Addressing accuracy and precision issues in iTRAQ quantitation

iTRAQ (isobaric tags for relative or absolute quantitation) is a mass spectrometry technology that allows quantitative comparison of protein abundance by measuring peak intensities of reporter ions released from iTRAQ-tagged peptides by fragmentation during MS/MS. However, current data analysis techniques for iTRAQ struggle to report reliable relative protein abundance estimates and suffer with problems of precision and accuracy. The precision of the data is affected by variance heterogeneity: low signal data have higher relative variability; however, low abundance peptides dominate data sets. Accuracy is compromised as ratios are compressed toward 1, leading to underestimation of the ratio. This study investigated both issues and proposed a methodology that combines the peptide measurements to give a robust protein estimate even when the data for the protein are sparse or at low intensity. Our data indicated that ratio compression arises from contamination during precursor ion selection, which occurs at a consistent proportion within an experiment and thus results in a linear relationship between expected and observed ratios. We proposed that a correction factor can be calculated from spiked proteins at known ratios. Then we demonstrated that variance heterogeneity is present in iTRAQ data sets irrespective of the analytical packages, LC-MS/MS instrumentation, and iTRAQ labeling kit (4-plex or 8-plex) used. We proposed using an additive-multiplicative error model for peak intensities in MS/MS quantitation and demonstrated that a variance-stabilizing normalization is able to address the error structure and stabilize the variance across the entire intensity range. The resulting uniform variance structure simplifies the downstream analysis. Heterogeneity of variance consistent with an additive-multiplicative model has been reported in other MS-based quantitation including fields outside of proteomics; consequently the variance-stabilizing normalization methodology has the potential to increase the capabilities of MS in quantitation across diverse areas of biology and chemistry.

LC-MS/MS quantitative determination of tetrapterys mucronata alkaloids, a plant occasionally used in ayahuasca preparation

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Neutron activation analysis for assessing chemical composition of dry dog foods

Brazil holds the second largest population of domestic dogs in the world, with 33 million dogs, only behind the United States. The annual consumption of dog food in the country is 1.75 million tons, corresponding to the World's sixth in trade turnover. Dog food is supposed to be a complete and balanced diet, formulated with high quality ingredients. All nutrients and minerals required for an adequate nutrition of dogs are added to the formulation to ensure longevity and welfare. In this context, the present study aimed at assessing the chemical composition of dry dog foods commercialized in Brazil. Thirty-four samples were acquired in the local market of Piracicaba and analyzed by instrumental neutron activation analysis (INAA) to determine the elements As, Br, Ca, Co, Cr, Cs, Fe, K, La, Na, Rb, Sb, Sc, Se, U, and Zn. In general, the concentrations of Ca, Fe, K, Na, and Zn complied with the values required by the Association of American Feed Control Officials (AAFCO). To evaluate the safety of dog food commercialized in Brazil, further investigation is necessary to better understand the presence of toxic elements found in this study, i.e. Sb and U. INAA was useful for the screening analysis of different types and brands of dry dog foods for the determination of both essential and toxic elements.

Investigation of the composition of linear alkylbenzenes with emphasis on the identification and quantitation of some trace compounds using GS/MS system in both electron impact and chemical ionization modes

Linear alkylbenzenes, LAB, formed by the Alel3 or HF catalyzed alkylation of benzene are common raw materials for surfactant manufacture. Normally they are sulphonated using S03 or oleum to give the corresponding linear alkylbenzene sulphonates In >95 % yield. As concern has grown about the environmental impact of surfactants,' questions have been raised about the trace levels of unreacted raw materials, linear alkylbenzenes and minor impurities present in them. With the advent of modem analytical instruments and techniques, namely GCIMS, the opportunity has arisen to identify the exact nature of these impurities and to determine the actual levels of them present in the commercial linear ,alkylbenzenes. The object of the proposed study was to separate, identify and quantify major and minor components (1-10%) in commercial linear alkylbenzenes. The focus of this study was on the structure elucidation and determination of impurities and on the qualitative determination of them in all analyzed linear alkylbenzene samples. A gas chromatography/mass spectrometry, (GCIMS) study was performed o~ five samples from the same manufacturer (different production dates) and then it was followed by the analyses of ten commercial linear alkylbenzenes from four different suppliers. All the major components, namely linear alkylbenzene isomers, followed the same elution pattern with the 2-phenyl isomer eluting last. The individual isomers were identified by interpretation of their electron impact and chemical ionization mass spectra. The percent isomer distribution was found to be different from sample to sample. Average molecular weights were calculated using two methods, GC and GCIMS, and compared with the results reported on the Certificate of Analyses (C.O.A.) provided by the manufacturers of commercial linear alkylbenzenes. The GC results in most cases agreed with the reported values, whereas GC/MS results were significantly lower, between 0.41 and 3.29 amu. The minor components, impurities such as branched alkylbenzenes and dialkyltetralins eluted according to their molecular weights. Their fragmentation patterns were studied using electron impact ionization mode and their molecular weight ions confirmed by a 'soft ionization technique', chemical ionization. The level of impurities present i~ the analyzed commercial linear alkylbenzenes was expressed as the percent of the total sample weight, as well as, in mg/g. The percent of impurities was observed to vary between 4.5 % and 16.8 % with the highest being in sample "I". Quantitation (mg/g) of impurities such as branched alkylbenzenes and dialkyltetralins was done using cis/trans-l,4,6,7-tetramethyltetralin as an internal standard. Samples were analyzed using .GC/MS system operating under full scan and single ion monitoring data acquisition modes. The latter data acquisition mode, which offers higher sensitivity, was used to analyze all samples under investigation for presence of linear dialkyltetralins. Dialkyltetralins were reported quantitatively, whereas branched alkylbenzenes were reported semi-qualitatively. The GC/MS method that was developed during the course of this study allowed identification of some other trace impurities present in commercial LABs. Compounds such as non-linear dialkyltetralins, dialkylindanes, diphenylalkanes and alkylnaphthalenes were identified but their detailed structure elucidation and the quantitation was beyond the scope of this study. However, further investigation of these compounds will be the subject of a future study.

High precision and selectivity for quantitation of enrofloxacin and ciprofloxacin in five chicken tissues using solid phase extraction and ESI LC-MS/MS for application in monitoring residues

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Development of an LC-MS/MS method for the quantitation of 55 compounds prescribed in combined cardiovascular therapy

This paper reports an LC-MS/MS method with positive electrospray ionization for the screening of commonly prescribed cardiovascular drugs in human plasma, including compounds with antihypertensive (57), antidiabetic (12), hypolipemiant (5), anticoagulant (2) and platelet anti-aggregation (2) effects. Sample treatment consisted of a simple protein precipitation with MeOH/0.1 M ZnSO₄ (4:1, v/v) solution after the addition of internal standard, followed by evaporation and reconstitution. Analytes separation was performed on a Polar-RP column (150 m x 2 mm, 4 μm) using a gradient elution of 15 min. The MS system was operated in MRM mode, monitoring one quantitation and one confirmation transition for each analyte. The recovery of the protein precipitation step ranged from 50 to 70% for most of the compounds, while some were considerably affected by matrix effects. Since several analytes fulfilled the linearity, accuracy and precision values required by the ICH guidelines, the method proved to be suitable for their quantitative analysis. The limits of quantitation varied from 0.38 to 9.1 μg/L and the limits of detection from 0.12 to 5.34 μg/L. The method showed to be suitable for the detection of plasma samples of patients under cardiovascular treatment with the studied drugs, and for 55 compounds reliable quantitative results could be obtained.

Determination of free fatty acids in soil and bryophyte plants by precolumn derivatization via HPLC with fluorescence detection and tandem mass spectrometry (HPLC-MS/MS)

A sensitive method for the determination of 30 kinds of free fatty acids (FFAs, C-1-C-30) with 1-[2-(p-toluenesulfonate)-ethyl]-2-phenylimidazole-[4,5-f] 9,10-phenan- threne (TSPP) as labeling reagent and using high performance liquid chromatography with fluorescence detection and identification by online postcolumn mass spectrometry with atmospheric pressure chemical ionization (APCI) source in positive-ion mode (HPLC/MS/APCI) has been developed. TSPP could easily and quickly label FFAs in the presence of K2CO3 catalyst at 90 degrees C for 30 min in N,N-dimethylformamide (DMF) solvent, and maximal labeling yields close to 100% were observed with a 5-fold excess of molar reagent. Derivatives were stable enough to be efficiently analyzed by high performance liquid chromatography. TSPP was introduced into fatty acid molecules and effectively augmented MS ionization of fatty acid derivatives and led to regular MS and MS/MS information. The collision induced cleavage of protonated molecular ions formed specific fragment ions at m/z [MH](+)(molecular ion), m/z [M'+CH2CH2](+)(M' was molecular mass of the corresponding FFA) and m/z 295.0 (the, mass of protonated molecular core structure of TSPP). Fatty acid derivatives were separated on a reversed-phase Eclipse XDB-C-8 column (4.6 x 150 mm, 5 mu m, Agilent) with a good baseline resolution in combination with a gradient elution. Linear ranges of 30 FFAs are 2.441 x 10(-3) to 20 mu mol/L, detection limits are 3.24 similar to 36.97 fmol (injection volume 10 mu L, at a signal-to-noise ratio of 3, S/N 3:1). The mean interday precision ranged from 93.4 to 106.2% with the largest mean coefficients of variation (R.S.D.) < 7,5%. The mean intraday precision for all standards was < 6.4% of the expected concentration. Excellent linear responses were observed with correlation coefficients of > 0.9991. Good compositional data could be obtained from the analysis of extracted fatty acids from as little as 200 mg of bryophyte plant samples.Therefore, the facile TSPP derivatization coupled with HPLC/MS/APCI analysis allowed the development of a highly sensitive method for the quantitation of trace levels of short and long chain fatty acids from biological and natural environmental samples.

Determination of long-chain fatty acids in bryophyte plants extracts by HPLC with fluorescence detection and identification with MS

A sensitive method for the determination of long-chain fatty acids (LCFAs) (>C20) using 1-[2-(p-toluenesulfonate)-ethyl]-2-phenylimidazole-[4.5-f]-9,10-phenanthrene (TSPP) as tagging reagent with fluorescence detection and identification with post-column APCI/MS has been developed. The LCFAs in bryophyte plant samples were obtained based on distillation extraction with 1: 1 (v/v) chloroform/methanol as extracting solvent. TSPP could easily and quickly label LCFAs at 90 degrees C in the presence of K2CO3 catalyst in DMF. Eleven free LCFAs from the extracts of bryophyte plants were sensitively determined. Maximal labeling yields close to 100% were observed with a five-fold excess of molar reagent. Separation of the derivatized fatty acids exhibited a good baseline resolution in combination with a gradient elution on a reversed-phase Eclipse XDB-C-8 column. Calculated detection limits from 1.0 pmol injection, at a signal-to-noise ratio of 3, were 26.19-76.67 fmol. Excellent linear responses were observed with coefficients of >0.9996. Good compositional data were obtained from the analysis of the extracted LCFAs containing as little as 0.2 g of bryophyte plant samples. Therefore, the facile TSPP derivatization coupled with HPLC/APCI/MS analysis allowed the development of a highly sensitive method for the quantitation of trace levels of LCFAs from biological and natural environmental samples. (c) 2006 Elsevier B.V. All rights reserved.

Validation of an ultra high performance liquid chromatography-tandem mass spectrometry method for detection and quantitation of 19 endocrine disruptors in milk

An endocrine disruptor (ED) is an exogenous compound that interferes with the body's endocrine system. Exposure to EDs may result in adverse health effects such as infertility and cancer. EDs are composed of a vast group of chemicals including compounds of natural origin such as phytoestrogens or mycotoxins and a wide range of man-made chemicals such as pesticides. Synthetic compounds may find their way into the food chain where a number of them can biomagnify. Additionally, processing activities and food contact materials may add further to the already existing pool of food contaminants. Thus, our diet is considered to be one of the main exposure routes to EDs. Some precautionary legislation has already been introduced to control production and/or application of some persistent organic pollutants with ED characteristics. However, newly emerging EDs with bioaccumulative properties have recently been reported to appear at lower tiers of the food chain but have not been monitored at the grander scale. Milk and dairy products are a major component of our diet, thus it is important to monitor them for EDs. However, most methods developed to date are devoted to one group of compounds at a time. The UHPLC-MS/MS method described here has been validated according to EC decision 2002/657/EC and allows simultaneous extraction, detection, quantitation and confirmation of 19 EDs in milk. The method calibration range is between 0.50 and 20.0 μg kg with coefficients of determination above 0.99 for all analytes. Precision varied from 4.7% to 23.4% in repeatability and reproducibility studies. Established CCα and CCβ values (0.11-0.67 μg kg) facilitate fast, reliable, quantitative and confirmatory analysis of sub μg kg levels of a range of EDs in milk.

Determination of the Mycotoxin Content in Distiller's Dried Grain with Solubles Using a Multianalyte UHPLC-MS/MS Method

There are more than 300 potential mycotoxins that can contaminate food and feed and cause adverse effects in humans and animals. The data on the co-occurrence of mycotoxins in novel animal feed materials, such as distiller's dried grain with solubles (DDGS), are limited. Thus, a UHPLC-MS/MS method for the quantitation of 77 mycotoxins and other fungal metabolites was used to analyze 169 DDGS samples produced from wheat, maize, and barley and 61 grain samples. All DDGS samples analyzed were contaminated with 13-34 different mycotoxins. Fumonisins were present in all 52 maize DDGS samples (81.0-6890 μg/kg for fumonisin B1), and deoxynivalenol was present in all 99 wheat DDGS samples (39.3-1120 μg/kg). A number of co-occurring mycotoxins were also identified. Due to the high co-occurrence of mycotoxins, routine screening of the animal feed ingredients is highly recommended to allow the highlighted risks to be effectively managed.

Fully automated software solution for protein quantitation by global metabolic labeling with stable isotopes

Metabolic stable isotope labeling is increasingly employed for accurate protein (and metabolite) quantitation using mass spectrometry (MS). It provides sample-specific isotopologues that can be used to facilitate comparative analysis of two or more samples. Stable Isotope Labeling by Amino acids in Cell culture (SILAC) has been used for almost a decade in proteomic research and analytical software solutions have been established that provide an easy and integrated workflow for elucidating sample abundance ratios for most MS data formats. While SILAC is a discrete labeling method using specific amino acids, global metabolic stable isotope labeling using isotopes such as (15)N labels the entire element content of the sample, i.e. for (15)N the entire peptide backbone in addition to all nitrogen-containing side chains. Although global metabolic labeling can deliver advantages with regard to isotope incorporation and costs, the requirements for data analysis are more demanding because, for instance for polypeptides, the mass difference introduced by the label depends on the amino acid composition. Consequently, there has been less progress on the automation of the data processing and mining steps for this type of protein quantitation. Here, we present a new integrated software solution for the quantitative analysis of protein expression in differential samples and show the benefits of high-resolution MS data in quantitative proteomic analyses.

Rapid qualitative and quantitative analysis of proanthocyanidin oligomers and polymers by UPLC-MS/MS.

This paper presents the development of a rapid method with ultraperformance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) for the qualitative and quantitative analyses of plant proanthocyanidins directly from crude plant extracts. The method utilizes a range of cone voltages to achieve the depolymerization step in the ion source of both smaller oligomers and larger polymers. The formed depolymerization products are further fragmented in the collision cell to enable their selective detection. This UPLC-MS/MS method is able to separately quantitate the terminal and extension units of the most common proanthocyanidin subclasses, that is, procyanidins and prodelphinidins. The resulting data enable (1) quantitation of the total proanthocyanidin content, (2) quantitation of total procyanidins and prodelphinidins including the procyanidin/prodelphinidin ratio, (3) estimation of the mean degree of polymerization for the oligomers and polymers, and (4) estimation of how the different procyanidin and prodelphinidin types are distributed along the chromatographic hump typically produced by large proanthocyanidins. All of this is achieved within the 10 min period of analysis, which makes the presented method a significant addition to the chemistry tools currently available for the qualitative and quantitative analyses of complex proanthocyanidin mixtures from plant extracts.

Assessing melatonin and its oxidative metabolites amounts in biological fluid and culture medium by liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)