identified to be a major compound in the headspace of medical infusion sets; and (2) the differentiation and quantification of propanal and acetone in three synthetic mixtures with different ratios. This study presents a potential method to distinguish and quantify isobars/isomers conveniently in practical applications of PTR-MS analysis without additional instrumental configurations.     

ESI-MS differential fragmentation of positional isomers of sulfated oligosaccharides derived from carrageenans and agarans

We have prepared a number of isomeric red seaweed galactan-derivative sulfated oligosaccharides to determine whether there were diagnostic differences among the isomeric mass spectra obtained using ESI CID MS/MS (triple quadrupole instrument). Fragmentation of the single or multicharged molecular ions from di-, tetra-, and hexasaccharides indicated that the relative positioning of the sulfate groups and type of monosaccharide unit affect the rate of cleavage of the glycosidic bonds. We also performed a comparative [M-Na]⁻ fragmentation study of positional isomers of sulfated disaccharides that present all four monosulfation possibilities on the galactopyranosidic ring. In this case, negative-ion ESI CID MS/MS approach gave diagnostic product ions from cross-ring cleavages along with the same main B₁ ion (from sulfated Gal_p), at m/z 241, for all isomers. The isomeric disaccharides were also submitted to increased spray energy conditions inducing in-source fragmentation; preformed B₁ ions were then fragmented to give similar product ions as those found in [M-Na]⁻ analysis. Evaluation of the relative abundances mainly for cross-ring fragment ions at m/z 138, 139, 151, 153 allowed clear distinction among the members of the disaccharide series. The different ratios for m/z 151/153 ions were consistent with the predominance of m/z 153 being related to the cases when the bond involved in the cleavage process links a sulfated carbon. A quadrupole ion trap instrument (MSⁿ analysis) was also utilized to compare the results obtained with the triple quadrupole instrument.     

Detection of Ketones by a Novel Technology: Dipolar Proton Transfer Reaction Mass Spectrometry (DP-PTR-MS)

Proton transfer reaction mass spectrometry (PTR-MS) has played an important role in the field of real-time monitoring of trace volatile organic compounds (VOCs) due to its advantages such as low limit of detection (LOD) and fast time response. Recently, a new technology of proton extraction reaction mass spectrometry (PER-MS) with negative ions OH^– as the reagent ions has also been presented, which can be applied to the detection of VOCs and even inorganic compounds. In this work, we combined the functions of PTR-MS and PER-MS in one instrument, thereby developing a novel technology called dipolar proton transfer reaction mass spectrometry (DP-PTR-MS). The selection of PTR-MS mode and PER-MS mode was achieved in DP-PTR-MS using only water vapor in the ion source and switching the polarity. In this experiment, ketones (denoted by M) were selected as analytes. The ketone (molecular weight denoted by m) was ionized as protonated ketone [M + H]⁺ [mass-to-charge ratio (m/z) m + 1] in PTR-MS mode and deprotonated ketone [M – H]^– (m/z m – 1) in PER-MS mode. By comparing the m/z value of the product ions in the two modes, the molecular weight of the ketone can be positively identified as m. Results showed that whether it is a single ketone sample or a mixed sample of eight kinds of ketones, the molecular weights can be detected with DP-PTR-MS. The newly developed DP-PTR-MS not only maintains the original advantages of PTR-MS and PER-MS in sensitive and rapid detection of ketones, but also can estimate molecular weight of ketones.

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Graphical Abstract ?

     

Differentiation of the Stereochemistry and Anomeric Configuration for 1-3 Linked Disaccharides Via Tandem Mass Spectrometry and <Superscript>18</Superscript>O-labeling

Collision-induced dissociation (CID) of deprotonated hexose-containing disaccharides (m/z 341) with 1–2, 1–4, and 1–6 linkages yields product ions at m/z 221, which have been identified as glycosyl-glycolaldehyde anions. From disaccharides with these linkages, CID of m/z 221 ions produces distinct fragmentation patterns that enable the stereochemistries and anomeric configurations of the non-reducing sugar units to be determined. However, only trace quantities of m/z 221 ions can be generated for 1–3 linkages in Paul or linear ion traps, preventing further CID analysis. Here we demonstrate that high intensities of m/z 221 ions can be built up in the linear ion trap (Q3) from beam-type CID of a series of 1–3 linked disaccharides conducted on a triple quadrupole/linear ion trap mass spectrometer. ¹⁸O-labeling at the carbonyl position of the reducing sugar allowed mass-discrimination of the “sidedness” of dissociation events to either side of the glycosidic linkage. Under relatively low energy beam-type CID and ion trap CID, an m/z 223 product ion containing ¹⁸O predominated. It was a structural isomer that fragmented quite differently than the glycosyl-glycolaldehydes and did not provide structural information about the non-reducing sugar. Under higher collision energy beam-type CID conditions, the formation of m/z 221 ions, which have the glycosyl-glycolaldehyde structures, were favored. Characteristic fragmentation patterns were observed for each m/z 221 ion from higher energy beam-type CID of 1–3 linked disaccharides and the stereochemistry of the non-reducing sugar, together with the anomeric configuration, were successfully identified both with and without ¹⁸O-labeling of the reducing sugar carbonyl group.     

Application of a Self-developed Proton Transfer Reaction-Mass Spectrometer to On-line Monitoring Trace Volatile Organic Compounds in Ambient Air

Real-time and on-line monitoring volatile organic compounds(VOCs) are valuable for real-time evalua- ting air quality and monitoring the key source of pollution. A self-developed proton transfer reaction-mass spectrometer(PTR-MS) was constructed and applied to on-line monitoring trace VOCs in ambient air in Hefei, China. With the help of a self-developed catalytic converter, the background signal of the instrument was detected and the stability of the instrument was evaluated. The relative standard deviation of signal at m/z 21 was only 0.74% and the detection limit of PTR-MS was 97 part per trillion(97×10^-12, volume ratio). As a case of the air monitoring in Hefei, the ambient air at Dongpu reservoir spot was on-line monitored for 13 d with our self-developed PTR-MS. Meanwhile, a solid-phase micro-extraction(SPME) technique coupled to gas chromatography-mass spectrometry/mass spectrometry (GC-MS/MS) was also used for the off-line detection of the air. The results show that our self-developed PTR-MS can be used for the on-line and long-term monitoring of VOCs in air at part per trillion level, and the change trend of VOCs concentration monitored with PTR-MS was consistent with that detected with the conventional SPME-GC-MS. This self-developed PTR-MS can fully satisfy the requirements of air quality monitoring and real-time monitoring of the key pollution sources.     

多反应离子的质子转移反应质谱

在无放射性辉光放电离子源内, 采用不同试剂气体进行放电, 为质子转移反应质谱(PTR-MS)新增了强度在10⁵ cps量级的3种反应离子NH₄⁺, NO⁺和O₂⁺, 纯度大于95%; 测试了这3种反应离子的离子-分子反应特征. 采用H₃O⁺, NH₄⁺, NO⁺和O₂⁺等4种反应离子对同分异构体丙醛/丙酮进行检测发现, H₃O⁺和NH₄⁺均不能区分的丙醛/丙酮可采用NO⁺或O₂⁺进行区分. 结果表明, 增加反应离子不仅使PTR-MS的可检测有机物范围不再局限于质子亲和势(PA)大于H₂O的有机物, 还提高了PTR-MS区分同分异构体的能力.     

Site of alkylation of N-methyl- and N-ethylaniline in the gas phase: a tandem mass spectrometric study

N-Methylaniline (NMA) was ethylated and N-ethylaniline (NEA) was methylated under chemical ionization conditions using C₂H₅I and CH₃I, respectively, as reagent gases. The structures of the resulting m/z 136 adduct ions have been probed using metastable ion and collision-induced dissociation (CID) methods. From the similarity of the spectra obtained and from the presence of structure-diagnostic ions at m/z 59 (CH₃NHC₂H₅^+•) and m/z 44 (CH₃NHCH₂⁺), it is concluded that predominantly N-alkylation occurs in both systems. This interpretation was aided by the use of C₂D₅I and CD₃I as reagents. Adduct ions of m/z 136 were also formed by ethylation of the isomeric toluidines and by methylation of the ring-ethylanilines. The resulting CID mass spectra were distinctly different from those obtained for the m/z 136 ions obtained by alkylation of NMA and NEA. Protonation of N-ethyl-N-methylaniline using CH₃C(O)CH₃ as Brønsted acid reagent produced an m/z 136 species whose CID mass spectrum also featured intense ion signals at m/z 59 and 44. This observation led to the conclusion that protonation with acetone as reagent results, in this case, in dominant N-protonation. However, the CID mass spectrum of the m/z 136 ion formed when CH₃OH was the protonating agent featured a weak signal at m/z 44 and no signal at m/z 59. Hence it was concluded that the latter m/z 136 ion contains a larger contribution from the ring-protonated adduct. Copyright © 2004 John Wiley & Sons, Ltd.     

Does deprotonated benzoic acid lose carbon monoxide in collision-induced dissociation?

Decarboxylation is known to be the major fragmentation pathway for the deprotonated carboxylic acids in collision-induced dissociation (CID). However, in the CID mass spectrum of deprotonated benzoic acid (m/z 121) recorded on a Q-orbitrap mass spectrometer, the dominant peak was found to be m/z 93 instead of the anticipated m/z 77. Based on theoretical calculations, ¹⁸O-isotope labeling and MS³ experiments, we demonstrated that the fragmentation of benzoate anion begins with decarboxylation, but the initial phenide anion (m/z 77) can react with trace O₂ in the mass analyzer to produce phenolate anion (m/z 93) and other oxygen-containing ions. Thus oxygen adducts should be considered when annotating the MS/MS spectra of benzoic acids.     

Collision induced dissociation in a flowing afterglow-tandem mass spectrometer for the selective detection of C5 unsaturated alcohols and isoprene

A flowing afterglow-tandem mass spectrometer (FA-TMS) was used to study a series of C₅ unsaturated alcohols and isoprene. The analytical procedure was validated through collision induced dissociation (CID) experiments on proton hydrates. In the FA, reagent H₃O⁺ ions were used to chemically ionize the alcohols under study and isoprene. Chemical ionization (CI) by H₃O⁺ is widely used, especially in PTR-MS instruments, and produces a main peak at m/z 69 for all studied compounds, implying the impossibility to distinguish them by a simple quadrupole mass filter. The CID of these ions at m/z 69 resulted in daughter ions with the same masses but with different intensities depending on the organic compound, the collision energy and the Ar target gas pressure in the collision cell. From these observations, pentenols were easily distinguished from methylbutenols and 3-methyl-3-buten-1-ol from the other compounds. CID experiments were also performed on the protonated alcohol, which is only a stable ion for 1-penten-3-ol, 2-methyl-3-buten-2-ol and 3-methyl-3-buten-1-ol, showing different CID patterns as a function of the collision energy. The coupling between a FA reactor and a TMS has proven to be a valuable approach to identify C₅ unsaturated alcohols and isoprene.     

An online ultra-high sensitivity Proton-transfer-reaction mass-spectrometer combined with switchable reagent ion capability (PTR + SRI − MS)

Proton-transfer-reaction mass-spectrometry (PTR-MS) developed in the 1990s is used today in a wide range of scientific and technical fields. PTR-MS allows for real-time, online determination of absolute concentrations of volatile (organic) compounds (VOCs) in air with high sensitivity (into the low pptv range) and a fast response time (in the 40–100 ms time regime). Most PTR-MS instruments employed so far use an ion source consisting of a hollow cathode (HC) discharge in water vapour which provides an intense source of proton donor H₃O⁺ ions. As the use of other ions, e.g. NO⁺ and O₂⁺, can be useful for the identification of VOCs and for the detection of VOCs with proton affinities (PA) below that of H₂O, selected ion flow tube mass spectrometry (SIFT-MS) with mass selected ions has been applied in these instances. SIFT-MS suffers, however, from at least two orders lower reagent ion counts rates and therefore SIFT-MS suffers from lower sensitivity than PTR-MS.Here we report the development of a PTR-MS instrument using a modified HC ion source and drift tube design, which allows for the easy and fast switching between H₃O⁺, NO⁺ and O₂⁺ ions produced in high purity and in large quantities in this source. This instrument is capable of measuring low concentrations (with detection limits approaching the ppqv regime) of VOCs using any of the three reagent ions investigated in this study. Therefore this instrument combines the advantages of the PTR-MS technology (the superior sensitivity) with those of SIFT-MS (detection of VOCs with PAs smaller than that of the water molecule and the capability to distinguish between isomeric compounds).We will first discuss the setup of this new PTR+SRI-MS mass spectrometer instrument, its performance for aromates, aldehydes and ketones (with a sensitivity of up to nearly 1000 cps/ppbv and a detection limit of about several 100 ppqv) and finally give some examples concerning the ability to distinguish structural isomeric compounds.     

Low-energy tandem mass spectrometry of the molecular ion derived from fatty acid methyl esters: A novel method for analysis of branched-chain fatty acids

Low-energy collision-induced dissociation (CID) of the molecular ions of fatty acid methyl esters obtained by electron ionization (70 eV) decompose in the tandem quadrupole mass spectrometer to yield a regular homologous series of carbomethoxy ions. Even at energies up to 200 eV (E _lab), primarily carbomethoxy ions are present, with the most abundant found at m/z 101 at hi her energies. The lack of any other CID ions, including m/z 74 (McLafferty rearrangement) or m/z 87, suggest a rearranged molecular ion structure on leaving the first quadrupole mass analyzer. Analyses of various stable isotope variants support the hypothesis of alkyl radical migration to the carboxy carbonyl oxygen atom, with subsequent radical site directed cleavage either with or without a cyclization event. Decomposition of the molecular ions (70 eV) of several methyl branched fatty acid methyl esters, including phytanic acid, iso-methyl and anteiso-methyl branched acids, and tuberculostearic acid, reveals enhanced radical site cleavage at the alkyl branching positions. This method can be used to readily determine methyl (or alkyl) branching positions in a saturated fatty acid methyl ester.     

Selective detection of specific protein-ligand complexes by electrosonic spray-precursor ion scan tandem mass spectrometry

A novel mass spectrometric method for the selective detection of specific protein-ligand complexes is presented. The new method is based on electrosonic spray ionization of samples containing protein and ligand molecules, and mass spectrometric detection using the precursor ion scanning function on a triple quadrupole instrument. Mass-selected intact protein-ligand complex ions are subjected to fragmentation by means of collision-induced dissociation in the collision cell of the instrument, while the second mass analyzer is set to the m/z of protonated ligand ions or their alkali metal adducts. The method allows for the detection of only those ions which yield ions characteristic of the ligand molecules upon fragmentation. Since the scan range of first analyzer is set well above the m/z of the ligand ion, and the CID conditions are established to permit fragmentation of only loosely bound, noncovalent complexes, the method is specific to the detection of protein-ligand complexes under described conditions. Behavior of biologically specific and nonspecific complexes was compared under various instrumental settings. Parameters were optimized to obtain maximal selectivity for specific complexes. Specific and nonspecific complexes were found to show markedly different fragmentation characteristics, which can be a basis for selective detection of complexes with biological relevance. Preparation of specific and nonspecific complexes containing identical building blocks was attempted. Complex ions with identical stoichiometry but different origin showed the expected difference in fragmentation characteristics, which gives direct evidence for the different mechanism of specific versus nonspecific complex ion formation.     

Selective detection of the tolyl cation among other [C7H7]+ isomers by ion/molecule reaction with dimethyl ether

The ion/molecule reaction of the tolyl cation with dimethyl ether has been investigated using triple quadrupole mass spectrometry. Three isomers with [C₇H₇]⁺ composition, the 3-tolyl, benzyl, and tropylium cations, were individually selected and reacted with dimethyl ether at a pressure of 1 mtorr in the second quadrupole (Q₂) collision cell. Only the tolyl ion reacted to yield a methoxylated product ion peak at m/z 122. This reaction product having m/z 122 is postulated to be identical in structure with the molecular ion of 3-methyl anisole, as supported by thermochemical data and the similarity of the collision induced dissociation (CID) daughter ion mass spectra of the product ion and the molecular ion of authentic 3-methyl anisole. The daughter ion mass spectra of the three [C₇H₇]⁺ isomers during CID, by using a triple quadrupole mass spectrometer, are nearly identical; on the other hand, the analytical approach based on the ion/molecule reaction with dimethyl ether clearly exhibits distinct gas-phase chemistry reflecting structural differences among the isomers. Sot     

Structural determination by atmospheric pressure photoionization tandem mass spectrometry of some compounds isolated from the SARA fractions obtained from bitumen

We have identified compounds obtained from the SARA fractions of bitumen by using atmospheric pressure photoionization mass spectrometry and low‐energy collision tandem mass spectrometric analyses with a QqToF‐MS/MS hybrid instrument. The identified compounds were isolated from the maltene saturated oil and the aromatic fractions of the SARA components of a bitumen. The QqToF instrument had sufficient mass resolution to provide accurate molecular weight information and to enhance the tandem mass spectrometry results. The APPI‐QqToF‐MS analysis of the separated compounds showed a series of protonated molecules [M + H]⁺ and molecular ions [M]^+? of the same mass but having different chemical structures, in the maltene saturated oil and the aromatic SARA fractions. These isobaric ions were a molecular ion [M₂]^+? at m/z 418.2787 and a protonated molecule [M₅ + H]⁺ at m/z 287.1625 in the saturated oil fraction, and molecular ions [M₆]^+? at m/z 418.1584 and [M₇]^+? at m/z 287.1285 in the aromatic fraction. The identification of this series of chemical compounds was achieved by performing CID‐MS/MS analyses of the molecular ions [M]^+? ([M₁]^+? at m/z 446. 2980, [M₂]^+? at m/z 418.2787, [M₃]^+? at m/z 360.3350 and [M₄]^+? at m/z 346.2095) in the saturated oil fraction and of the [M₅ + H]⁺ ion at m/z 287.1625 also in the saturated oil fraction. The observed CID‐MS/MS fragmentation differences were explained by proposed different breakdown processes of the precursor ions. The presented tandem mass spectrometric study shows the capability of MS/MS experiments to differentiate between different classes of chemical compounds of the SARA components of bitumen and to explain the reasons for the observed mass spectrometric differences. However, greater mass resolution than that provided by the QqToF‐MS/MS instrument would be required for the analysis of the asphaltene fraction of bitumen. Copyright © 2011 John Wiley & Sons, Ltd.     

Identification of Proteins and Phosphoproteins Using Pulsed Q Collision Induced Dissociation (PQD)

Pulsed Q collision induced dissociation (PQD) was developed to facilitate detection of low-mass reporter ions from labeling reagents (e.g., iTRΑQ) in peptide quantification using an LTQ mass spectrometer (MS). Despite the large number of linear ion traps worldwide, the use and optimization of PQD for protein identification have been limited, in part due to less effective ion fragmentation relative to the collision induced dissociation (CID). PQD expands the m/z coverage of fragment ions to the lower m/z range by circumventing the typical low mass cut-off of an ion trap MS. Since database searching relies on the matching between theoretical and observed spectra, it is not clear how ion intensity and peak number might affect the outcomes of a database search. In this report, we systematically evaluated the attributes of PQD mass spectra, performed intensity optimization, and assessed the benefits of using PQD on the identification of peptides and phosphopeptides from an LTQ. Based on head-to-head comparisons between CID (higher intensity) and PQD (better m/z coverage), peptides identified using PQD generally have Xcorr scores lower than those using CID. Such score differences were considerably diminished by the use of 0.1% m-nitrobenzyl alcohol (m-NBA) in mobile phases. The ion intensities of both CID and PQD were adversely affected by increasing m/z of the precursor, with PQD more sensitive than CID. In addition to negating the 1/3 rule, PQD enhances direct bond cleavage and generates patterns of fragment ions different from those of CID, particularly for peptides with a labile functional group (e.g., phosphopeptides). The higher energy fragmentation pathway of PQD on peptide fragmentation was further compared to those of CID and the quadrupole-type activation in parallel experiments.     

Phase-resolved real-time breath analysis during exercise by means of smart processing of PTR-MS data

Separation of inspiratory, mixed expired and alveolar air is indispensable for reliable analysis of VOC breath biomarkers. Time resolution of direct mass spectrometers often is not sufficient to reliably resolve the phases of a breathing cycle. To realise fast on-line breath monitoring by means of direct MS utilising low-fragmentation soft ionisation, a data processing algorithm was developed to identify inspiratory and alveolar phases from MS data without any additional equipment. To test the algorithm selected breath biomarkers (acetone, isoprene, acetaldehyde and hexanal) were determined by means of quadrupole proton transfer reaction mass spectrometry (PTR-MS) in seven healthy volunteers during exercise on a stationary bicycle. The results were compared to an off-line reference method consisting of controlled alveolar breath sampling in Tedlar® bags, preconcentration by solid-phase micro extraction (SPME), separation and identification by GC-MS. Based on the data processing method, quantitative attribution of biomarkers to inspiratory, alveolar and mixed expiratory phases was possible at any time during the experiment, even under respiratory rates up to 60/min. Alveolar concentrations of the breath markers, measured by PTR-MS ranged from 130 to 2,600 ppb (acetone), 10 to 540 ppb (isoprene), 2 to 31 ppb (acetaldehyde), whereas the concentrations of hexanal were always below the limit of detection (LOD) of 3 ppb. There was good correlation between on-line PTR-MS and SPME-GC-MS measurements during phases with stable physiological parameters but results diverged during rapid changes of heart rate and minute ventilation. This clearly demonstrates the benefits of breath-resolved MS for fast on-line monitoring of exhaled VOCs.

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Figure Experimental setup showing bicycle ergometer and analytical pathways: Right side PTR-MS: identification of respiratory phases by means of the new algorithm. Left side: confirmation of PTR-MS data for exhaled isoprene by means of GC-MS analysis

     

Discrimination of cancerous and non-cancerous cell lines by headspace-analysis with PTR-MS

Proton transfer reaction mass spectrometry (PTR-MS) has been used to analyze the volatile organic compounds (VOCs) emitted by in-vitro cultured human cells. For this purpose, two pairs of cancerous and non-cancerous human cell lines were selected:1. lung epithelium cells A-549 and retinal pigment epithelium cells hTERT-RPE1, cultured in different growth media; and 2. squamous lung carcinoma cells EPLC and immortalized human bronchial epithelial cells BEAS2B, cultured in identical growth medium. The VOCs in the headspace of the cell cultures were sampled: 1. online by drawing off the gas directly from the culture flask; and 2. by accumulation of the VOCs in PTFE bags connected to the flask for at least 12 h. The pure media were analyzed in the same way as the corresponding cells in order to provide a reference. Direct comparison of headspace VOCs from flasks with cells plus medium and from flasks with pure medium enabled the characterization of cell-line-specific production or consumption of VOCs. Among all identified VOCs in this respect, the most outstanding compound was m/z = 45 (acetaldehyde) revealing significant consumption by the cancerous cell lines but not by the non-cancerous cells. By applying multivariate statistical analysis using 42 selected marker VOCs, it was possible to clearly separate the cancerous and non-cancerous cell lines from each other.     

Commercial formaldehyde standard for mass calibration in mass spectrometry

Common calibration standards for mass spectrometry can be a source of many problems including instrument contamination, ionization suppression and formation of unidentified ions during subsequent analysis. In this article, we present a new approach for the calibration of mass analyzers such as a quadrupole–time‐of‐flight mass spectrometry using a diluted solution of commercial formaldehyde. Formaldehyde is an inexpensive and commonly used solvent, and its intrinsic polymerization leads to the formation of polyoxymethylene (POM) oligomers, which are excellent multiple calibration standards for a low‐mass spectral region (up to m/z 400) in the positive and negative mode of electrospray ionization. We explore the nature and origin of these polymeric species and attributed them to chemical reactions of formaldehyde and stabilizing agents in commercial formaldehyde solutions and during electrospray ionization. In contrast to other calibrants, POM oligomers do not contaminate the instrument and can easily be removed from the sample delivery system. Using tandem mass spectrometry, we elucidate the structures of the detected POM oligomers and report their reference masses, which are tightly spaced by 30 mass units. In our calibration method, mass errors of <5 ppm can be obtained from m/z 20–400 using external calibration with a simple one‐point zero‐order correction of spectral data and without the need for operation of a dual spray or internal calibrants. Our approach will be particularly useful for those interested in the analysis of fragile ions with low m/z values and can function at instrumental conditions required for analysis of the most labile metabolites and environmental contaminants. Copyright © 2015 John Wiley & Sons, Ltd.     

Optimized orbitrap HCD for quantitative analysis of phosphopeptides

Despite the tremendous commercial success of radio frequency quadrupole ion traps for bottom-up proteomics studies, there is growing evidence that peptides decorated with labile post-translational modifications are less amenable to low-energy, resonate excitation MS/MS analysis. Moreover, multiplexed stable isotope reagents designed for MS/MS-based quantification of peptides rely on accurate and robust detection of low-mass fragments for all precursors. Collectively these observations suggest that beam-type or tandem in-space MS/MS measurements, such as that available on traditional triple quadrupole mass spectrometers, may provide beneficial figures of merit for quantitative proteomics analyses. The recent introduction of a multipole collision cell adjacent to an Orbitrap mass analyzer provides for higher energy collisionally activated dissociation (HCD) with efficient capture of fragment ions over a wide mass range. Here we describe optimization of various instrument and post-acquisition parameters that collectively provide for quantification of iTRAQ-labeled phosphorylated peptides isolated from complex cell lysates. Peptides spanning a concentration dynamic range of 100:1 are readily quantified. Our results indicate that appropriate parameterization of collision energy as a function of precursor m/z and z provides for optimal performance in terms of peptide identification and relative quantification by iTRAQ. Using this approach, we readily identify activated signaling pathways downstream of oncogenic mutants of Flt-3 kinase in a model system of human myeloid leukemia.     

Proton transfer reaction ion trap mass spectrometer

Proton transfer reaction mass spectrometry is a relatively new field that has attracted a great deal of interest in the last few years. This technique uses H(3)O(+) as a chemical ionization (CI) reagent to measure volatile organic compounds (VOCs) in the parts per billion by volume (ppbv) to parts per trillion by volume (pptv) range. Mass spectra acquired with a proton transfer reaction mass spectrometer (PTR-MS) are simple because proton transfer chemical ionization is "soft" and results in little or no fragmentation. Unfortunately, peak identification can still be difficult due to isobaric interferences. A possible solution to this problem is to couple the PTR drift tube to an ion trap mass spectrometer (ITMS). The use of an ITMS is appealing because of its ability to perform MS/MS and possibly distinguish between isomers and other isobars. Additionally, the ITMS duty cycle is much higher than that of a linear quadrupole so faster data acquisition rates are possible that will allow for detection of multiple compounds. Here we present the first results from a proton transfer reaction ion trap mass spectrometer (PTR-ITMS). The aim of this study was to investigate ion injection and storage efficiency of a simple prototype instrument in order to estimate possible detection limits of a second-generation instrument. Using this prototype a detection limit of 100 ppbv was demonstrated. Modifications are suggested that will enable further reduction in detection limits to the low-ppbv to high-pptv range. Furthermore, the applicability of MS/MS in differentiating between isobaric species was determined. MS/MS spectra of the isobaric compounds methyl vinyl ketone (MVK) and methacrolein (MACR) are presented and show fragments of different mass making differentiation possible, even when a mixture of both species is present in the same sample. However, MS/MS spectra of acetone and propanal produce fragments with the same molecular masses but with different intensity ratios. This allows quantitative distinction only if one species is predominant. Fragmentation mechanisms are proposed to explain the results.