LC-MS/MS signal suppression effects in the analysis of pesticides in complex environmental matrices

The application of LC separation and mobile phase additives in addressing LC-MS/MS matrix signal suppression effects for the analysis of pesticides in a complex environmental matrix was investigated. It was shown that signal suppression is most significant for analytes eluting early in the LC-MS analysis. Introduction of different buffers (e.g. ammonium formate, ammonium hydroxide, formic acid) into the LC mobile phase was effective in improving signal correlation between the matrix and standard samples. The signal improvement is dependent on buffer concentration as well as LC separation of the matrix components. The application of LC separation alone was not effective in addressing suppression effects when characterizing complex matrix samples. Overloading of the LC column by matrix components was found to significantly contribute to analyte-matrix co-elution and suppression of signal. This signal suppression effect can be efficiently compensated by 2D LC (LC-LC) separation techniques. The effectiveness of buffers and LC separation in improving signal correlation between standard and matrix samples is discussed.     

LC-MS/MS signal suppression effects in the analysis of pesticides in complex environmental matrices

The application of LC separation and mobile phase additives in addressing LC-MS/MS matrix signal suppression effects for the analysis of pesticides in a complex environmental matrix was investigated. It was shown that signal suppression is most significant for analytes eluting early in the LC-MS analysis. Introduction of different buffers (e.g. ammonium formate, ammonium hydroxide, formic acid) into the LC mobile phase was effective in improving signal correlation between the matrix and standard samples. The signal improvement is dependent on buffer concentration as well as LC separation of the matrix components. The application of LC separation alone was not effective in addressing suppression effects when characterizing complex matrix samples. Overloading of the LC column by matrix components was found to significantly contribute to analyte-matrix co-elution and suppression of signal. This signal suppression effect can be efficiently compensated by 2D LC (LC-LC) separation techniques. The effectiveness of buffers and LC separation in improving signal correlation between standard and matrix samples is discussed.     

基于超高效液相色谱-高分辨质谱的非衍生化法测定面粉和燕麦中草甘膦及氨甲基膦酸残留

建立了固相萃取-超高效液相色谱-高分辨质谱（UPLC-HRMS）快速准确测定面粉和燕麦中残留草甘膦（GLY）及其代谢物氨甲基膦酸（AMPA）的分析方法。面粉和燕麦样品经水涡旋和超声提取,用混合阳离子交换固相萃取（MCX）小柱净化与乙腈沉淀蛋白质后,以5 mmol/L乙酸铵水溶液（pH=10.5）和乙腈溶液作为流动相在Dikma Polyamino HILIC色谱柱（150 mm×2.0 mm,5 μm）上进行梯度洗脱与分离,采用电喷雾电离源、负离子模式和平行反应监测（PRM）模式下,内标法定量分析。系统优化了液相色谱与高分辨质谱等仪器条件和样品前处理条件对GLY及其代谢物AMPA测定的影响,并比对了不同分析方法的基质效应,研究了进样系统残留。实验结果表明,GLY和AMPA在5.0~100.0 μg/L范围内呈现良好的线性关系（线性相关系数R²>0.999）,检出限分别为0.005和0.05 mg/kg;低（0.1 mg/kg）、中（0.5 mg/kg）、高（2.0 mg/kg）3个添加水平下,GLY和AMPA的加标回收率分别为93.8%~115%和89.8%~110%,相对标准偏差均小于10%。基质效应实验结果表明,利用同位素内标物能有效降低方法的基质抑制效应（基质效应参数|η|<3%）;进样系统的残留率小于1.0%。本方法与文献报道的衍生化法方法进行比对,结果表明,两种检测方法与靶值的相对偏差分别为2.19%和3.07%。将该方法用于弗帕斯（FAPAS）能力验证样品的测定（编号为09122,燕麦中GLY的测定）,结果满意,测定值与真值之间的偏离程度（z值）=0.2。FAPAS质控样品（编号为T09119QC,面粉中GLY的测定）检测结果显示本方法的准确度为102.2%。该方法具有快速、简便、灵敏和准确等优点,适合面粉与燕麦样品中GLY及其代谢物AMPA的日常监测。     

Systematic investigation of ion suppression and enhancement effects of fourteen stable‐isotope‐labeled internal standards by their native analogues using atmospheric‐pressure chemical ionization and electrospray ionization and the relevance for multi‐analyte liquid chromatographic/mass spectrometric procedures

In clinical and forensic toxicology, multi‐analyte procedures are very useful to quantify drugs and poisons of different classes in one run. For liquid chromatographic/tandem mass spectrometric (LC/MS/MS) multi‐analyte procedures, often only a limited number of stable‐isotope‐labeled internal standards (SIL‐ISs) are available. If an SIL‐IS is used for quantification of other analytes, it must be excluded that the co‐eluting native analyte influences its ionization. Therefore, the effect of ion suppression and enhancement of fourteen SIL‐ISs caused by their native analogues has been studied. It could be shown that the native analyte concentration influenced the extent of ion suppression and enhancement effects leading to more suppression with increasing analyte concentration especially when electrospray ionization (ESI) was used. Using atmospheric‐pressure chemical ionization (APCI), methanolic solution showed mainly enhancement effects, whereas no ion suppression and enhancement effect, with one exception, occurred when plasma extracts were used under these conditions. Such differences were not observed using ESI. With ESI, eleven SIL‐ISs showed relevant suppression effects, but only one analyte showed suppression effects when APCI was used. The presented study showed that ion suppression and enhancement tests using matrix‐based samples of different sources are essential for the selection of ISs, particularly if used for several analytes to avoid incorrect quantification. In conclusion, only SIL‐ISs should be selected for which no suppression and enhancement effects can be observed. If not enough ISs are free of ionization interferences, a different ionization technique should be considered. Copyright © 2010 John Wiley & Sons, Ltd.     

Investigation of matrix effects in bioanalytical high-performance liquid chromatography/tandem mass spectrometric assays: application to drug discovery

A series of studies was performed to investigate some of the causes for matrix effects ('ion suppression' or 'ion enhancement') in bioanalytical high-performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS) assays. Previous studies have reported that matrix effects are mainly due to endogenous components in biological fluids and are a greater concern for electrospray ionization (ESI) than for atmospheric pressure chemical ionization (APCI). In this report we demonstrate that: (1) matrix effects can also be caused by exogenous materials, such as polymers contained in different brands of plastic tubes, or Li-heparin, a commonly used anticoagulant; (2) matrix effects are not only ionization mode (APCI or ESI) dependent, but also source design (Sciex, Finnigan, Micromass) dependent; and (3) for at least one vendor's design, we found the APCI mode to be more sensitive to matrix effects than the ESI mode. Based on these findings, we have proposed the following simple strategies to avoid matrix effects: (1) select the same brand of plastic tubes for processing and storing plasma samples and spiked plasma standards; (2) avoid using Li-heparin as the anticoagulant; and (3) try switching the ionization mode or switching to different mass spectrometers when matrix effects are encountered. These three strategies have allowed us to use protein precipitation and generic fast LC techniques to generate reliable LC/MS/MS data for the support of pharmacokinetic studies at the early drug discovery stage.     

Determination of glyphosate in water samples by multi-pumping flow system coupled to a liquid waveguide capillary cell

A simple screening method was developed for the determination of glyphosate in water samples using a multi-pumping flow system. The proposed method is based on the reaction between glyphosate and p-dimethylaminocinnamaldehyde (p-DAC), in an acid medium where the reaction product can be measured spectrophotometrically at λ(max) = 495 nm. An experimental design methodology was used to optimize the measurement conditions. The proposed method was applied to the determination of glyphosate in water samples in a concentration range from 0.5 to 10 μg mL(-1). The limit of detection and quantification were 0.17 and 0.53 μg mL(-1), respectively. The results obtained (88.5 to 104.5%) in recovery studies for the determination of glyphosate in different water samples indicated good accuracy and no matrix effect for the developed method. Samples were also analyzed by a confirmatory HPLC method, and agreement within the two set of results was found.     

ICP-MS测量环境样品中铀的非质谱干扰内标校正研究

内标的合理应用直接关系到测量结果的可靠性,通过外标与内标校正相结合的方法,实验研究了Y,Rh,In,Tb,Yb,Tl,Bi,Re作为内标对ICP-MS测量铀的非质谱干扰的校正效果。对于非抑制/增强基体效应,各内标元素校正结果明显优于无内标校正结果,高质量数内标元素Tb,Yb,Re,Tl,Bi可获得较好的校正效果,校正偏差优于5%,其中以Tl为最佳;对于盐度较高的样品溶液,由于基体对待测元素和内标元素产生了明显不同的抑制/增强效应,因此各内标校正结果均不理想,这表明内标对可溶性固体引起的抑制/增强效应的校正能力有限。在铀的测量中,对于含盐度在300～500μg/mL的样品,内标校正造成的偏差可达到5%～10%;对于盐度在500μg/mL以上的样品,内标校正造成的偏差很可能超过10%或者更高。     

Effect of liquid chromatography separation of complex matrices on liquid chromatography-tandem mass spectrometry signal suppression

The effect of liquid chromatography separation on liquid chromatography-tandem mass spectrometry (LC-MS-MS) signal response for the characterization of low-molecular-mass compounds in a complex matrix was investigated. Matrix induced signal suppression appears throughout the entire LC-MS-MS analysis of wheat forage extract, with greatest suppression occurring at early retention times. Experimental results show that co-elution of matrix components and analytes from the LC column may be most strongly attributed to column overloading rather than similar analyte and matrix retention behavior. As a result, two-dimensional (LC-LC) separation can be a highly effective approach to address signal suppression effects for the quantitative LC-MS-MS analysis of complex matrix samples.     

MALDI-TOF mass spectrometry of a combinatorial peptide library: effect of matrix composition on signal suppression

The effect of matrix composition on signal suppression caused by a dominant compound under MALDI ionization was studied using the combinatorial TQTXT pentapeptide library as a model system. The peptide library is composed of 19 components with all proteinogenic amino acids except cysteine in position X. From these compounds, only the Arg peptide (TQTRT) was detected with sufficient intensity in the MALDI-TOF mass spectrum under typical MALDI conditions (CCA matrix). The analysis of a set of compounds utilized as different matrix components, additives and a cationizing agent revealed that the composition of the matrix is a critical point in signal suppression. Highly improved ion yields were achieved by using a CCA/DHB mixture as a matrix. The addition of K(+) as a cationizing agent to the CCA matrix resulted in MALDI-TOF mass spectra with relative ion intensities very similar to those obtained by electrospray ionization.     

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.     

直接进样超高效液相色谱-三重四极杆质谱法快速测定环境水样中草甘膦、氨甲基膦酸、草铵膦及乙烯利残留

建立了一种简便、直接进样的超高效液相色谱-三重四极杆质谱法（UPLC-MS/MS）快速测定环境水样中草甘膦、氨甲基膦酸、草铵膦及乙烯利的残留。环境水样经0.22 μm滤膜过滤或冷冻离心去除杂质后,滤液无需衍生化直接进行定量分析。4种农药通过Metrosep A Supp 5柱（150 mm×4.0 mm,5 μm）分离,以碳酸氢铵-氨水溶液为流动相进行梯度洗脱,在负离子模式下以MRM方式进行检测。结果表明,4种农药在0.50~50.0 μg/L范围内相关系数（r）均大于0.999,线性关系良好,方法检出限为0.05~0.09 μg/L。实际水样在低、中、高3种加标浓度水平下,回收率分别为76.3%~108%、83.0%~107%和87.0%~105%,相对标准偏差分别为2.0%~12.3%、2.4%~5.6%和2.7%~6.8%。使用该方法对海南省34个水样进行测定,其中30个饮用水源地水样中均未检出4种农药,槟榔园附近3个水样均检出草甘膦和氨甲基膦酸,香蕉园附近的1个水样检出草铵膦和氨甲基膦酸。与传统的衍生化方法比较,该方法操作简便,重现性好,准确性高,不受基体干扰,适用于环境水样中草甘膦、氨甲基膦酸、草铵膦及乙烯利的残留检测。     

A study of common discovery dosing formulation components and their potential for causing time-dependent matrix effects in high-performance liquid chromatography tandem mass spectrometry assays

Hydroxyproyl-beta-cyclodextran (HPBCD), methyl cellulose (MC), Tween 80 and PEG400 are commonly used in dosing formulations in pharmacokinetic (PK) studies during the early drug discovery stage. A series of studies was designed to evaluate the potential matrix effects of these dosing vehicles when the samples are assayed by high-performance liquid chromatography combined with tandem mass spectrometry (HPLC/MS/MS). These dosing vehicles were dosed into the rats via either an intravenous (IV) or an oral route (PO) and plasma samples were collected for a 24-h post-dose period. Five test compounds with CLog P values ranging from 0.9 to 5.4 were spiked into the collected rat plasma. After protein precipitation, these samples were analyzed using a generic fast-gradient HPLC/MS/MS method. Three popular mass spectrometers (Thermo-Finnigan Quantum with ESI and APCI, AB-Sciex API 3000 with ESI and APCI, and Waters-Micromass Quattro Ultima with ESI) were used to test these plasma samples. Results indicated that there was no observed matrix effect for all five compounds when 20% HPBCD or 0.4% MC was used as the vehicle in either the IV or the PO route, respectively. In addition, 0.1% Tween 80 dosed either IV or PO caused significant ion suppression (50-80%, compared to results obtained from plasma samples free from vehicles) for compounds that eluted at the beginning of the chromatogram. Also, PEG400 when used in an oral formulation caused significant ion suppression (30-50%) for early eluting compounds. These matrix effects were not only ionization mode (ESI or APCI) dependent, but also source design (Thermo-Finnigan, AB-Sciex or Waters-Micromass) dependent. Overall, the APCI mode proved to be less vulnerable to matrix effects than the ESI mode. Some possible mechanisms of these matrix effects are proposed and simple strategies to avoid these matrix effects are discussed.     

Matrix effects during analysis of plasma samples by electrospray and atmospheric pressure chemical ionization mass spectrometry: practical approaches to their elimination

Some cases of occurrence of matrix effects (mostly ion suppression) in protein-precipitated plasma samples, and their influence on the validity of plasma concentrations and pharmacokinetic parameters, are discussed. The comparison of matrix effects using either electrospray (TurboIonspray, TISP) or atmospheric pressure chemical ionization (APCI) indicated that APCI is less prone to matrix effects. Nevertheless, TISP is usually the first choice of ionization technique since unknown thermally labile metabolites might be present in the plasma samples causing erroneous results. A high impact of ion suppression on the plasma concentrations after intravenous (i.v.) administration was found, depending on the drug formulation (vehicle). Since ion suppression caused significantly lower plasma concentrations (by a factor of up to 5.5) after i.v. dosing, the area under the curve (AUC) was underestimated and the plasma clearance was consequently erroneously high, with an impact on drug candidate selection. By simple stepwise dilution (e.g. 10-fold and 50-fold) of the supernatant of protein-precipitated plasma samples, including all calibration and quality control samples, the matrix effects were recognized and eliminated.     

Matrix suppression and analyte suppression effects of quaternary ammonium salts in matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry: an investigation of suppression mechanism

In the matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI TOF MS) analysis of some quaternary ammonium salts (QASs), very clean spectra of the quaternary ammonium ions were recorded with a strong matrix suppression effect (MSE). The QASs also showed a considerable analyte suppression effect (ASE). It was demonstrated that the MSE and ASE of the QASs can be explained well by the cluster ionization model. According to this model, MALDI ions are formed from charged matrix/analyte clusters. Various analyte ions and matrix ions might coexist in the cluster, and they will compete for the limited number of net charges available. If enough quaternary ammonium ions are present in the cluster, they will take away the net charges, thus resulting in the MSE and ASE. Our results also suggest that ‘the cluster ionization model’ is not in conflict with ‘the theory of ionization via secondary gas‐phase reactions’. The initial MALDI ions produced from charged matrix/analyte clusters will collide with other molecules or ions in the MALDI plume. Depending on the properties of the initial ions and the composition of the MALDI plume, secondary gas‐phase reactions might result from these collisions. The final ions observed are the combined results of ‘cluster ionization’ and ‘ionization via secondary gas‐phase reactions’. Copyright © 2009 John Wiley & Sons, Ltd.     

Determination of ergot alkaloids from grains with UPLC‐MS/MS

A simple and rapid method for determining six ergot alkaloids and four of their respective epimers was developed for rye and wheat. The analytes were extracted from the sample matrix with ACN/ammonium carbonate solution. The extract was purified with a commercial push‐through SPE column (Mycosep^® 150 Ergot). After concentration and filtration steps, the final separation of the analytes was achieved with ultra‐performance LC‐MS/MS. The chromatographic separation of the ergot alkaloids was achieved in 4.5 min. The method performance proved satisfactory in the preliminary validation. The calculated LOQs were low ranging from 0.01 to 1.0 μg/kg for wheat and from 0.01 to 10.0 μg/kg for rye. At the concentration levels of 10, 50 and 200 μg/kg, the recoveries were between 80 and 120% in most cases and the within‐day repeatability (expressed as RSD) ranged between 1.3 and 13.9%. Despite the cleanup of the samples, some matrix effect was observed in the MS, highlighting the necessity of using matrix‐assisted standards. This is the first article to describe the application of the push‐through columns and ultra‐performance LC in the analysis of ergot alkaloids.     

Combating matrix effects in LC/ESI/MS: The extrapolative dilution approach

Liquid chromatography electrospray mass spectrometry - LC/ESI/MS—a primary tool for analysis of low volatility compounds in difficult matrices - suffers from the matrix effects in the ESI ionization. It is well known that matrix effects can be reduced by sample dilution. However, the efficiency of simple sample dilution is often limited, in particular by the limit of detection of the method, and can strongly vary from sample to sample.In this study matrix effect is investigated as the function of dilution. It is demonstrated that in some cases dilution can eliminate matrix effect, but often it is just reduced. Based on these findings we propose a new quantitation method based on consecutive dilutions of the sample and extrapolation of the analyte content to the infinite dilution, i.e. to matrix-free solution.The method was validated for LC/ESI/MS analysis of five pesticides (methomyl, thiabendazole, aldicarb, imazalil, methiocarb) in five matrices (tomato, cucumber, apple, rye and garlic) at two concentration levels (0.5 and 5.0 mg kg⁻¹). Agreement between the analyzed and spiked concentrations was found for all samples. It was demonstrated that in terms of accuracy of the obtained results the proposed extrapolative dilution approach works distinctly better than simple sample dilution.The main use of this approach is envisaged for (a) method development/validation to determine the extent of matrix effects and the ways of overcoming them and (b) as a second step of analysis in the case of samples having analyte contents near the maximum residue limits (MRL).     

固相基底电喷雾电离质谱分析固状与粘稠状药物的基质效应

固状与粘稠状辅剂常用于制造颗粒、片剂、胶囊或膏状药品,并能有效地保持药效成分活性的稳定性。基于固相基底的敞开式电喷雾电离质谱技术已被发展用于药品的直接分析。然而,固状与粘稠状基质对药物分子直接质谱检测的影响规律还不明确。该研究构建了不同黏度和不同溶解度的基质体系,采用木签(牙签)为代表的固相基底电喷雾电离质谱考察了几种模式药物分子在固状与粘稠状基质中的质谱响应规律。结果发现,易溶解的基质电离产生显著的离子干扰和抑制效应,而难溶的基质尽管不产生离子干扰,但在溶剂作用下可变成粘稠状从而抑制药物的离子化。进一步研究表明,药物分子的质谱信号随着基质的黏度增加(1~500 cP)呈幂函数降低(r 2>0.95)。该研究将增进理解固体与粘稠样品直接质谱分析的基质效应与信号响应规律。     

High-performance liquid chromatography coupled to direct analysis in real time mass spectrometry: investigations on gradient elution and influence of complex matrices on signal intensities

Direct analysis in real time (DART) time-of-flight mass spectrometry (TOF-MS) has been tested for its suitability as a detector for gradient elution HPLC. Thereby a strong dependency of signal intensity on the amount of organic solvent present in the eluent could be observed. Adding a make-up liquid (iso-propanol) post-column to the HPLC effluent greatly enhanced detection limits for early eluting compounds. Limits of detection achieved employing this approach were in the range of 7-27 μg L(-1) for the parabene test mixture and 15-87 μg L(-1) for the pharmaceuticals. In further investigations DART ionization was compared to several other widely used atmospheric pressure ionization methods with respect to signal suppression phenomena occurring in when samples with problematic matrices are analyzed. For this purpose extracts from environmental and waste water samples were selected as model matrices which were subsequently spiked with a set of six substances commonly present in personal care products as well as six pharmaceuticals at concentration levels between 100 μg L(-1) and 500 μg L(-1) corresponding to 100 ng L(-1) and 500 ng L(-1) respectively in the original sample. With ionization suppression of less than 11% for most analytes investigated, DART ionization showed similar to even somewhat superior behavior compared to atmospheric pressure chemical ionization (APCI) and atmospheric pressure photo ionization (APPI) for the Danube river water extract; for the more challenging matrix of the sewage plant effluent extract DART provided better results with ion suppression being less than 11% for 9 out of 12 analytes while values for APCI were lying between 20% and >90%. Electrospray ionization (ESI) was much more affected by suppression effects than DART with values between 26% and 80% for Danube river water; in combination with the sewage plant effluent matrix suppression >50% was observed for all analytes.     

Using calibration approaches to compensate for remaining matrix effects in quantitative liquid chromatography/electrospray ionization multistage mass spectrometric analysis of phytoestrogens in aqueous environmental samples

Signal suppression is a common problem in quantitative liquid chromatography/electrospray ionization multistage mass spectrometric (LC/ESI-MS(n)) analysis in environment samples, especially in highly loaded wastewater samples with highly complex matrix. Optimization of sample preparation and improvement of chromatographic separation are prerequisite to improve reproducibility and selectivity. Matrix components are reduced if not eliminated by optimization of sample preparation steps. However, extensive sample preparation may be time-consuming and risk the significant loss of some trace analytes. The best way to further compensate matrix effects is the use of an internal standard for each analyte. However, in a multi-component analysis, finding appropriate internal standards for every analyte is often difficult. In this present study, a more practical alternative option was sought. Matrix effects were assessed using the post-extraction addition method. By comparison of three different calibration approaches, it was found that matrix-matched calibration combined with one internal standard provides a satisfactory method for compensating for any residual matrix effects on all the analytes. Validating experiments on different sewage treatment plant (STP) influent samples analyzing for a range of phytoestrogens showed that this calibration method provided satisfactory results with concentration ratio 96.1-105.7% compared to those by standard addition.     

Effects of common surfactants on protein digestion and matrix-assisted laser desorption/ionization mass spectrometric analysis of the digested peptides using two-layer sample preparation

While surfactants are commonly used in preparing protein samples, their presence in a protein sample can potentially affect the enzymatic digestion process and the subsequent analysis of the resulting peptides by mass spectrometry. The extent of the tolerance of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to surfactant interference in peptide analysis is very much dependent on the matrix/sample preparation method. In this work the effects of four commonly used surfactants, namely n-octyl glucoside (OG), Triton X-100 (TX-100), 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) and sodium dodecyl sulfate (SDS), for biological sample preparation on trypsin digestion and MALDI-MS of the resulting digest are examined in detail within the context of using a two-layer method for MALDI matrix/sample preparation. Non-ionic and mild surfactants, such as OG, TX-100 or CHAPS, are found to have no significant effect on trypsin digestion with surfactant concentrations up to 1%. However, TX-100 and CHAPS interfere with the subsequent peptide analysis by MALDI-MS and should be removed prior to peptide analysis. OG is an MS-friendly surfactant and no effect is observed for MALDI peptide analysis. The effect of SDS on trypsin digestion in terms of the number of peptides generated and the overall protein sequence coverage by these peptides is found to be protein dependent. The use of SDS to solubilize hydrophobic membrane proteins, followed by trypsin digestion in the presence of 0.1% SDS, results in a peptide mixture that can be analyzed directly by MALDI-MS. These peptides are shown to provide better sequence coverage compared with those obtained without the use of SDS in the case of bacteriorhodopsin, a very hydrophobic transmembrane protein. This work illustrates that MALDI-MS with the two-layer sample preparation method can be used for direct analysis of protein digests with no or minimum sample cleanup after proteins are digested in a solution containing surfactants.