Assessment of the various ionization methods in the analysis of metal salen complexes by mass spectrometry

Metal salen complexes are one of the most frequently used catalysts in enantioselective organic synthesis. In the present work, we compare a series of ionization methods that can be used for the mass spectral analysis of two types of metalosalens: ionic complexes (abbreviated as Com⁺X^?) and neutral complexes (NCom). These methods include electron ionization and field desorption (FD) which can be applied to pure samples and atmospheric pressure ionization techniques: electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI) and atmospheric pressure photoionization (APPI) which are suitable for solutions. We found that FD is a method of choice for recording molecular ions of the complexes containing even loosely bonded ligands. The results obtained using atmospheric pressure ionization methods show that the results depend mainly on the structure of metal salen complex and the ionization method. In ESI spectra, Com⁺ ions were observed, while in APCI and APPI spectra both Com⁺ and [Com + H]⁺ ions are observed in the ratio depending on the structure of the metal salen complex and the solvent used in the analysis. For complexes with tetrafluoroborate counterion, an elimination of BF₃ took place, and ions corresponding to complexes with fluoride counterion were observed. Experiments comparing the relative sensitivity of ESI, APCI and APPI (with and without a dopant) methods showed that for the majority of the studied complexes ESI is the most sensitive one; however, the sensitivity of APCI is usually less than two times lower and for some compounds is even higher than the sensitivity of ESI. Both methods show very high linearity of the calibration curve in a range of about 3 orders of magnitude of the sample concentration. Copyright © 2014 John Wiley & Sons, Ltd.     

Evaluation of the optimization space for atmospheric pressure photoionization (APPI) in comparison with APCI

The usefulness of atmospheric pressure photoionization (APPI) is difficult to evaluate for unknowns due to the fragmented literature. Specifically, the variation of dopants with a wide set of compounds or the use of APPI in the negative mode have rarely been explored. Thirty compounds were selected that were not suitable for ESI with a wide variety of functional groups and investigated with atmospheric pressure chemical ionization (APCI) and APPI in the positive and negative ion modes. The influence of the mobile phase (eluents containing acetonitrile or methanol) and – for APPI – four different dopants (acetone, chlorobenzene, toluene, and toluene/anisole) were explored. Stepwise variation of the organic mobile phase allowed to elucidate the ionization mechanism. Atmospheric pressure photoionization was especially useful for compounds, where the M^●+ and not the [M + H]⁺ was formed. The dopants chlorobenzene and anisole promoted the formation of molecular ions M^●+ for about half of the compounds, and its formation was also positively influenced by the use of mobile phases containing methanol. In the negative ion mode, APPI offered no advantage toward APCI. Best results were generally achieved with the dopant chlorobenzene, establishing that this dopant is suitable for a wide set of compounds. For one quarter of the compounds, significantly better results were achieved with mobile phases containing methanol for both APPI and APCI than those with acetonitrile, but only in the positive mode. With either of the methods – APPI or APCI – about 10% of the compounds were not detected. Strategies to get results quickly with difficult unknowns will be discussed. Copyright © 2014 John Wiley & Sons, Ltd.     

Drug impurity profiling by capillary electrophoresis/mass spectrometry using various ionization techniques

Capillary electrophoresis/mass spectrometry (CE/MS) is predominantly carried out using electrospray ionization (ESI). Recently, atmospheric pressure chemical ionization (APCI) and atmospheric pressure photoionization (APPI) have become available for CE/MS. With the VUV lamp turned off, the APPI source may also be used for CE/MS by thermospray ionization (TSI). In the present study the suitability of ESI, APCI, APPI and TSI for drug impurity profiling by CE/MS in the positive ion mode is evaluated. The drugs carbachol, lidocaine and proguanil and their potential impurities were used as test compounds, representing different molecular polarities. A background electrolyte of 100 mM acetic acid (pH 4.5) provided baseline separation of nearly all impurities from the respective drugs. APPI yielded both even‐ and odd‐electron ions, whereas the other ionization techniques produced even‐electron ions only. In‐source fragmentation was more pronounced with APCI and APPI than with ESI and TSI, which was most obvious for proguanil and its impurities. In general, ESI and TSI appeared the most efficient ionization techniques for impurities that are charged in solution achieving detection limits of 100 ng/mL (full‐scan mode). APPI and APCI showed a lower efficiency, but allowed ionization of low and high polarity analytes, although quaternary ammonium compounds (e.g. carbachol) could not be detected. Largely neutral compounds, such as the lidocaine impurity 2,6‐dimethylaniline, could not be detected by TSI, and yielded similar detection limits (500 ng/mL) for ESI, APPI and APCI. In many cases, impurity detection at the 0.1% (w/w) level was possible when 1 mg/mL of parent drug was injected with at least one of the CE/MS systems. Overall, the tested CE/MS systems provide complementary information as illustrated by the detection and identification of an unknown impurity in carbachol. Copyright © 2009 John Wiley & Sons, Ltd.     

Determination of carotenoids by liquid chromatography/mass spectrometry: effect of several dopants

Various carotenoids were analyzed by ultra-high-pressure liquid chromatography with tandem mass spectrometry detection (UHPLC-MS/MS). Three different techniques to ionize the carotenoids were compared: electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI) and atmospheric pressure photoionization (APPI). For all of the carotenoids tested, it was possible to obtain characteristic transitions for their unequivocal identification using each ionization technique. APCI was shown to be a more powerful technique to ionize the carotenoids than ESI or APPI. Transitions to differentiate carotenoids that coelute were determined to distinguish antheraxanthin from astaxanthin and lutein from zeaxanthin. In addition, four dopants were evaluated to improve ionization and enhance the carotenoid signal strength in APPI. These dopants were acetone, toluene, anisole, and chlorobenzene. Carotenoids improved their response in almost all cases when a dopant was used. The use of dopants allowed the enhancement of the carotenoid signals strength up to 178-fold.     

Atmospheric pressure photoionization liquid chromatographic-mass spectrometric determination of idoxifene and its metabolites in human plasma

This paper describes a comparison between atmospheric pressure chemical ionization (APCI) and the recently introduced atmospheric pressure photoionization (APPI) interface for the LC–MS determination of idoxifene and its major metabolite, SB245419 (SB19), in human plasma. The results indicate that analyte response in APPI is highly dependent on the solvent composition, especially to water in the mobile phase. Other parameters investigated are the mobile phase flow-rate, the chemical noise, and signal suppression by matrix interferences. APPI appears to be six to eight times more sensitive than APCI for idoxifene and its SB245419 metabolite; the response for the SB245420 metabolite is considerably better than for APCI conditions, but still not sufficient for trace level pharmacokinetic determinations in human plasma. The LOQ for the parent drug and its major metabolite were 10 and 25 ng/ml, respectively, in human plasma. From post-column infusion experiments we conclude that there is little difference in matrix suppression between APCI and APPI. From these studies we suggest APPI may be an additional tool in pharmaceutical LC–MS applications.     

Effect of organic mobile phase composition on signal responses for selected polyalkene additive compounds by liquid chromatography-mass spectrometry

The high performance liquid chromatography (HPLC) separation methodology employed in the study of polyalkene additive compounds by atmospheric pressure ionization mass spectrometry (API-MS) was undertaken. Both atmospheric pressure chemical ionization (APCI) and atmospheric pressure photoionization (APPI) were examined. APPI (including dopant-assisted APPI) was found to be an inferior ionization technique to APCI in all cases. APCI ion responses were found to be highly dependent upon the organic solvent type used in the HPLC separations. Namely, employing a water/methanol gradient in place of a water/acetonitrile or a water/acetone gradient yielded improvements in analyte ion intensities between 2.3- and 52-fold for the liquid chromatography-mass spectrometry (LC-MS) experiments. Analyte and mobile phase solvent ionization energies were found to be only partially responsible, whereas mobile phase cluster formation and hydration was also implicated. Mobile phase component modification is demonstrated to be an important consideration when developing new, or modifying existing HPLC separations for use in LC-MS experiments in order to enhance analyte sensitivity for a wide variety of common polyalkene additives.     

Advantages of atmospheric pressure photoionization mass spectrometry in support of drug discovery

The performance of the atmospheric pressure photoionization (APPI) technique was evaluated against five sets of standards and drug-like compounds and compared to atmospheric pressure chemical ionization (APCI) and electrospray ionization (ESI). The APPI technique was first used to analyze a set of 86 drug standards with diverse structures and polarities with a 100% detection rate. More detailed studies were then performed for another three sets of both drug standards and proprietary drug candidates. All 60 test compounds in these three sets were detected by APPI with an overall higher ionization efficiency than either APCI or ESI. Most of the non-polar compounds in these three sets were not ionized by APCI or ESI. Analysis of a final set of 201 Wyeth proprietary drug candidates by APPI, APCI and ESI provided an additional comparison of the ionization techniques. The detection rates in positive ion mode were 94% for APPI, 84% for APCI, and 84% for ESI. Combining positive and negative ion mode detection, APPI detected 98% of the compounds, while APCI and ESI detected 91%, respectively. This analysis shows that APPI is a valuable tool for day-to-day usage in a pharmaceutical company setting because it is able to successfully ionize more compounds, with greater structural diversity, than the other two ionization techniques. Consequently, APPI could be considered a more universal ionization method, and therefore has great potential in high-throughput drug discovery especially for open access liquid chromatography/mass spectrometry (LC/MS) applications.     

Negative ion-atmospheric pressure photoionization-mass spectrometry

The ionization mechanism in the novel atmospheric pressure photoionization mass spectrometry (APPI-MS) in negative ion mode was studied thoroughly by the analysis of seven compounds in 17 solvent systems. The compounds possessed either gas-phase acidity or positive electron affinity, whereas the solvent systems had different polarities and gas-phase acidities and some of them positive electron affinities. The analytes that possessed gas-phase acidity formed deprotonated ions in proton transfer; in addition, fragments and solvent adducts were observed. The compounds of positive electron affinity formed negative molecular ions by electron capture or charge exchange and substitution products of form [M - X + O](-) by substitution reactions. The efficiency of deprotonation was decreased if the solvent used possessed higher gas-phase acidity than the analyte. Solvents of positive electron affinity captured thermal electrons and deteriorated the ionization of all the analytes. Also, the proportion of substitution products was affected by the solvent. Finally, the performances of negative ion APPI and negative ion APCI were compared. The sensitivity for the studied compounds was better in APPI, but the formation of substitution products was lower in APCI.     

Gas chromatography coupled to atmospheric pressure ionization mass spectrometry (GC-API-MS): Review

Although the coupling of GC/MS with atmospheric pressure ionization (API) has been reported in 1970s, the interest in coupling GC with atmospheric pressure ion source was expanded in the last decade. The demand of a “soft” ion source for preserving highly diagnostic molecular ion is desirable, as compared to the “hard” ionization technique such as electron ionization (EI) in traditional GC/MS, which fragments the molecule in an extensive way. These API sources include atmospheric pressure chemical ionization (APCI), atmospheric pressure photoionization (APPI), atmospheric pressure laser ionization (APLI), electrospray ionization (ESI) and low temperature plasma (LTP). This review discusses the advantages and drawbacks of this analytical platform. After an introduction in atmospheric pressure ionization the review gives an overview about the history and explains the mechanisms of various atmospheric pressure ionization techniques used in combination with GC such as APCI, APPI, APLI, ESI and LTP. Also new developments made in ion source geometry, ion source miniaturization and multipurpose ion source constructions are discussed and a comparison between GC-FID, GC-EI-MS and GC-API-MS shows the advantages and drawbacks of these techniques. The review ends with an overview of applications realized with GC-API-MS.     

Effect of eluent on the ionization process in liquid chromatography-mass spectrometry

The most widely used ionization techniques in liquid chromatography-mass spectrometry (LC-MS) are electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI) and atmospheric pressure photoionization (APPI). All three provide user friendly coupling of LC to MS. Achieving optimal LC-MS conditions is not always easy, however, owing to the complexity of ionization processes and the many parameters affecting mass spectrometric sensitivity and chromatographic performance. The selection of eluent composition requires particular attention since a solvent that is optimal for analyte ionization often does not provide acceptable retention and resolution in LC. Compromises must then be made between ionization and chromatographic separation efficiencies. The review presents an overview of studies concerning the effect of eluent composition on the ionization efficiency of ESI, APCI and APPI in LC-MS. Solvent characteristics are discussed in the light of ionization theories, and selected analytical applications are described. The aim is to provide practical background information for the development and optimization of LC-MS methods.     

Atmospheric pressure photoionization mechanisms. 2. The case of benzene and toluene

Benzene and toluene have been proposed previously as dopants in atmospheric pressure photoionization (APPI) experiments on compounds exhibiting ionization energies higher than the energy of photons used for irradiation. Their low ionization energies lead to their easy photoionization and the ions so formed lead to the ionization of analytes through charge exchange. However, some measurements have shown that some protonation reactions also take place, and a series of experiments was undertaken to investigate this unexpected behavior. It was shown that, when benzene is irradiated in the APPI source, the odd-electron molecular ions of phenol, diphenyl ether and phenoxyphenol are produced in high yield, together with protonated diphenyl ether and protonated phenoxyphenol. These results have been confirmed by deuterium labelling and MS(n) experiments. A possible mechanism is proposed, based on a radical attack by benzene molecular ions on oxygen molecules present inside the APPI source, analogous to that proposed in the literature for phenyl radicals. Similar results have been obtained with toluene, proving that APPI is able to activate a series of reactions leading to highly reactive species which are highly effective in promoting ionization of molecules with ionization energies higher than the photon energy.     

Comparison of APPI, APCI and ESI for the LC-MS/MS analysis of bezafibrate, cyclophosphamide, enalapril, methotrexate and orlistat in municipal wastewater

The applicability of three different ionization techniques: atmospheric pressure photoionization (APPI), atmospheric pressure chemical ionization (APCI) and electrospray ionization (ESI) was tested for the liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of five target pharmaceuticals (cyclophosphamide, methotrexate, bezafibrate, enalapril and orlistat) in wastewater samples. Performance was compared both by flow injection analysis (FIA) and on-column analysis in deionized water and wastewater samples. A column switching technique for the on-line extraction and analysis of water samples was used. For both FIA and on-column analysis, signal intensity and signal-to-noise (S/N) ratio of the target analytes in the three sources were studied. Limits of detection and matrix effects during the analysis of wastewater samples were also investigated. ESI generated significantly larger peak areas and higher S/N ratios than APCI and APPI in FIA and in on-column analysis. ESI was proved to be the most suitable ionization method as it enabled the detection of the five target compounds, whereas APCI and APPI ionized only four compounds.     

Dimerization of ionized 4‐(methyl mercapto)‐phenol during ESI,APCI and APPI mass spectrometry

A novel ion/molecule reaction was observed to occur under electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI), and atmospheric pressure photo ionization (APPI) conditions, leading to dimerization of ionized 4‐(methyl mercapto)‐phenol followed by fast H^· loss. The reaction is particularly favored during ESI, which suggests that this ion/molecule reaction can occur both in the solution inside the ESI‐charged droplets and in the gas‐phase environment of most other atmospheric pressure ionization techniques. The dimerization reaction is inherent to the electrolytic process during ESI, whereas it is more by ion/molecule chemistry in nature during APCI and APPI. From the tandem mass spectrometry (MS/MS) data, accurate mass measurements, hydrogen/deuterium (H/D) exchange experiments and density functional theory (DFT) calculations, two methyl sulfonium ions appear to be the most likely products of this electrophilic aromatic substitution reaction. The possible occurrence of this unexpected reaction complicates mass spectral data interpretation and can be misleading in terms of structural assignment as reported herein for 4‐(methyl mercapto)‐phenol. Copyright © 2009 John Wiley & Sons, Ltd.     

Effect of eluent on the ionization efficiency of flavonoids by ion spray, atmospheric pressure chemical ionization, and atmospheric pressure photoionization mass spectrometry.

The effect of nine different eluent compositions on the ionization efficiency of five flavonoids was studied using ion spray (IS), atmospheric pressure chemical ionization (APCI), and the novel atmospheric pressure photoionization (APPI), in positive and negative ion modes. The eluent composition had a great effect on the ionization efficiency, and the optimal ionization conditions were achieved in positive ion IS and APCI using 0.4% formic acid (pH 2.3) as a buffer, and in negative ion IS and APCI using ammonium acetate buffer adjusted to pH 4.0. For APPI work, the eluent of choice appeared to be a mixture of organic solvent and 5 mM aqueous ammonium acetate. The limits of detection (LODs) were determined in scan mode for the analytes by liquid chromatography/mass spectrometry using IS, APCI and APPI interfaces. The results show that negative ion IS with an eluent system consisting of acidic ammonium acetate buffer provides the best conditions for detection of flavonoids in mass spectrometry mode, their LODs being between 0.8 and 13 microM for an injection volume of 20 microl.     

Atmospheric pressure photoionization. II. Dual source ionization

In this paper we describe results based on the combination of atmospheric pressure photoionization (APPI) with atmospheric pressure chemical ionization (APCI) and electrospray ionization (ESI). The main purpose of combining more than one ionizer is to extend the range of compounds that can be simultaneously analyzed. Three modes of operation are presented; use of either ionizer, simultaneous use of two ionizers, and rapid switching between ionizers during a single chromatographic run. The dual ionizer configurations only minimally affect the performance of either ionizer relative to the standard single-ionizer sources. However, it is observed that the operation of both ionizers together does not typically give the sum signal from either source operating alone. For APCI/APPI the signal can range from less than that of either source alone to the sum of the two individual sources. For ESI/APPI, we observed large suppressions of the ESI multiply-charged signal of proteins when the APPI source was on. These behaviors are presumed to be due to the interaction of the initially formed ions by both sources and attests to the importance of ion-molecule reactions that occur during and after the primary ionization events. We give examples of compounds that are preferentially ionized by either APPI, APCI or ESI and present thermochemical arguments based on molecular structure and functionality to explain this behavior. The dual source is also shown to be able to operate in negative ion mode opening up the potential to conduct wide ranging chemical analyses.     

Atmospheric-pressure laser ionization: a novel ionization method for liquid chromatography/mass spectrometry

We report on the development of a new laser-ionization (LI) source operating at atmospheric pressure (AP) for liquid chromatography/mass spectrometry (LC/MS) applications. APLI is introduced as a powerful addition to existing AP ionization techniques, in particular atmospheric-pressure chemical ionization (APCI), electrospray ionization (ESI), and atmospheric pressure photoionization (APPI). Replacing the one-step VUV approach in APPI with step-wise two-photon ionization strongly enhances the selectivity of the ionization process. Furthermore, the photon flux during an ionization event is drastically increased over that of APPI, leading to very low detection limits. In addition, the APLI mechanism generally operates primarily directly on the analyte. This allows for very efficient ionization even of non-polar compounds such as polycyclic aromatic hydrocarbons (PAHs). The APLI source was characterized with a MicroMass Q-Tof Ultima II analyzer. Both the effluent of an HPLC column containing a number of PAHs (benzo[a]pyrene, fluoranthene, anthracene, fluorene) and samples from direct syringe injection were analyzed with respect to selectivity and sensitivity of the overall system. The liquid phase was vaporized by a conventional APCI inlet (AP probe) with the corona needle removed. Ionization was performed through selective resonance-enhanced multi-photon ionization schemes using a high-repetition-rate fixed-frequency excimer laser operating at 248 nm. Detection limits well within the low-fmol regime are readily obtained for various aromatic hydrocarbons that exhibit long-lived electronic states at the energy level of the first photon. Only molecular ions are generated at the low laser fluxes employed ( approximately 1 MW/cm(2)). The design and performance of the laser-ionization source are presented along with results of the analysis of aromatic hydrocarbons.     

Liquid chromatography/negative ion atmospheric pressure photoionization mass spectrometry: a highly sensitive method for the analysis of organic explosives

Gas chromatography/mass spectrometry (GC/MS) is applied to the analysis of volatile and thermally stable compounds, while liquid chromatography/atmospheric pressure chemical ionization mass spectrometry (LC/APCI‐MS) and liquid chromatography/electrospray ionization mass spectrometry (LC/ESI‐MS) are preferred for the analysis of compounds with solution acid‐base chemistry. Because organic explosives are compounds with low polarity and some of them are thermally labile, they have not been very well analyzed by GC/MS, LC/APCI‐MS and LC/ESI‐MS. Herein, we demonstrate liquid chromatography/negative ion atmospheric pressure photoionization mass spectrometry (LC/NI‐APPI‐MS) as a novel and highly sensitive method for their analysis. Using LC/NI‐APPI‐MS, limits of quantification (LOQs) of nitroaromatics and nitramines down to the middle pg range have been achieved in full MS scan mode, which are approximately one order to two orders magnitude lower than those previously reported using GC/MS or LC/APCI‐MS. The calibration dynamic ranges achieved by LC/NI‐APPI‐MS are also wider than those using GC/MS and LC/APCI‐MS. The reproducibility of LC/NI‐APPI‐MS is also very reliable, with the intraday and interday variabilities by coefficient of variation (CV) of 0.2–3.4% and 0.6–1.9% for 2,4,6‐trinitrotoluene (2,4,6‐TNT). Copyright © 2008 John Wiley & Sons, Ltd.     

LC‐MS analysis of estradiol in human serum and endometrial tissue: Comparison of electrospray ionization,atmospheric pressure chemical ionization and atmospheric pressure photoionization

Accurate measurement of estradiol (E2) is important in clinical diagnostics and research. High sensitivity methods are critical for specimens with E2 concentrations at low picomolar levels, such as serum of men, postmenopausal women and children. Achieving the required assay performance with LC–MS is challenging due to the non‐polar structure and low proton affinity of E2. Previous studies suggest that ionization has a major role for the performance of E2 measurement, but comparisons of different ionization techniques for the analysis of clinical samples are not available. In this study, female serum and endometrium tissue samples were used to compare electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI) and atmospheric pressure photoionization (APPI) in both polarities. APPI was found to have the most potential for E2 analysis, with a quantification limit of 1 fmol on‐column. APCI and ESI could be employed in negative polarity, although being slightly less sensitive than APPI. In the presence of biological background, ESI was found to be highly susceptible to ion suppression, while APCI and APPI were largely unaffected by the sample matrix. Irrespective of the ionization technique, background interferences were observed when using the multiple reaction monitoring transitions commonly employed for E2 (m/z 271 > 159; m/z 255 > 145). These unidentified interferences were most severe in serum samples, varied in intensity between ionization techniques and required efficient chromatographic separation in order to achieve specificity for E2. Copyright © 2013 John Wiley & Sons, Ltd.     

The Ionization Mechanisms in Direct and Dopant-Assisted Atmospheric Pressure Photoionization and Atmospheric Pressure Laser Ionization

A novel, gas-tight API interface for gas chromatography–mass spectrometry was used to study the ionization mechanism in direct and dopant-assisted atmospheric pressure photoionization (APPI) and atmospheric pressure laser ionization (APLI). Eight analytes (ethylbenzene, bromobenzene, naphthalene, anthracene, benzaldehyde, pyridine, quinolone, and acridine) with varying ionization energies (IEs) and proton affinities (PAs), and four common APPI dopants (toluene, acetone, anisole, and chlorobenzene) were chosen. All the studied compounds were ionized by direct APPI, forming mainly molecular ions. Addition of dopants suppressed the signal of the analytes with IEs above the IE of the dopant. For compounds with suitable IEs or Pas, the dopants increased the ionization efficiency as the analytes could be ionized through dopant-mediated gas-phase reactions, such as charge exchange, proton transfer, and other rather unexpected reactions, such as formation of [M?+?77]⁺ in the presence of chlorobenzene. Experiments with deuterated toluene as the dopant verified that in case of proton transfer, the proton originated from the dopant instead of proton-bound solvent clusters, as in conventional open or non-tight APPI sources. In direct APLI using a 266 nm laser, a narrower range of compounds was ionized than in direct APPI, because of exceedingly high IEs or unfavorable two-photon absorption cross-sections. Introduction of dopants in the APLI system changed the ionization mechanism to similar dopant-mediated gas-phase reactions with the dopant as in APPI, which produced mainly ions of the same form as in APPI, and ionized a wider range of analytes than direct APLI. Graphical Abstract

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New perspective on the determination of flame retardants in sewage sludge by using ultrahigh pressure liquid chromatography–tandem mass spectrometry with different ion sources

Analysis of 11 polybrominated diphenyl ethers (PBDEs), tetrabromobisphenol A bis 2,3-dibromopropylether (TBBPA-bis), tetrachlorobisphenol A (TCBPA), tetrabromobisphenol A (TBBPA) and hexabromocyclododecanes (HBCDs) was optimized by ultrahigh pressure liquid chromatography/tandem mass spectrometry (UPLC–MS/MS) operating in negative ion (NI) mode. Electrospray ionization (ESI), atmospheric pressure photoionization (APPI) and atmospheric pressure chemical ionization (APCI) sources were tested and for PBDEs APCI gave higher sensitivity than APPI while for TBBPA-bis APCI and APPI showed similar performance. ESI was the best option for TCBPA, TBBPA and HBCDs. Detection limits were between 20 and 59 fg for the compounds analyzed by ESI, 0.10 and 0.72 pg for PBDEs and 6 pg for TBBPA-bis. The matrix effect of sewage sludge extract was also tested showing negligible ion suppression for APCI and an increase of the background level of all investigated pollutants leading to a worsening of the limits of quantification by a factor between 1.2 and 3.3. The UPLC-APCI/MS/MS method for PBDEs, after pressurized liquid extraction (PLE), was validated by comparison with the concentration values from the NIST 1944 standard reference material. The advantages of the methods include low detection limits, PBDE congeners specificity using selected multiple reaction monitoring (MRM) transitions, and the absence of thermal degradation of higher PBDE congeners, especially BDE-209. The methods were applied for the determination of the above reported flame retardants in sewage sludge in order to get more information about the degradation on PBDEs (in particular BDE-209) during municipal wastewater treatments.