Fluorogenic Derivatization Reagents Suitable for Isolation and Identification of Cysteine-Containing Proteins Utilizing High-Performance Liquid Chromatography−Tandem Mass Spectrometry

The Ginsenoside Rg1 Rescues Mitochondrial Disorders in Aristolochic Acid-Induced Nephropathic Mice

Chronic exposure to aristolochic acid (AA) leads to renal interstitial fibrosis and nephropathy. In this study, we aimed to investigate the renoprotective effects of Panax ginseng extract (GE) and ginsenoside saponin (GS) on AA-induced nephropathy (AAN) in mice. Eighty female C3H/He mice were randomly divided into eight groups, including normal; AA (3 μg/mL for 56 days); AA with GE (125, 250, or 500 mg/kg/d for 14 days); and AA with important GE ingredients, Rg₁, Rb₁, or Rd (5 mg/kg/d for 14 days). Compared with the AA group, renal injuries were significantly decreased in the GE (250 mg/kg/d), Rb₁, and Rg₁ treatment groups. Rg₁ exhibited the best renoprotection among all GS-treated groups. There were 24 peaks significantly altered among normal, AA, and AA + Rg₁ groups, and four mitochondrial proteins were identified, including acyl-CoA synthetase medium-chain family member 2, upregulated during skeletal muscle growth 5 (Usmg5), mitochondrial aconitase 2 (ACO2), and cytochrome c oxidase subunit Va preprotein (COX5a). We demonstrated for the first time that the AAN mechanism and renoprotective effects of Rg₁ are associated with expression of mitochondrial proteins, especially ACO2, Usmg5, and COX5a.

Recent Progress in FD-LC-MS/MS Proteomics Method

Through the course of our bio-analytical chemistry studies, we developed a novel proteomics analysis method, FD-LC-MS/MS (fluorogenic derivatization-liquid chromatography-tandem mass spectrometry). This method consists of fluorogenic derivatization (FD), LC separation, and detection/quantification of the derivatized proteins, followed by isolation, tryptic digestion of the isolated proteins, and final identification of the isolated proteins using electrospray ionization nano-LC-MS/MS of the generated peptide mixtures with a probability-based protein identification algorithm. In this review, we will present various examples where this method has been used successfully to identify expressed proteins in individual human cells. FD-LC-MS/MS is also suitable for differential proteomics analysis. Here, two biological samples are treated by the same steps mentioned above, and the two chromatograms obtained are compared to identify peaks with different intensities (variation in protein levels). Associated peak fractions are then isolated, and the differentially expressed proteins between the two samples are identified by LC-MS/MS. Several biomarkers for cancers have been identified by FD-LC-MS/MS. For more efficient separation, nano-flow LC with a phenyl-bonded monolithic silica-based capillary column was adopted for cell-expressed intact protein analysis. The derivatized human cell proteins (K562) and yeast cell (Saccharomyces cerevisiae) proteins as model intact cell proteins were analyzed by nano-flow LC with fluorescence detection. More than 1,300 protein peaks were separated/detected from both cells. For straightforward comparison of multiple peak separation profiles, a novel type of chromatogram display, termed the “spiderweb” chromatogram, was developed. A nano-LC-FD-LC-mass spectrometry trial for molecular weight estimation of FD proteins has also been conducted.

Serum Albumin Redox States: More Than Oxidative Stress Biomarker

Serum albumin is the most abundant circulating protein in mammals including humans. It has three isoforms according to the redox state of the free cysteine residue at position 34, named as mercaptalbumin (reduced albumin), non-mercaptalbumin-1 and -2 (oxidized albumin), respectively. The serum albumin redox state has long been viewed as a biomarker of systemic oxidative stress, as the redox state shifts to a more oxidized state in response to the severity of the pathological condition in various diseases such as liver diseases and renal failures. However, recent ex vivo studies revealed oxidized albumin per se could aggravate the pathological conditions. Furthermore, the possibility of the serum albumin redox state as a sensitive protein nutrition biomarker has also been demonstrated in a series of animal studies. A paradigm shift is thus ongoing in the research field of the serum albumin. This article provides an updated overview of analytical techniques for serum albumin redox state and its association with human health, focusing on recent findings.

Phenyl-bonded monolithic silica capillary column liquid chromatographic separation and detection of fluorogenic derivatized intact proteins

Prior to the identification of proteins for proteomics analysis in human cells, separation of fluorogenic derivatized proteins with a fluorogenic reagent, 7-chloro-N-[2-(dimethylamino)ethyl]-2,1,3-benzoxadiazole-4-sulfonamide, has typically been performed by using a conventional reversed-phase HPLC column. However, the number of proteins in human cells (HepaRG) that are separated by this conventional approach is limited to approximately 500. In this study, a nanoflow liquid chromatography system with an evaluated phenyl-bonded monolithic silica capillary column (0.1 mm i.d., 700 mm length) was used to increase the number of separated fluorogenic derivatized proteins. This system was used to separate derivatized human cell proteins (K562) and yeast (Saccharomyces cerevisiae) proteins as model cell proteomes. More than 1,300 protein peaks were separated/detected from both cell proteomes. We present a straightforward comparison of multiple separation profiles using a novel chromatogram display approach, termed the "spiderweb" chromatogram. In addition, to validate that the detected peaks are derived from proteins, a mass spectrometer was connected to the capillary column and deconvolution of the obtained mass spectra was performed. Furthermore, different molecular weight distribution profiles of the expressed proteins were observed between the two cell proteomes.

Recent Research in Ocular Cystinosis: Drug Delivery Systems, Cysteamine Detection Methods and Future Perspectives

Cystinosis is a rare genetic disorder characterized by the accumulation of cystine crystals in different tissues and organs. Although renal damage prevails during initial stages, the deposition of cystine crystals in the cornea causes severe ocular manifestations. At present, cysteamine is the only topical effective treatment for ocular cystinosis. The lack of investment by the pharmaceutical industry, together with the limited stability of cysteamine, make it available only as two marketed presentations (Cystaran® and Cystadrops®) and as compounding formulations prepared in pharmacy departments. Even so, new drug delivery systems (DDSs) need to be developed, allowing more comfortable dosage schedules that favor patient adherence. In the last decades, different research groups have focused on the development of hydrogels, nanowafers and contact lenses, allowing a sustained cysteamine release. In parallel, different determination methods and strategies to increase the stability of the formulations have also been developed. This comprehensive review aims to compile all the challenges and advances related to new cysteamine DDSs, analytical determination methods, and possible future therapeutic alternatives for treating cystinosis.

Challenges for cysteamine stabilization, quantification, and biological effects improvement

The aminothiol cysteamine, derived from coenzyme A degradation in mammalian cells, presents several biological applications. However, the bitter taste and sickening odor, chemical instability, hygroscopicity, and poor pharmacokinetic profile of cysteamine limit its efficacy. The use of encapsulation systems is a good methodology to overcome these undesirable properties and improve the pharmacokinetic behavior of cysteamine. Besides, the conjugation of cysteamine to the surface of nanoparticles is generally proposed to improve the intra-oral delivery of cyclodextrin-drug inclusion complexes, as well as to enhance the colorimetric detection of compounds by a gold nanoparticle aggregation method. On the other hand, the detection and quantification of cysteamine is a challenging mission due to the lack of a chromophore in its structure and its susceptibility to oxidation before or during the analysis. Derivatization agents are therefore applied for the quantification of this molecule. To our knowledge, the derivatization techniques and the encapsulation systems used for cysteamine delivery were not reviewed previously. Thus, this review aims to compile all the data on these methods as well as to provide an overview of the various biological applications of cysteamine focusing on its skin application.

Effect of prednisolone on glyoxalase 1 in an inbred mouse model of aristolochic acid nephropathy using a proteomics method with fluorogenic derivatization-liquid chromatography-tandem mass spectrometry

Prednisolone is involved in glucose homeostasis and has been used for treatment for aristolochic acid (AA) nephropathy (AAN), but its effect on glycolysis in kidney has not yet been clarified. This study aims to investigate the effect in terms of altered proteins after prednisolone treatment in a mice model of AAN using a proteomics technique. The six-week C3H/He female mice were administrated AA (0.5 mg/kg/day) for 56 days. AA+P group mice were then given prednisolone (2 mg/kg/day) via oral gavage for the next 14 days, and AA group mice were fed water instead. The tubulointerstitial damage was improved after prednisolone treatment comparing to that of AA group. Kidney homogenates were harvested to perform the proteomics analysis with fluorogenic derivatization-liquid chromatography-tandem mass spectrometry method (FD-LC-MS/MS). On the other hand, urinary methylglyoxal and D-lactate levels were determined by high performance liquid chromatography with fluorescence detection. There were 47 altered peaks and 39 corresponding proteins on day 14 among the groups, and the glycolysis-related proteins, especially glyoxalase 1 (GLO1), fructose-bisphosphate aldolase B (aldolase B), and triosephosphate isomerase (TPI), decreased in the AA+P group. Meanwhile, prednisolone decreased the urinary amount of methylglyoxal (AA+P: 2.004 ± 0.301 μg vs. AA: 2.741 ± 0.630 μg, p < 0.05), which was accompanied with decrease in urinary amount of D-lactate (AA+P: 54.07 ± 5.45 μmol vs. AA: 86.09 ± 8.44 μmol, p < 0.05). Prednisolone thus alleviated inflammation and interstitial renal fibrosis. The renal protective mechanism might be associated with down-regulation of GLO1 via reducing the contents of methylglyoxal derived from glycolysis. With the aid of proteomics analysis and the determination of methylglyoxal and its metabolite-D-lactate, we have demonstrated for the first time the biochemical efficacy of prednisolone, and urinary methylglyoxal and its metabolite-D-lactate might be potential biomarkers for AAN.

[Clinical Pharmaceutical Research Based on New Proteome Analysis Based on Chromatographic Separation]

Comprehensive identification of antigens in immune complexes (IC-antigens) is beneficial to provide insights into pathophysiology and could form the basis for novel diagnostic and treatment strategies for many immune-related diseases. Immune complexome analysis is a method for comprehensively identifying and profiling IC-antigens in biological fluids (such as serum and cerebrospinal fluid). We applied this strategy to the analysis of circulating ICs in autoimmune diseases (rheumatoid arthritis, Sjögren's syndrome, systemic scleroderma, and systemic lupus erythematosus), infectious diseases, and cancers. Fluorogenic derivatization-liquid chromatography-tandem mass spectrometry (FD-LC-MS/MS) consists of fluorogenic derivatization of proteins, followed by HPLC of the derivatized proteins, isolation of the proteins differentially expressed in a certain group, enzymatic digestion of the isolated proteins followed by LC-tandem MS using a database-searching algorithm for protein identification. We have applied this method to understand the cardioprotective effect of pre-administration of docetaxel in adriamycin/docetaxel combination anti-cancer therapy, and the cellular processes that are affected by non-steroidal anti-inflammatory drugs (NSAIDs) in mouse stomach tissue during ulcer formation.

Proteomic analysis and ATP assay reveal a positive effect of artificial cerebral spinal fluid perfusion following microdialysis sampling on repair of probe-induced brain damage

BACKGROUND

Microdialysis (MD) is conventionally used to measure the in vivo levels of various substances and metabolites in extracellular and cerebrospinal fluid of brain. However, insertion of the MD probe and subsequent perfusion to obtain samples cause damage in the vicinity of the insertion site, raising questions regarding the validity of the measurements.

NEW METHOD

We used fluorogenic derivatization liquid chromatography-tandem mass spectrometry, that quantifies both high and low abundance proteins, to differentiate the effects of perfusion from the effects of probe insertion on the proteomic profiles of expressed proteins in rat brain.

RESULTS

We found that the expression levels of five proteins were significantly lower in the perfusion group than in the non-perfusion group. Three of these proteins are directly involved in ATP synthesis. In contrast to decreased levels of the three proteins involved in ATP synthesis, ATP assays show that perfusion, following probe insertion, even for a short time (3 h) increased ATP level up to 148% that prior to perfusion, and returned it to normal state (before probe insertion).

COMPARISON WITH EXISTING METHOD

There is essentially no information regarding which observed changes are due to probe insertion and which to perfusion.

CONCLUSIONS

Our findings partially demonstrate that the influence of whole MD sampling process may not significantly compromise brain function and subsequent analytical results may have physiological equivalence to normal, although energy production is transiently damaged by probe insertion.

Proteomics analysis of altered proteins in kidney of mice with aristolochic acid nephropathy using the fluorogenic derivatization-liquid chromatography-tandem mass spectrometry method

Aristolochic acid (AA) causes interstitial renal fibrosis, called aristolochic acid nephropathy (AAN). There is no specific indicator for diagnosing AAN, so this study aimed to investigate the biomarkers for AAN using a proteomics method. The C3H/He female mice were given ad libitum AA-distilled water (0.5 mg/kg/day) and distilled water for 56 days in the AA and normal groups, respectively. The AA-induced proteins in the kidney were investigated using a proteomics study, including fluorogenic derivatization with 7-chloro-N-[2-(dimethylamino)ethyl]-2,1,3-benzoxadiazole-4-sulfonamide, followed by high-performance liquid chromatography analysis and liquid chromatography tandem mass spectrometry with a MASCOT database searching system. There were two altered proteins, thrombospondin type 1 (TSP1) and G protein-coupled receptor 87 (GPR87), in the kidney of AA-group mice on day 56. GPR87, a tumorigenesis-related protein, is reported for the first time in the current study. The renal interstitial fibrosis was certainly induced in the AA-group mice under histological examination. Based on the results of histological examination and the proteomics study, this model might be applied to AAN studies in the future. TSP1 might be a novel biomarker for AAN, and the further role of GPR87 leading to AA-induced tumorigenesis should be researched in future studies.

Readily functionalizable phosphonium-tagged fluorescent coumarins for enhanced detection of conjugates by mass spectrometry

Fluorescent coumarins are an important class of small-molecule organic fluorophores ubiquitous in different well-established and emerging fields of research including, among others, biochemistry and chemical biology. The present work aims at covering the poor detectability of coumarin-based conjugates by mass spectrometry while keeping important photophysical properties of the coumarin core. In this context, the synthesis of readily functionalizable phosphonium-tagged coumarin derivatives enabling a dual mass-tag and fluorescence labelling of analytes or (bio)molecules of interest through a single-step protocol, is reported. The utility of these coumarins is illustrated through the preparation of fluorogenic substrates that facilitated identification of the peptide fragment released by specific proteolytic cleavages.

Structural and functional insights into S-thiolation of human serum albumins

Human serum albumin (HSA) is the most abundant serum protein, contributing to the maintenance of redox balance in the extracellular fluids. One single free cysteine residue at position 34 is believed to be a target of oxidation. However, the molecular details and functions of oxidized HSAs remain obscure. Here we analyzed serum samples from normal subjects and hyperlipidemia patients and observed an enhanced S-thiolation of HSA in the hyperlipidemia patients as compared to the control individuals. Both cysteine and homocysteine were identified as the low molecular weight thiols bound to the HSAs. Intriguingly, S-thiolations were observed not only at Cys34, but also at multiple cysteine residues in the disulfide bonds of HSA. When the serum albumins from genetically modified mice that exhibit high levels of total homocysteine in serum were analyzed, we observed an enhanced S-homocysteinylation at multiple cysteine residues. In addition, the cysteine residues in the disulfide bonds were also thiolated in recombinant HSA that had been treated with the disulfide molecules. These findings and the result that S-homocysteinylation mediated increased surface hydrophobicity and ligand binding activity of HSA offer new insights into structural and functional alternation of serum albumins via S-thiolation.

A proteomics method using immunoaffinity fluorogenic derivatization-liquid chromatography/tandem mass spectrometry (FD-LC-MS/MS) to identify a set of interacting proteins

Biological functions in organisms are usually controlled by a set of interacting proteins, and identifying the proteins that interact is useful for understanding the mechanism of the functions. Immunoprecipitation is a method that utilizes the affinity of an antibody to isolate and identify the proteins that have interacted in a biological sample. In this study, the FD-LC-MS/MS method, which involves fluorogenic derivatization followed by separation and quantification by HPLC and finally identification of proteins by HPLC-tandem mass spectrometry, was used to identify proteins in immunoprecipitated samples, using heat shock protein 90 (HSP90) as a model of an interacting protein in HepaRG cells. As a result, HSC70 protein, which was known to form a complex with HSP90, was isolated, together with three different types of HSP90-beta. The results demonstrated that the proposed immunoaffinity-FD-LC-MS/MS method could be useful for simultaneously detecting and identifying the proteins that interact with a certain protein.

Straightforward proteomic analysis reveals real dynamics of proteins in cells

To reveal real dynamics of proteins in cells, we have developed a novel type of straightforward proteomic analysis named FD-LC-MS/MS. This technique consists of fluorogenic derivatization (FD) of intact proteins, followed by high performance liquid chromatographic (LC) separation, detection and quantification of the derivatized proteins, isolation of the subject proteins, enzymatic digestion of the isolated proteins, and identification of the proteins using HPLC and MS/MS with a database-searching algorithm. The method is uncomplicated, sensitive, reproducible, and easily quantifies and identifies intact proteins in tissues and cells. Additionally, in contrast to other proteomic approaches, our method does not require any pretreatment steps, such as precipitation and clean-up, except for the derivatization, resulting in high reproducibility and the same or higher detectability than that of other methods. In this article, after a brief review of other types of proteomic analyses, we introduce the development and application of the FD-LC-MS/MS method. We also discuss the features and perspectives of this method.

Drug absorption efficiency in Caenorhbditis elegans delivered by different methods

BACKGROUND

Caenorhbditis elegans has being vigorously used as a model organism in many research fields and often accompanied by administrating with various drugs. The methods of delivering drugs to worms are varied from one study to another, which make difficult in comparing results between studies.

METHODOLOGY/PRINCIPAL FINDINGS

We evaluated the drug absorption efficiency in C. elegans using five frequently used methods with resveratrol with low aqueous solubility and water-soluble 5-Fluoro-2'-deoxyuridine (FUDR) as positive compounds. The drugs were either applied to the LB medium with bacteria OP50, before spreading onto Nematode Growth Medium (NGM) plates (LB medium method), or to the NGM with live (NGM live method) or dead bacteria (NGM dead method), or spotting the drug solution to the surface of plates directly (spot dead method), or growing the worms in liquid medium (liquid growing method). The concentration of resveratrol and FUDR increased gradually within C. elegans and reached the highest during 12 hours to one day and then decreased slowly. At the same time point, the higher the drug concentration, the higher the metabolism rate. The drug concentrations in worms fed with dead bacteria were higher than with live bacteria at the same time point. Consistently, the drug concentration in medium with live bacteria decreased much faster than in medium with dead bacteria, reach to about half of the original concentration within 12 hours.

CONCLUSION

Resveratrol with low aqueous solubility and water-soluble FUDR have the same absorption and metabolism pattern. The drug metabolism rate in worms was both dosage and time dependent. NGM dead method and liquid growing method achieved the best absorption efficiency in worms. The drug concentration within worms was comparable with that in mice, providing a bridge for dose translation from worms to mammals.

Comprehensive fluorogenic derivatization-liquid chromatography/tandem mass spectrometry proteomic analysis of colorectal cancer cell to identify biomarker candidate

Existing colorectal cancer biomarkers are insufficient for providing a quick and accurate diagnosis, which is critical for a good prognosis. More appropriate biomarkers are thus needed. To identify new colorectal cancer biomarker candidates, we conducted a comprehensive differential proteomic analysis of six cancer cell lines and a normal cell line, utilizing a fluorogenic derivatization-liquid chromatography-tandem mass spectrometry (FD-LC-MS/MS) approach. Two sets of intracellular biomarker candidates were identified: one for colorectal cancer, and the other for metastatic colorectal cancer. Our results suggest that cooperative expression of FABP5 and cyclophilin A might be linked to Her2 signaling. Upregulation of LDHB and downregulation of GAPDH suggest the existence of a specific nonglycolytic energy production pathway in metastatic colorectal cancer cells. Downregulation of 14-3-3ζ/δ, cystatin-B, Ran and thioredoxin could be a result of their secretion, which then stimulates metastasis via activity in the sera and ascitic fluids. We propose a possible flow scheme to describe the dynamics of protein expression in colorectal cancer cells leading to tumor progression and metastasis via cell proliferation, angiogenesis, disorganization of actin filaments and epithelial-mesenchymal transition. Our results suggest that colorectal tumor progression may be regulated by signaling mediated by Her2, hypoxia, and TGFβ.

Proteome analysis of altered proteins in streptozotocin-induced diabetic rat kidney using the fluorogenic derivatization-liquid chromatography-tandem mass spectrometry method

To find new molecular markers for early diagnosis of diabetic nephropathy, we applied fluorogenic derivatization-liquid chromatography-tandem mass spectrometry to identify the differentially expressed proteins in the kidney of control and streptozotocin-induced diabetic rats. The Sprague-Dawley rats were injected with the sodium citrate buffer or streptozotocin and then killed after 1, 4, 12 and 24 weeks. The results showed that seven proteins were significantly changed after 1 week of injection. Only one protein had significantly changed after 4 weeks of injection. However, after 12 weeks of injection, the number of altered proteins rose to 10. After 24 weeks of injection, 18 proteins had altered significantly. Five common proteins were significantly altered at week 12 and 24 after injection, respectively. Importantly, these proteins appeared prior to microalbuminuria and may serve as new biomarkers that are able to improve early detection of and new drug development for diabetic-related nephropathy.

Toxicoproteomic analysis of a mouse model of nonsteroidal anti-inflammatory drug-induced gastric ulcers

Nonsteroidal anti-inflammatory drugs (NSAIDs) are valuable agents; however, their use has been limited by their association with mucosal damage in the upper gastrointestinal tract. NSAIDs inhibit cyclooxygenase and consequently block the synthesis of prostaglandins, which have cytoprotective effects in gastric mucosa; these effects on prostaglandins have been thought to be major cause of NSAID-induced ulceration. However, studies indicate that additional NSAID-related mechanisms are involved in formation of gastric lesions. Here, we used a toxicoproteomic approach to understand cellular processes that are affected by NSAIDs in mouse stomach tissue during ulcer formation. We used fluorogenic derivatization-liquid chromatography-tandem mass spectrometry (FD-LC-MS/MS)-which consists of fluorogenic derivatization, separation and fluorescence detection by LC, and identification by LC-tandem mass spectrometry-in this proteomic analysis of pyrolic stomach from control and diclofenac (Dic)-treated mice. FD-LC-MS/MS results were highly sensitive; 10 differentially expressed proteins were identified, and all 10 were more highly expressed in Dic-treated mice than in control mice. Specifically, expression levels of 78 kDa glucose-regulated protein (GRP78), heat shock protein beta-1 (HSP27), and gastrin were more than 3-fold higher in Dic-treated mice than in control mice. This study represents a first step to ascertain the precise actors of early NSAID-induced ulceration.

Synthesis and evaluation of a fluorogenic reagent for proteomic studies: 7-fluoro-N-[2-(dimethylamino)ethyl]-2,1,3-benzoxadiazole-4-sulfonamide (DAABD-F)

Since the successful selection of fluorogenic derivatization reagent 7-chloro-N-[2-(dimethylamino)ethyl]-2,1,3-benzoxadiazole-4-sulfonamide (DAABD-Cl) as a component of a novel method (FD-LC-MS/MS method) for proteomics studies, a further reactive reagent has been required to obtain more species of proteins: DAABD-Cl reacts with only thiol moieties of proteins to give fluorescence at 505 nm with excitation at 395 nm. Here, we synthesized reagent 7-fluoro-N-[2-(dimethylamino)ethyl]-2,1,3-benzoxadiazole-4-sulfonamide, DAABD-F, having a 7-fluorine moiety instead of the 7-chlorine moiety in DAABD-Cl, expecting it to exhibit high reactivity to amino moieties of proteins. As expected, the reaction rates of low molecular thiols with DAABD-F were 50 times higher than those with DAABD-Cl. DAABD-F was able to react with the amino moiety of a low molecular amine, beta-alanine, producing fluorescence at 554 nm with excitation at 432 nm. The reaction with DAABD-F of a typical model protein, bovine serum albumin (BSA), needed a lower amount of reagent (DAABD-F) than DAABD-Cl to produce a single fluorescent derivative (fluorescence at 495 nm with excitation at 390 nm) that was demonstrated to be solely a cysteinyl residue modified product. A derivatization reaction with DAABD-F towards a soluble extract of a normal human mammary epithelial cell (HMEC) resulted in the same fluorescent protein profiles as those with DAABD-Cl except one (AHNAK nucleoprotein isoform1) that was produced by the derivatization at a lysinyl residue (4761Lys) and was identified according to the usual procedure of isolation and tryptic digestion of the fluorescent protein peak on the chromatogram and final LC-MS/MS with a database-searching algorithm.

Differential labeling of free and disulfide-bound thiol functions in proteins

A method for the simultaneous determination of the number of free cysteine groups and disulfide-bound cysteine groups in proteins has been developed based on the sequential labeling of free and bound thiol functionalities with two ferrocene-based maleimide reagents. Liquid chromatography/electrochemistry/mass spectrometry was used to assign the N-(2-ferroceneethyl)maleimide (FEM) labeled free cysteine functionalities in a tryptic digest mixture, whereas a precursor ion scan enables the detection of peptides with ferrocenecarboxylic acid-(2-maleimidoyl)ethylamide (FMEA) labeled disulfide-bound cysteine groups after reduction. Fragment spectra of the labeled peptides yield an excellent coverage of b-type and y-type ions. The ferrocene labeled cysteines were fragmented as 412 Da (FEM) and 455 Da (FMEA). These fragment masses are significantly higher than unlabeled amino acids or dipeptides and are easily detected. The position of free and disulfide-bound cysteine may therefore be assigned in an amino acid sequence.

Synthesis of 4-[2-(N,N-dimethylamino)ethylaminosulfonyl]-7-N-methylhydrazino-2,1,3-benzoxadiazole (DAABD-MHz) as a derivatization reagent for aldehydes in liquid chromatography/electrospray ionization–tandem mass spectrometry

Benzofurazan derivatization reagent, 4-[2-(N,N-dimethylamino)ethylaminosulfonyl]-7-N-methylhydrazino-2,1,3-benzoxadiazole (DAABD-MHz), for aldehydes in liquid chromatography/electrospray ionization-tandem mass spectrometry (LC/ESI-MS/MS), was synthesized. DAABD-MHz reacted with aliphatic aldehydes under mild conditions. The generated derivatives were separated on a reversed-phase column and detected by ESI-MS/MS with detection limits of 30-60 fmol on-column. Upon collision-induced dissociation, a single and intense fragment ion at m/z 151 was observed. These results suggested that DAABD-MHz was suitable as a derivatization reagent in LC/ESI-MS/MS.

A Proteomics Method Revealing Disease-Related Proteins in Livers of Hepatitis-Infected Mouse Model

In this post-genome era, a sensitive quantitative method is required for differential profiling analyses of clinical proteomes to understand the disease progress. Here, we adopt the FD-LC-MS/MS method, consisting of fluorogenic derivatization (FD), separation by liquid chromatography (LC), and identification by LC-tandem mass spectrometry (MS/MS), to reveal disease-related proteins in livers of hepatocarcinogenesis in transgenic (Tg) and non-transgenic (NTg) mice at three developmental stages. After 6 months, the expression of apoptosis-related proteins is suppressed. After 12 months, proteins related to respiration, the electron-transfer system, and anti-oxidation are significantly up-regulated. After 16 months, proteins related to defense, beta-oxidation, and apoptosis are significantly suppressed. This fluctuating expression of proteins could explain the progression of hepatocarcinogenesis. The method would be useful for clinical proteomics analysis because of its high resolution, sensitivity, and reproducibility.

Precolumn derivatization of cysteine residues for quantitative analysis of five major cytochrome P450 isoenzymes by liquid chromatography/tandem mass spectrometry

The development of a novel method for absolute quantification of the five most clinically relevant CYP450 isoenzymes is described based on chemical derivatization of cysteine residues. The sulfhydryl-reactive reagents, 2-bromo-4'-chloroacetophenone (p-CPB) and 2-bromo-4'-bromoacetophenone (p-BPB), are proposed for use in quantitative proteomics. After reducing and denaturing, the P450s are derivatized with p-CPB for sulfhydryl alkylation then subjected to trypsin digestion. The resulting p-CPB-attached peptides are enriched using a phenyl resin solid-phase cartridge, then separated on a Zorbax 300SB reversed-phase column, and detected under positive electrospray ionization in the multiple reaction monitoring mode. Quantification is achieved using p-BPB-modified peptides as internal standards. Validation results demonstrated that this method showed good linearity between the concentration range of 10 fmol/microg to 5 pmol/microg for the six selected peptides in a complex matrix (rat liver microsomal protein). Intra-day and inter-day precision, expressed by relative standard deviation, were all less than 18%. Assay accuracy was within +/- 20% in terms of relative error. The quantitative derivatization approach proved to be reproducible, cost-effective and readily suitable for high-throughput assays. The reliability of this method for quantification of intact P450s was demonstrated through comparing with the well-applied isotope-coded affinity tag (ICAT) method.

Existence of low-molecular-weight thiols inCaenorhabditis elegans demonstrated by HPLC-fluorescene detection utilizing 7-chloro-N-[2-(dimethylamino)ethyl]-2,1,3-benzoxadiazole-4-sulfonamide

A highly sensitive and simple method using HPLC-fluorescence detection with 7-chloro-N-[2-(dimethylamino)ethyl]-2,1,3-benzoxadiazole-4-sulfonamide (DAABD-Cl) as a fluorogenic reagent demonstrated the existence of the low-molecular-weight thiols in the extract of Caenorhabditis elegans (C. elegans). The method includes derivatization of the thiols with DAABD-Cl at 40 degrees C for 10 min in borate buffer (pH 9.0) containing TCEP, CHAPS and EDTA, separation of the derivatives on an ODS column and fluorometric determination of the derivatives at 510 +/- 15 nm with excitation at 400 +/- 15 nm. The identification of the thiols was made by HPLC-electrospray ionization mass spectrometry (LC-MS) following isolation of the derivatives using HPLC-fluorescence detection. Low-molecular-weight thiols were found to exist in the extract of C. elegans, such as cysteine, cysteinylglycine, gamma-glutamylcysteine, reduced glutathione and two other unidentified thiol compounds, confirming the existence of the 'glutathione cycle' in C. elegans similar to the mammalian body.

Synthesis of benzofurazan derivatization reagents for carboxylic acids in liquid chromatography/electrospray ionization–tandem mass spectrometry

The applicability of benzofurazan derivatization regents to carboxylic acids analysis in LC/ESI-MS/MS (high-performance liquid chromatography/electrospray ionization tandem mass spectrometry) was examined. The product ion spectra of DAABD-AE {4-[2-(N,N-dimethylamino)ethylaminosulfonyl]-7-(2-aminoethylamino)-2,1,3-benzoxadiazole}, DAABD-PZ {4-[2-(N,N-dimethylamino)ethylaminosulfonyl]-7-N-piperazino-2,1,3-benzoxadiazole}, DAABD-PiCZ {4-[4-carbazoylpiperidin-1-yl]-7-[2-(N,N-dimethylamino)ethylaminosulfonyl]-2,1,3-benzoxadiazole}, DAABD-ProCZ {4-[2-carbazoylpyrrolidin-1-yl]-7-[2-(N,N-dimethylamino) ethylaminosulfonyl]-2,1,3-benzoxadiazole} and DAABD-Apy {4-[2-(N,N-dimethylamino)ethylaminosulfonyl]-7-(3-aminopyrrolidin-1-yl)-2,1,3-benzoxadiazole}, and their acetylated compounds were obtained. An intense fragment ion at m/z 151 corresponding to (dimethylamino)ethylaminosulfonyl moiety was observed in each spectra, suggesting that these reagents were suitable for ESI-MS/MS analysis. DAABD-AE, DAABD-APy and DAABD-PZ were applied to the analysis of octanoic acid and it was found that DAABD-AE and DAABD-APy gave high signal intensity suitable for LC/ESI-MS/MS.

Combining Fluorescence Detection and Mass Spectrometric Analysis for Comprehensive and Quantitative Analysis of Redox-Sensitive Cysteines in Native Membrane Proteins

Monobromobimane (MBB) is a lipophilic reagent that selectively modifies free cysteine residues in proteins. Because of its lipophilic character, MBB is capable of labeling cysteine residues in membrane proteins under native conditions. Reaction of MBB with the sulfhydryl groups of free cysteines leads to formation of highly fluorescent derivatives. Here we describe a procedure for the detection and relative quantitation of MBB-labeled cysteines using fluorescence and mass spectrometric analyses, which allow determination of free cysteine content and unambiguous identification of MBB-modified cysteine residues. We have applied this approach to the analysis of the free and redox-sensitive cysteine residues of a large membrane protein, the sarcoplasmic reticulum Ca2+ release channel with a molecular mass of 2.2 million Da. Labeling was performed under physiologic conditions where the channel complex is in its native environment and is functionally active. The purified MBB-labeled channel complex was enzymatically digested, and the resulting peptides were separated by reversed-phase high-performance chromatography. MBB-labeled peptides were detected by fluorescence and identified by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. Under MALDI conditions, partial photolytic fragmentation of the MBB-peptide bound occurred, thus allowing convenient screening for the MBB-modified peptides in the MS spectrum by detection of the specific mass increment of 190.07 Da for MBB-modified cysteine residues. Modification of the peptides was further confirmed by tandem mass spectrometric analysis, utilizing sequencing information and the presence of the specific immonium ion for the MBB-modified cysteine residues at m/z 266.6. Quantitative information was obtained by comparison of both fluorescence and MS signal intensities of MBB-modified peptides. Combination of fluorescence with MS detection and analysis of MBB-labeled peptides supported by a customized software program provides a convenient method for identifying and quantifying redox-sensitive cysteines in membrane proteins of native biological systems. Identification of one redox-sensitive cysteine (2327) in the native membrane-bound sarcoplasmic reticulum Ca2+ release channel is described.

Synthesis and evaluation of fluorogenic reagents for simultaneous detection of peptides and proteins by HPLC in two different samples

To find the pairs of fluorogenic reagents having similar retention times in HPLC but with different fluorescent characteristics, six fluorogenic reagents bearing benzoxadiazole or benzoselenadiazole skeletons were synthesized. The resultant derivatives obtained from the reaction of peptides and proteins with reagents which have a benzoselenadiazole skeleton showed different fluorescence characteristics from those with a benzoxadiazole skeleton. Since each corresponding derivatives of trypsin inhibitor and BSA with DAABD-Cl and 7-fluoro-N-[2-(diethylamino)ethyl]-2,1,3-benzoselenadiazole-4-sulfonamide (DEAEABSeD-F) have similar retention times, the pair of reagents was adopted for the sensitive simultaneous detection of proteins in two different samples. When the soluble fraction of mouse hippocampus was divided into the two samples (A and B), each was reacted with DEAEABSeD-F for A and DAABD-Cl for B, respectively. The two reaction solutions were combined and subjected to HPLC analysis with two fluorescent detectors in series (excitation and emission at different wavelengths for A and B, respectively). The resultant two chromatograms had quite similar patterns for each other. The new pair of fluorogenic reagents (DAABD-Cl and DEAEABSeD-F) would be applicable to proteomics studies using the previously reported FD-LC-MS/MS method.

A further study on the combined use of internal standard and isotope-labeled derivatization reagent for expansion of linear dynamic ranges in liquid chromatography–electrospray mass spectrometry

The combined use of a so-called internal standard and the isotope-labeled derivatization reagent for the quantification of analytes for liquid chromatography-mass spectrometry (LC/MS) was further studied. The sample solution (containing the analytes and an internal standard) was derivatized with the light form of the derivatization reagent, 7-(N,N-dimethylaminosulfonyl)-4-(aminoethyl)piperazino-2,1,3-benzoxadiazole (DBD-PZ-NH(2)) or 7-(N,N-dimethylaminosulfonyl)-4-piperazino-2,1,3-benzoxadiazole (DBD-PZ). A standard solution of the analytes (containing an internal standard) was derivatized with the isotope (d(6))-labeled derivatization reagent, DBD-PZ-NH(2) (D) or DBD-PZ (D), and served as the isotope-labeled internal standards. The peak heights of the targeted analytes derivatives in the sample solution were corrected using those of the internal standard and the heavy form derivatives of the standards, and the calibration curves were constructed. The curve bending of the calibration curves caused by the ion suppression at the ion source was suppressed and the linear dynamic ranges of the calibration curves were expanded. The derivatives of DBD-PZ-NH(2) were about 10 times more sensitively detected than those of DBD-PZ derivatives and, therefore, DBD-PZ-NH(2) might be suitable for sensitive detection.

Synthesis of the isotope-labeled derivatization reagent for carboxylic acids, 7-(N,N-dimethylaminosulfonyl)-4-(aminoethyl)piperazino-2,1,3-benzoxadiazole (d6) [DBD-PZ-NH2 (D)], and its application to the quantification and the determination of relative amount of fatty acids in rat plasma samples by high-performance liquid chromatography/mass spectrometry

The isotope-labeled benzofurazan derivatization reagent for carboxylic acids, 7-(N,N-dimethylaminosulfonyl)-4-(aminoethyl)piperazino-2,1,3-benzoxadiazole (d6) [DBD-PZ-NH2 (D)] was synthesized. DBD-PZ-NH2 (D) was used for the accurate quantification of fatty acids by liquid chromatography/mass spectrometry (LC/MS). The standard fatty acids were derivatized with DBD-PZ-NH2 (D) to the stable isotope-labeled compounds for the fatty acids derivatives of DBD-PZ-NH2 and used for the internal standards. The obtained calibration curves for fatty acids were linear over the range 0.1-200 microM (r2 > 0.999). Fatty acids in plasma samples were determined after derivatization with DBD-PZ-NH2 and analyzed by LC/MS using standard fatty acid DBD-PZ-NH2 (D) derivatives as internal standards. Furthermore, the relative amounts of fatty acids in two plasma samples were determined after derivatization with DBD-PZ-NH2 and DBD-PZ-NH2) (D). The isotope-labeled derivatization reagent was useful for accurate quantification and the determination of relative amounts of the metabolites in biological samples having the target functional group.