High-performance Liquid Chromatography Run Research Articles

Quantification of serine residue stereoinversion in a short peptide by reversed-phase high-performance liquid chromatography: analysis of mechanisms promoting serine stereoinversion.

Stereoinversion of Ser residues within proteins, which has been identified in long-lived proteins, influences protein function. To quantify the stereoinversion of Ser residues, we investigated the potential adaptation of our direct peptide analytical method originally established for analyzing the isomerization of asparaginyl/aspartyl residues. Peptide pairs containing L-Ser or D-Ser residues with lengths of four or five residues were synthesized. Separation conditions for these peptide pairs were systematically examined by precisely adjusting the pH of the elution solvent using reverse-phase high-performance liquid chromatography (HPLC). Optimal separation conditions were successfully developed for all peptide pairs, enabling the direct quantification of Ser residue stereoinversion through a single HPLC run. Subsequently, the degree of Ser stereoinversion within the model peptide, Gly-Ser-Gly-Tyr, was determined using the method established in this study. Surprisingly, the stereoinversion of Ser residues occurred only when the absolute configurations of Ser and Tyr residues of the peptide differed from each other, whereas no stereoinversion was observed when their absolute configurations were identical. The experiments using peptides similar to the model peptide reveal that both the N-terminal amino group and the hydroxyl group of the C-terminal Tyr residue are involved in the stereoinversion of the Ser residue. By applying a simple method to quantify the stereoinversion of Ser residues, valuable insights into the mechanisms governing these stereoinversions were obtained.

Temperature-programmed capillary high-performance liquid chromatography with atmospheric pressure chemical ionization mass spectrometry for analysis of fatty acid methyl esters.

A new capillary high-performance liquid chromatography method with atmospheric pressure chemical ionization mass spectrometry was developed for the analysis of fatty acid methyl esters and long-chain alcohols. The chromatographic separation was achieved using a Zorbax SB-C18 HPLC column (0.3 × 150mm, 3.5μm) with a mobile phase composed of acetonitrile and formic acid and delivered isocratically at a flow rate of 10μL/min. The column temperature was programmed simply, using a common column oven. Good reproducibility of the temperature profile and retention times were achieved. The temperature programming during the isocratic high-performance liquid chromatography run had a similar effect as a solvent gradient; it reduced retention times of later eluting analytes and improved their detection limits. Two atmospheric pressure chemical ionization sources of the mass spectrometry detector were compared: an enclosed conventional ion source and an in-house made ion source with a glass microchip nebulizer. The enclosed source provided better detectability of saturated fatty acid methyl esters and made it possible to determine the double bond positions using acetonitrile-related adducts, while the open chip-based source provided better analytical figures of merit for unsaturated fatty acid methyl esters. Temperature-programmed capillary high-performance liquid chromatography is a promising method for analyzing neutral lipids in lipidomics and other applications.

High-performance liquid chromatography assay with programmed flow elution for cisatracurium in human plasma: Application to pharmacokinetics in infants and children

A high-performance liquid chromatography (HPLC) assay with fluorescence detection (FLD) for quantification of cisatracurium in human plasma was developed and fully validated. Liquid-liquid extraction was employed for sample preparation. The separation was carried out on a C18 column with ternary mobile phase composed of 30mmolL(-1) phosphate buffer (pH 3.0), acetonitrile and methanol (60:35:5, v/v/v). Verapamil was used as the internal standard. The isocratic elution with programmed flow rate was employed by setting at 0.8mLmin(-1) from 0 to 3.5min, 0.5mLmin(-1) from 3.5 to 6min, and 1.0mLmin(-1) from 6 to 10min. The fluorescence detection was performed at 236nm for excitation and 324nm for emission. The assay was linear from 50 to 2800ngmL(-1), with a detection limit of 12ngmL(-1). The correlation coefficient (r) for linear regression was 0.9997. The intra-day coefficients of variation (CVs) were less than 2.0%, and the inter-day CVs were less than 4.0%. The mean recoveries were in the range of 92.1-100.4%. The total HPLC run time was less than 10min. The developed HPLC method was fast, simple, sensitive, accurate and suitable for studying the pharmacokinetics of cisatracurium in infants and children after intravenous administration.

Stabilities of hemoglobins A and S in dried blood spots stored under controlled conditions

ObjectiveWe aimed to measure separately the contributions of heat and humidity to changes in levels of hemoglobins A and S in dried-blood-spot (DBS) samples. Design and methodsWe stored paired sets of DBSs at 37°C for predetermined intervals in low-humidity and high-humidity environments. Hemoglobin A and S levels of all samples in each complete set were measured in a single high performance liquid chromatography run. ResultsDuring the one-month storage intervals, both hemoglobin species lost about 35% of initial levels in low-humidity storage and almost all of initial levels in high-humidity storage. ConclusionsMinimizing both humidity and temperature in the transportation and storage environments of DBS samples is essential to maintaining the integrity of the hemoglobin tetramer molecules.

Purification of meta-cresol purple and cresol red by flash chromatography: Procedures for ensuring accurate spectrophotometric seawater pH measurements

Impurities in sulphonephthalein indicator salts can result in significant errors in seawater pH determinations. To ensure suitable measurement accuracy and intercomparability on a global basis, impurities must be removed from all indicators used for oceanographic CO2 system analyses. Previous work has described an effective HPLC (high-performance liquid chromatography) procedure for purification of meta-cresol purple, but the technique is labor-intensive, with each HPLC run producing only a small batch of purified indicator. This work describes the use of flash chromatography to more efficiently produce large batches of purified meta-cresol purple (mCP) and cresol red (CR), the preferred indicators for direct water column determinations of seawater pH.Several batches of unrefined mCP and CR of independent origin were prepared by flash chromatography. Indicator purity was then assessed in two ways: by (a) HPLC verification and (b) pH measurements of highly buffered solutions. HPLC chromatograms of the various flash-prepared mCPs indicated that the process did not always result in a completely pure product. In terms of performance, however – i.e., pH measurements of highly buffered solutions – no differences were observed between an HPLC-purified reference mCP and the flash-purified mCPs. HPLC examination of the flash-purified CRs indicated that every product was free of detectable impurities. No differences were seen in comparative pH measurements made with the purified CRs. The flash chromatography procedures outlined in this work are suitable for producing bulk quantities of mCP and CR for use in high-precision spectrophotometric pH measurements in seawater.

Comprehensive analysis of the major lipid classes in sebum by rapid resolution high-performance liquid chromatography and electrospray mass spectrometry

Sebum is a complex lipid mixture that is synthesized in sebaceous glands and excreted on the skin surface. The purpose of this study was the comprehensive detection of the intact lipids that compose sebum. These lipids exist as a broad range of chemical structures and concentrations. Sebum was collected with SebuTape(TM) from the foreheads of healthy donors, and then separated by HPLC on a C8 stationary phase with sub 2 µm particle size. This HPLC method provided high resolution and excellent reproducibility of retention times (RT). Compound mining was performed with time of flight (TOF) and triple quadrupole (QqQ) mass spectrometers (MS), which allowed for the classification of lipids according to their elemental composition, degree of unsaturation, and MS/MS fragmentation. The combination of the two MS systems detected 95 and 29 families of triacylglycerols (TAG) and diacylglycerols (DAG), respectively. Assignment was carried out regardless of positional isomerism. Among the wax esters (WE), 28 species were found to contain the 16:1 fatty acyl moiety. This method was suitable for the simultaneous detection of squalene and its oxygenated derivative. A total of 9 cholesterol esters (CE) were identified and more than 48 free fatty acids (FFA) were detected in normal sebum. The relative abundance of each individual lipid within its own chemical class was determined for 12 healthy donors. In summary, this method provided the first characterization of the features and distribution of intact components of the sebum lipidome.

Improved Assay for the Nonradioactive Determination of Inosine 5'-Monophosphate Dehydrogenase Activity in Peripheral Blood Mononuclear Cells

Mycophenolic acid (MPA) inhibits the enzyme inosine 5'-monophosphate dehydrogenase (IMPDH). Thus, the measurement of IMPDH activity could serve as a specific pharmacodynamic (PD) tool for monitoring MPA therapy. At present, however, monitoring of pharmacokinetic parameters is preferred over that of PD parameters because, in general, PD assays are labor-intensive and poorly reproducible. Currently, cell count or protein concentration is widely accepted as methods to normalize enzyme activity. In the present study, we have attempted to further improve a method for the determination of IMPDH activity to increase the robustness and reproducibility of the IMPDH activity assay itself, without making the assay more labor-intensive. Therefore, several aspects of the IMPDH method were investigated regarding their influence on the reproducibility and also modified to increase the feasibility and consistency of the assay. The isolation of peripheral blood mononuclear cells (PBMCs) of whole blood samples was found to be the most variable step. Normalization on cell count is labor-intensive and at the same time has a poor reproducibility. Determination of the protein content in cell extracts is impaired by contamination with extracellular proteins and non-PBMCs. Alternatively, the intracellular substance adenosine monophosphate (AMP) was investigated to normalize the newly generated xanthosine monophosphate. Among various subject groups, no significant differences in mean AMP concentration were found. To simplify the procedure, PBMCs were diluted to a fixed volume after isolation from sample of whole blood, and the IMPDH activity was normalized to the AMP concentration quantified in the same high-performance liquid chromatography run as xanthosine monophosphate was quantified. The within-run and total imprecision (coefficient of variation) ranged from 4.2% to 10.6% and from 6.6% to 11.9%, respectively. In conclusion, the modified method described here for the measurement of IMPDH activity can be used reliably in multicenter trials and in longitudinal studies to evaluate the additional value of any PD monitoring among a diversity of patients treated with MPA.

An optimized fast-performance liquid chromatography method for analyzing lipoprotein profiles using microliter volumes of serum

Plasma or serum lipoprotein analysis is commonly carried out with a conventional size-exclusion fast-performance liquid chromatography method that requires large sample volumes (1–2 ml). To determine lipoprotein profiles of mice with this method, plasma or serum samples have to be pooled from a group of animals, which often requires sacrificing animals. Here we report an optimized anion-exchange chromatography method with simplified cholesterol collection and detection system. After 5–10 μl serum was injected for anion-exchange chromatography, a stepwise gradient was applied and fractions were collected on a 96-well plate. Cholesterol content in each well was measured using a fluorescence-based detection method. With this method, distinct lipoprotein peaks corresponding to high-density lipoprotein, low-density lipoprotein, and very-low-density lipoprotein, can be easily separated and identified with excellent resolution. The entire high-performance liquid chromatography run takes about 30 min and the results are reproducible with a low variability. The small sample size allows analyzing the lipoprotein profile in a given mouse at a given time point with nonterminal bleeding. The method is simple to set up with commercially available parts and convenient to run.

Response Normalized Liquid Chromatography Nanospray Ionization Mass Spectrometry

The widely different LC-MS response observed for many structurally different compounds limits the use of LC-MS in full scan detection mode for quantitative determination of drugs and metabolites without using reference standard. The recently introduced nanospray ionization (NSI) technique shows comparable MS response for some compounds under non-LC-MS conditions. However, in the presence of numerous endogenous compounds commonly associated with biological samples such as urine, plasma, and bile, LC-MS is required to separate, detect, identify, and measure individual analytes. An LC-NSI-MS system was devised and the MS response obtained in this system for a variety of pharmaceutical drugs and their metabolites. The set-up involves two high-performance liquid chromatography (HPLC) systems, a chip-based NSI source and a quadrupole-time-of-flight (Q-TOF) mass spectrometer. Herein this is referred to as the response normalized-liquid chromatography NSI-MS (RNLC-NSI-MS) system. One HPLC unit performs the analytical separation, while the other unit adds solvent post-column with an exact reverse of the mobile phase composition such that the final composition entering the NSI source is isocratic throughout the entire HPLC run. The data obtained from four different structural classes of compounds [vicriviroc (VCV), desloratadine (DL), tolbutamide, and cocaine] and their metabolites indicate that by maintaining the solvent composition unchanged across the HPLC run, the influence of the solvent environment on the ionization efficiency is minimized. In comparison to responses obtained from radiochromatograms, responses from conventional LC-ESI-MS overestimated the VCV and DL responses, respectively, by 6- and 20-fold. Although VCV and DL responses obtained using LC-NSI-MS are within 2- to 6-fold from the respective radiochromatographic responses, the response normalization modification results in nearly uniform LC-NSI-MS response for all compounds evaluated.

A microplate solid scintillation counter as a radioactivity detector for high performance liquid chromatography in drug metabolism: Validation and applications

Sensitive radioactivity detection following high performance liquid chromatography (HPLC) separation remains a challenge in many drug metabolism studies with radiolabeled compounds. In this work, solid scintillation counting (SSC) after fraction collection into 96-well plates was evaluated as an off-line radioactivity detection method, in comparison with conventional liquid scintillation counting (LSC). The impact of counting time and biological matrix on the quantification of radiolabeled metabolites and parent drug in samples from animal and human absorption, distribution, metabolism and excretion (ADME) studies was investigated. Three different approaches were used to test whether reliable quantification by off-line SSC detection, which requires an approximately constant counting yield during the entire chromatographic run, can be realized: (i) the measurement of radioactivity-spiked biological blank samples without HPLC separation as an extreme case of biological background, (ii) the measurement of radioactivity-spiked HPLC fractions of biological blank samples and (iii) the comparison of radiochromatograms obtained by off-line SSC and LSC of real samples from ADME studies with radiolabeled compounds. Situations in which variations in SSC yield during an HPLC run are likely to lead to significant errors in quantitation were identified and are discussed. However, examples from a number of animal or human ADME studies showed that in the majority of cases off-line SSC provides very similar quantitative data, compared with the reference method of off-line LSC radioactivity detection. Approaches for validation of the off-line SSC approach in critical cases are discussed. The main advantages of off-line SSC, compared with off-line LSC, are lower detection limits and a substantially higher throughput. Several applications of off-line SSC detection in ADME studies are shown.

Enhanced Shutoff of Phototransduction in Transgenic Mice Expressing Palmitoylation-deficient Rhodopsin*♦

Palmitoylation is a reversible, post-translational modification observed in a number of G-protein-coupled receptors. To gain a better understanding of its role in visual transduction, we produced transgenic knock-in mice that expressed a palmitoylation-deficient rhodopsin (Palm(-/-)). The mutant rhodopsin was expressed at wild-type levels and showed normal cellular localization to rod outer segments, indicating that neither rhodopsin stability nor its intracellular trafficking were compromised. But Palm(-/-) rods had briefer flash responses and reduced sensitivity to flashes and to steps of light. Upon exposure to light, rhodopsin became phosphorylated at a faster rate in mutant than in wild-type retinas. Since quench of rhodopsin begins with its phosphorylation, these results suggest that palmitoylation may modulate rod photoreceptor sensitivity by permitting rhodopsin to remain active for a longer period.

Simultaneous separation and quantitation of amino acids and polyamines of forest tree tissues and cell cultures within a single high-performance liquid chromatography run using dansyl derivatization

The objective of the present study was to develop a rapid HPLC method for simultaneous separation and quantitation of dansylated amino acids and common polyamines in the same matrix for analyzing forest tree tissues and cell cultures. The major modifications incorporated into this method as compared to previously published HPLC methods for separation of only dansyl amino acids include: use of a 10 cm column to reduce the total run time by approximately 15 min; modification of the dansyl derivatization process and gradient profile to elute amino acids and common polyamines within the same run; addition of steps for column cleaning within each run; shorter re-equilibration time; and finally, column cleaning and physically reversing the column at the end of a loop of samples. These changes improved peak resolution and increased column longevity by several-fold. Over 1000 foliar samples from mature forest trees could be analyzed with the same column as compared to only 200–250 samples before the incorporation of these changes. This method eluted 22 amino acids within 40 min plus all three common polyamines between 44 and 47 min. The total run time is 53.6 min for amino acids only and 55.6 min for both amino acids and polyamines.

Simultaneous determination of indinavir, ritonavir and saquinavir in plasma by high-performance liquid chromatography.

Antiretroviral regimens consisting of a combination of protease inhibitors have been shown to be highly potent for the treatment of HIV infection. Therapeutic drug monitoring may ensure optimal drug levels to improve efficacy and minimize side effects. The purpose of this study was to establish a method for simultaneous determination of plasma concentrations of indinavir (IDV), ritonavir (RTV) and saquinavir (SQV) by high-performance liquid chromatography (HPLC) in a single run. A C(18) column and an ultraviolet detector set at 215 nm were used in the HPLC. The mobile phase consisted of phosphate buffer (50 mM, pH 5.6) and acetonitrile (55:45, v/v), and the flow rate was 1.5 mL/min. Plasma sample (0.5 mL) containing IDV, RTV, and SQV was alkalinized with ammonia water (10%) and propylparaben added as an internal standard (IS), which was then extracted with methyl tert.-butyl ether. The organic layer was taken and evaporated to dryness. The residue was dissolved in the mobile phase, and the solution was washed with n-hexane followed by HPLC analysis. The calibration curves were linear for each of the 3 drugs in the studied concentration range (0.1 to 5 microg/mL). The extraction recoveries were greater than 90%. One HPLC run takes less than 15 minutes. Analysis of plasma samples of patients treated with combinations of these drugs demonstrated that the calibration curves covered the clinical concentration range. This study established a simple and accurate method for simultaneous determination of IDV, RTV, and SQV in plasma by isocratic HPLC. The method is practical for therapeutic drug monitoring.

Detection and Identification of Simple Phenolics in Pistacia lentiscus Resin

Identification and quantification of a series of phenolic compounds in Pistacia lentiscus resin, commonly known as Chios mastic gum, has been achieved based on high performance liquid chromatography (HPLC) fractionation of polar extract of the resin prior to dual‐column gas chromatography‐mass spectrometry (GC‐MS) analysis. Polyphenols were extracted from the resin with methanol/water and the extract was fractionated by HPLC. Identification of tyrosol, p‐hydroxy‐benzoic, p‐hydroxy‐phenylacetic, vanillic, gallic, and trans‐cinnamic acids was performed on both HP‐5 and Innowax columns using GC‐MS at SIM mode. Also, the triterpenoids dihydroabietic acid, oleanolic and its isomer ursolic acid and hydroxy‐ursenal were detected in the same HPLC run with polyphenols, as a result of GC‐MS at full scan mode.

Mutual peak matching in a series of HPLC–DAD mixture analyses

One of the largest challenges in high performance liquid chromatography (HPLC) method development is the necessity for tracking the movement of peaks as separation conditions are changed. Peak increments are then used to build a mathematical model capable of minimizing the number of experiments in an optimization circuit. Method optimization for an unknown mixture is, moreover, complicated by the absence of any a priori information on component properties and retention times when direct signal assignment is not possible. On the contrary, achievement of the maximum separation becomes an important factor for successful identification or quantitation. In this case, the optimization may be based on assigning peaks of the same component chosen from different experiments to each other. In other words, mutual peak matching between the HPLC runs is required. A new method for mutual peak matching in a series of HPLC with diode array detector (HPLC–DAD) analyses of the same unknown mixture acquired at varying separation conditions has been developed. This approach, called mutual automated peak matching (MAP), does not require any prior knowledge of the mixture composition. Applying abstract factor analysis (AFA) and iterative key set factor analysis (IKSFA) on the augmented data matrix, the algorithm detects the number of mixture components and calculates the retention times of every individual compound in each of the input chromatograms. Every candidate component is then validated by target testing for presence in each HPLC run to provide quantitative criteria for the detection of “missing” peaks and non-analyte components as well as confirming successful matches. The matching algorithm by itself does not perform full curve resolution. However, its output may serve as a good initial estimate for further modeling. A common set of UV-Vis spectra of pure components can be obtained, as well as their corresponding concentration profiles in separate runs, by means of alternating least-square multivariate curve resolution (ALS MCR), resulting in reconstruction of overlapped peaks. The algorithms were programmed in MATLAB ® and tested on a number of sets of simulated data. Possible ways to improve the stability of results, reduce calculation time, and minimize operator interaction are discussed. The technique can be used to optimize HPLC analysis of a complex mixture without preliminary identification of its components.

Determination of the stoichiometry of noncovalent complexes using reverse-phase high-performance liquid chromatography coupled with electrospray ion trap mass spectrometry

An electrospray mass spectrometry-based methodology has been developed to have a fast and sensitive method for protein–cofactor stoichiometry determination. As model systems, we used two proteins which require the presence of cofactors for activity: TraR, a member of the LuxR family of quorum-sensing transcriptional regulators, which requires an acyl–homoserine lactone molecule called Agrobacterium autoinducer (AAI) as coinducer and the NS3 protease of hepatitis C virus which complexes with a NS4A cofactor peptide. Both TraR/AAI and NS3/NS4A are noncovalent complexes. Our method requires only nanomolar concentration of sample. A calibration curve of the cofactor is determined by high-performance liquid chromatography (HPLC) coupled on-line with an ion trap mass spectrometer operated in selected reaction monitoring mode. Subsequently, the complex is analyzed using the same experimental setup. During the HPLC run, the complex dissociates, and cofactor and protein elute at different retention times. The peak area of the cofactor is integrated and the molar concentration of cofactor in the complex is extrapolated from the calibration curve. The stoichiometry is consequently calculated by dividing the molar concentration of protein injected by that of cofactor measured. Both TraR/AAI and NS3/NS4A complexes have 1:1 stoichiometries, in line with those already reported in the literature.

Analytical Procedure for Simultaneous Use of Seven Fluorobenzoates in Multitracer Tests

An analytical procedure allowing simultaneous use of seven fluorobenzoate (FBA) isomers was developed and examined through column and field tracer experiments. The analytical method, based on high performance liquid chromatography (HPLC), included a reverse-phase separation method. This method was found to be very efficient for the FBA analysis, allowing accurate determination of seven FBAs in a single HPLC run, while avoiding analytical interference of other natural water constituents or pollutants. Consequently, this separation method allows the simultaneous use of seven isomers in multitracer tests in highly saline or contaminated environments. The mobility properties of the FBAs were examined in percolation experiments through a column filled with a mixture of crushed chalk and common fracture filling and coating material. The FBAs behaved conservatively as compared to bromid. All seven FBA isomers were successfully used in a multitracer test in a field percolation experiment designed to identify flowpath along a fracture plane.

An Improved Method for the Determination of Green and Black Tea Polyphenols in Biomatrices by High-Performance Liquid Chromatography with Coulometric Array Detection

Tea polyphenols are strong antioxidants and are believed to have beneficial health effects. However, the blood and tissue levels of these compounds are not well characterized because of a lack of suitable analytical methods for the biological resolution of these compounds. Previously, we developed methods for the analysis of three green tea catechins. Now we report an improved method for the measurement of the levels of the different catechins and theaflavins in biological fluids and tissues. The method includes digestion of the plasma, urine, or tissue samples with β-d-glucuronidase and sulfatase, followed by extraction with ethyl acetate and subsequent separation by reversed-phase high-performance liquid chromatography (HPLC). The polyphenols are identified on the basis of their retention times, spectral analysis, and electrochemical behavior across an array of electrodes. In a single HPLC run, it is possible to determine the major catechins and theaflavins as well as some of the catechin metabolites. The detection limits for catechins and theaflavins are from 5 to 10 ng/ml of saliva, plasma, or urine.

HPLC-integrated solid-phase extraction with photochemical post-column derivatization for the determination of oxacillin, cloxacillin and dicloxacillin in raw milk

An automated reversed-phase high-performance liquid chromatography (HPLC) method with UV detection at 300 nm after on-line coupled solid-phase extraction (SPE) and photochemical post-column derivatization was developed for the residue analysis of oxacillin, cloxacillin and dicloxacillin in raw milk. After a centrifugation step for defatting and ultrafiltration, a HPLC-integrated SPE using a restricted access sorbent, is performed. By operating the system in parallel mode, SPE and HPLC run are performed simultaneously. The procedure allows the analysis of about 30 samples within 24 h and was used to investigate the milk of cows which had been treated with oxacillin. The detection limit was 3 μg/kg for oxacillin and cloxacillin and 5 μg/kg for dicloxacillin. The recoveries were between 66% and 81% with coefficients of variation between 3.3% and 7.7%. Using an acetonitrile extraction procedure better recoveries of ≥90% were obtained with fortified samples, but more or less identical results were obtained for the samples with incurred residues after correction for recovery.

Mass spectrometric analysis of integral membrane proteins: application to complete mapping of bacteriorhodopsins and rhodopsin.

Integral membrane proteins have not been readily amenable to the general methods developed for mass spectrometric (or internal Edman degradation) analysis of soluble proteins. We present here a sample preparation method and high performance liquid chromatography (HPLC) separation system which permits online HPLC-electrospray ionization mass spectrometry (ESI-MS) and -tandem mass spectrometry (MS/MS) analysis of cyanogen bromide cleavage fragments of integral membrane proteins. This method has been applied to wild type (WT) bacteriorhodopsin (bR), cysteine containing mutants of bR, and the prototypical G-protein coupled receptor, rhodopsin (Rh). In the described method, the protein is reduced and the cysteine residues pyridylethylated prior to separating the protein from the membrane. Following delipidation, the pyridylethylated protein is cleaved with cyanogen bromide. The cleavage fragments are separated by reversed phase HPLC using an isopropanol/acetonitrile/aqueous TFA solvent system and the effluent peptides analyzed online with a Finnigan LCQ Ion Trap Mass Spectrometer. With the exception of single amino acid fragments and the glycosylated fragment of Rh, which is observable by matrix assisted laser desorption ionization (MALDI)-MS, this system permits analysis of the entire protein in a single HPLC run. This methodology will enable pursuit of chemical modification and crosslinking studies designed to probe the three dimensional structures and functional conformational changes in these proteins. The approach should also be generally applicable to analysis of other integral membrane proteins.