LC–MS bioanalysis of intact proteins and peptides

Bioanalysis assays that reliably quantify biotherapeutics and biomarkers in biological samples play pivotal roles in drug discovery and development. Liquid chromatography coupled with mass spectrometry (LC–MS), owing to its superior specificity, faster method development and multiplex capability, has evolved as one of the most important platforms for bioanalysis of biotherapeutics, particularly new scaffolds such as half-life extension platforms for proteins and peptides, as well as antibody drug conjugates. Intact LC–MS analysis is orthogonal to bottom-up surrogate peptide approach by providing whole molecule quantitation and high-level sequence and structure information. Here we review the latest development in LC–MS bioanalysis of intact proteins and peptides by summarizing recent publications and discussing the important topics such as the comparison between top-down intact analysis and bottom-up surrogate peptide approach, as well as simultaneous quantitation and catabolite identification. Key bioanalytical issues around intact protein bioanalysis such as sensitivity, data processing strategies, specificity, sample preparation and LC condition are elaborated. For peptides, topics including quantitation of intact peptide vs. digested surrogate peptide, metabolites, sensitivity, LC condition, assay performance, internal standard and sample preparation are discussed.     

Quantitation of hepcidin in serum using ultra‐high‐pressure liquid chromatography and a linear ion trap mass spectrometer

Hepcidin is a peptide hormone that functions as a key regulator of mammalian iron metabolism. Biological levels are increased in end‐stage renal disease and during inflammation but suppressed in hemochromatosis. Thus hepcidin levels have diagnostic importance. This study describes the development of an analytical method for the quantitative determination of the concentration of hepcidin in clinical samples. The fragmentation of hepcidin was investigated using triple quadrupole and linear ion trap mass spectrometers. A standard quantity of a stable isotopically labelled hepcidin internal standard was added to serum samples. Extraction was performed by protein precipitation and weak cation‐exchange magnetic nanoparticles. Chromatography was carried out on sub 2 µm particle stationary phase, using ultra‐high‐pressure liquid chromatography and a linear ion trap for quantitation. The lower limit of quantitation was 0.4 nmol/L with less than 20% accuracy and precision. The mean hepcidin concentration in sera for controls was 4.6 ± 2.7 nmol/L, in patients with sickle cell disease, 7.0 ± 8.9 nmol/L; in patients with end‐stage renal disease, 30.5 ± 15.7 nmol/L; and patients with penetrant hereditary hemochromatosis, 1.4 ± 0.8 nmol/L. Copyright © 2010 John Wiley & Sons, Ltd.     

A strategy for liquid chromatography/tandem mass spectrometry based quantitation of pegylated protein drugs in plasma using plasma protein precipitation with water-miscible organic solvents and subsequent trypsin digestion to generate surrogate peptides for detection

Recently, we have developed liquid chromatography/tandem mass spectrometry (LC/MS/MS)-based methods for the quantitation of pegylated therapeutic proteins in plasma. The methods are based on the LC/MS/MS detection of a surrogate peptide generated from trypsin digestion of the therapeutic protein. Various parameters related to the bioanalytical methods were evaluated and optimized, including the preparation of calibration standards and quality control samples, sample extraction, internal standard selection and its stage of addition, trypsin digestion, and non-specific binding. In this paper, we report the development of a method for a specific pegylated therapeutic protein and detail the various optimization steps undertaken. Simple extraction of the pegylated therapeutic protein from plasma was achieved via the precipitation of the endogenous proteins in plasma using acidic isopropanol and the resulting supernatant extract was subjected to trypsin digestion. A unique tryptic peptide arising from the pegylated therapeutic protein was used for LC/MS/MS-based detection and quantitation. A protein and a peptide were used as internal standards, with the former added before the sample extraction and the latter after the sample extraction. The method developed is simple, sensitive, specific and rugged, and has been implemented in a high throughput 96-well format to analyze plasma samples from in vivo studies. A required lower limit of quantitation (LLOQ) of 10 ng/mL, expressed in terms of the concentration of the protein drug, was easily achieved.     

Comparison of copper labeling followed by liquid chromatography-inductively coupled plasma mass spectrometry and immunochemical assays for serum hepcidin-25 determination

Hepcidin-25 has been defined as the key biomarker in iron metabolism. This peptide binds to the iron transporter ferroportin to cause its degradation. Therefore, the need for specific, accurate and precise methods for the quantification of hepcidin-25 in biological fluids is dramatically increasing. In this regard, the use of rapid immunochemical methods that provide low limit of quantification is desired for routine clinical use. However, such fast methodologies should be first analytically evaluated and compared with alternative strategies to check for their advantages and limitations. Here we compare the use of a commercial immunochemical assay for hepcidin determination with a novel analytical approach based on Cu-labeling of the peptide followed by Cu determination using liquid chromatography (HPLC) and plasma mass spectrometry (ICP-MS). The figures of merit of both systems reveal similar analytical characteristics and both seem to be adequate for the determination of the peptide at biologically relevant concentrations in human serum samples. The analysis of a larger number of samples (n = 50) by both techniques showed a good agreement in the concentrations found. Such finding permits to address the hepcidin recovery in the sample preparation procedure necessary for the HPLC-ICP-MS analysis in human serum that turn out to be 76–85%. Additionally, limitations due to cross-reactivity issues of the ELISA method could be addressed in some of the samples by using LC-ICP-MS and were confirmed by LC-Electrospray-MS.     

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

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

Simple and sensitive liquid chromatographic quantitative analysis of the novel marine anticancer drug Yondelis (ET-743, trabectedin) in human plasma using column switching and tandem mass spectrometric detection

The development of a simple and sensitive assay for the quantitative analysis of the marine anticancer agent Yondelis (ET-743, trabectedin) in human plasma using liquid chromatography (LC) with column switching and tandem mass spectrometric (MS/MS) detection is described. After protein precipitation with methanol, diluted extracts were injected on to a small LC column (10 x 3.0 mm i.d.) for on-line concentration and further clean-up of the sample. Next, the analyte and deuterated internal standard were back-flushed on to an analytical column for separation and subsequent detection in an API 2000 triple-quadrupole mass spectrometer. The lower limit of quantitation was 0.05 ng mL(-1) using 100 micro l of plasma with a linear dynamic range up to 2.5 ng ml(-1). Validation of the method was performed according to the most recent FDA guidelines for bioanalytical method validation. The time needed for off-line sample preparation has been reduced 10-fold compared with an existing LC/MS/MS method for ET-743 in human plasma, employing a labor-intensive solid-phase extraction procedure for sample pretreatment. The proposed column switching method was successfully applied in phase II clinical trials with Yondelis and pharmacokinetic monitoring.     

Large volume injection for the direct analysis of ionophores and avermectins in surface water by liquid chromatography-electrospray ionization tandem mass spectrometry

A simple method for the direct determination of residues of ionophore antibiotics and avermectin antiparasitics in surface water is reported. Using a large volume injector, a mixture of methanol and surface water is injected into an analytical liquid chromatography (LC) column and subsequently screened for residues of these veterinary pharmaceuticals using electrospray ionization tandem mass spectrometry. On-line sample enrichment and chromatographic separation are achieved using a single, short (20 mm) octadecylsilane LC column. The method permits the detection of four ionophores and two avermectins in surface water samples at low ng L⁻¹ concentrations. Minimal matrix effects were observed for a variety of surface water samples which permitted the use of reagent-based standards for quantitation.     

Quantitative analysis of the novel depsipeptide anticancer drug Kahalalide F in human plasma by high-performance liquid chromatography under basic conditions coupled to electrospray ionization tandem mass spectrometry

Kahalalide F (KF) is a novel cyclic depsipeptide anticancer drug, which has shown anticancer activity both in vitro and in vivo especially against human prostate cancer cell lines. To characterize the pharmacokinetics of KF during a phase I clinical trial in patients with androgen refractory prostate cancer, a method was developed and validated for the quantitative analysis of KF in human plasma using high-performance liquid chromatography (HPLC) coupled to positive electrospray ionization tandem mass spectrometry (ESI-MS/MS). Microbore reversed-phase liquid chromatography (LC) performed with mobile phases containing trifluoroacetic acid, an additive commonly used for separating peptides, resulted in substantial suppression of the signal for KF on ESI-MS/MS. An alternative approach employing a basic mobile phase provided an excellent response for KF when detected in the positive ion mode. Plasma samples were prepared for LC MS/MS by solid-phase extraction on C(18) cartridges. The LC separation was performed on a Zorbax Extend C(18) column (150 x 2.1 mm i.d., particle size 5 micro m) with acetonitrile -10 mM aqueous ammonia (85 : 15, v/v) as the mobile phase, at a flow-rate of 0.20 ml min(-1). A butyric acid analogue of KF was used as the internal standard. The lower limit of quantitation (LLQ) using a 500 micro l sample volume was 1 ng ml(-1) and the linear dynamic range extended to 1000 ng ml(-1). The inter-assay accuracy of the assay was -15.1% at the LLQ and between -2.68 and -9.05% for quality control solutions ranging in concentration from 2.24 to 715 ng ml(-1). The inter-assay precision was 9.91% or better at these concentrations. The analyte was stable in plasma under all relevant conditions evaluated and for a period of 16 h after reconstituting plasma extracts for LC analysis at ambient temperature.     

Development and validation of a direct plasma injection LC-MS method for YM087 and YM440 and metabolites in human plasma

Summary A fully automated, direct plasma-injection technique using an LC coupled to a quadrupole mass spectrometric detector with an on-line, sample clean-up procedure for two new pharmaceutical products, YM087 and YM440, has been developed. Plasma samples containing YM440 were mixed with internal standard or plasma containing YM087 and were injected into a chromatographic system based on two coupled columns. An extraction column packed with alkyl-diol-silica (ADS) was used for online sample cleanup. Using a back-flush technique analytes were subsequently transferred to an analytical column, for separation. Detection was based on tandem mass spectrometry either in electronspray or in APCI mode. Despite the relatively small volumes of plasma injected, reasonably low limits of quantitation were achieved. Validation of both assays was performed using guidelines concerning method validation. All parameters studied were within acceptance criteria. The methods were successfully applied to clinical pharmacokinetic studies.     

The development and validation of a high‐throughput LC–MS/MS method for the analysis of endogenous β‐hydroxy‐β‐methylbutyrate in human plasma

A high‐throughput, sensitive, and rugged liquid chromatography–tandem mass spectrometry (LC–MS/MS) method for the rapid quantitation of β ‐hydroxy‐β ‐methylbutyrate (HMB) in human plasma has been developed and validated for routine use. The method uses 100 μL of plasma sample and employs protein precipitation with 0.1% formic acid in methanol for the extraction of HMB from plasma. Sample extracts were analyzed using LC–MS/MS technique under negative mode electrospray ionization conditions. A ¹³C–labeled stable isotope internal standard was used to achieve accurate quantitation. Multiday validation was conducted for precision, accuracy, linearity, selectivity, matrix effect, dilution integrity (2×), extraction recovery, freeze–thaw sample stability (three cycles), benchtop sample stability (6 h and 50 min), autosampler stability (27 h) and frozen storage sample stability (146 days). Linearity was demonstrated between 10 and 500 ng/mL. Inter‐day accuracies and coefficients of variation (CV) were 91.2–98.1 and 3.7–7.8%, respectively. The validated method was proven to be rugged for routine use to quantify endogenous levels of HMB in human plasma obtained from healthy volunteers.     

Multi‐mycotoxin analysis in complex biological matrices using LC‐ESI/MS: Experimental study using triple stage quadrupole and LTQ‐Orbitrap

In the present study, we report the application of LC‐MS based on two different LC‐MS systems to mycotoxin analysis. The mycotoxins were extracted with an ACN/water/acetic acid mixture and directly injected into a LC‐MS/MS system without any dilution procedure. First, a sensitive and reliable HPLC‐ESI‐MS/MS method using selected reaction monitoring on a triple quadrupole mass spectrometer (TSQ Quantum Ultra AM) has been developed for determining 32 mycotoxins in crude extracts of wheat and maize. This method was operated both in positive and in negative ionization modes in two separate chromatographic runs. The method was validated by studies of spiked recoveries, linearity, matrix effect, intra‐assay precision and sensitivity. Further, we have developed and evaluated a method based on accurate mass measurements of extracted target ions in full scan mode using micro‐LC‐LTQ‐Orbitrap as a tool for fast quantitative analysis. Both instruments exhibited very high sensitivity and repeatability in positive ionization mode. Coupling of micro‐LC to Orbitrap technology was not applicable to the negatively ionizable compounds. The LC triple quadrupole MS method has proved to be stable in quantitation, as it is with respect to the matrix effects of grain samples.     

The validation of a simple LC/MS/MS method for determining the level of mevalonic acid in human plasma

A simple plasma extraction method coupled with liquid chromatography–tandem mass spectrometry (LC/MS/MS) detection was developed and validated for the analysis of endogenous mevalonic acid (MVA), a biomarker indicative of the rate of cholesterol biosynthesis, in human plasma samples. The analyte was extracted from the plasma matrix using a straightforward liquid–liquid sample preparation procedure. The extract supernatants were evaporated, reconstituted in aqueous solvent and injected into the LC/MS/MS system without further processing. The chromatographic separation was achieved on a reverse‐phase high‐performance liquid chromatography column. The accuracy and precision of the method was determined over the concentration range 0.25–25 ng/mL MVA from human plasma extracts in three validation batch runs. Inter‐assay precision (%CV) and accuracy (%RE) of the quality control samples were ≤7.00% (at lower limit quality control) and ≤6.10%, respectively. The sensitivity and throughput of this assay was significantly improved relative to previously published methods, resulting in smaller sample requirements and shorter analysis time. Assay results from a clinical study following the oral administration of an exploratory statin demonstrate that this procedure could potentially be used in the investigation of therapies associated with hypercholesterolemia. Copyright © 2010 John Wiley & Sons, Ltd.     

Application of fractional mass for the identification of peptide-oligonucleotide cross-links by mass spectrometry

A method has been developed to identify oligonucleotide-peptide heteroconjugates by accurate mass measurements using MS. The fractional mass (the decimal fraction mass value following the monoisotopic nominal mass) for peptides and oligonucleotides is different due to their differing molecular compositions. This property has been used to develop the general conditions necessary to differentiate peptides and oligonucleotides from oligonucleotide-peptide heteroconjugates. Peptides and oligonucleotides generated by the theoretical digestion of various proteins and nucleic acids were plotted as nominal mass versus fractional mass. Such plots reveal that three nucleotides cross-linked to a peptide produce enough change in the fractional mass to be recognized from non-cross-linked peptides at the same nominal mass. Experimentally, a Cytochrome c digest was spiked with an oligonucleotide-peptide heteroconjugate and conditions for analyzing the sample using liquid chromatography (LC)-MS were optimized. Upon analysis of this mixture, all detected masses were plotted on a fractional mass plot and the heteroconjugate could be readily distinguished from non-cross-linked peptides. The method developed here can be incorporated into a general proteomics-like scheme for identifying protein-nucleic acid cross-links, and this method is equally applicable to characterizing cross-links generated from protein-DNA and protein-RNA complexes.     

Method development and validation of LC–MS/MS-based assay for the simultaneous quantitation of trastuzumab and pertuzumab in cynomolgus monkey serum and its application in pharmacokinetic study

We present a simple and robust LC–MS/MS assay for the simultaneous quantitation of an antibody cocktail of trastuzumab and pertuzumab in monkey serum. The LC–MS/MS method saved costs, decreased the analysis time, and reduced quantitative times relative to the traditional ligand-binding assays. The serum samples were digested with trypsin at 50°C for 60 min after methanol precipitation, ammonium bicarbonate denaturation, dithiothreitol reduction, and iodoacetamide alkylation. The tryptic peptides were chromatographically separated using a C18 column (2.1 × 50 mm, 2.6 μm) with mobile phases of 0.1% formic acid in water and acetonitrile. The other monoclonal antibody, infliximab, was used as internal standards to minimize the variability during sample processing and detection. A unique peptide for each monoclonal antibody was simultaneously quantified using LC–MS/MS in the multiple reaction monitoring mode. Calibration curves were linear from 2.0 to 400 μg/mL. The intra- and inter-assay precision (%CV) was within 8.9 and 7.4% (except 10.4 and 15.1% for lower limit of quantitation), respectively, and the accuracy (%Dev) was within ±13.1%. The other validation parameters were evaluated, and all results met the acceptance criteria of the international guiding principles. Finally, the method was successfully applied to a pharmacokinetics study after a single-dose intravenous drip administration to cynomolgus monkeys.     

Quantitative analysis of terbinafine (Lamisil) in human and minipig plasma by liquid chromatography tandem mass spectrometry

A method using liquid chromatography/tandem mass spectrometry (LC/MS/MS) for the determination of terbinafine in human and minipig plasma has been developed and validated. The method used positive-ion mode for monitoring terbinafine, and used a stable isotope labelled terbinafine as the internal standard. Subsequent to acetonitrile protein precipitation, the supernatant was directly (unfiltered) injected onto the LC column (retention time approximately 4.3 min) for analysis. Interday and intraday accuracy and precision were assessed from the relative recoveries (observed concentration in percent of the nominal value) of spiked samples analyzed on three different days. The lower limit of quantitation (LLOQ) was 0.0679 ng/mL in human and minipig using a plasma sample volume of 0.08 mL. The method was fast, specific, and exhibited ruggedness. Furthermore, the use of turbulent flow chromatography (TurboFlow LC/MS/MS) coupled to mass spectrometry for direct analysis of terbinafine in plasma is discussed. The technique allowed direct introduction of plasma with satisfactory chromatographic peak shape and increased throughput.Copyright 2000 John Wiley & Sons, Ltd.     

Use of liquid chromatography-atmospheric pressure chemical ionization-ion trap mass spectrometry for identification of oleanolic acid and ursolic acid in Anoectochilus roxburghii (wall.) Lindl

Oleanolic acid (OA) and ursolic acid (UA) are the two important bioactive compounds in Anoectochilus roxburghii (wall) Lindl (A. roxburghii), which has been used as a traditional Chinese medicine. So far, there has been no report to indicate that A. roxburghii contains these two bioactive compounds. It is necessary to develop an effective method to extract and analyze OA and UA in A. roxburghii. In this paper, a quantitative method, consisting of supercritical fluid extraction (SFE) followed by liquid chromatography-atmospheric pressure chemical ionization-ion trap mass spectrometry (LC-APCI-IT-MS) analysis, was developed for identification of OA and UA in A. roxburghii. The extraction was carried out by using CO(2) as the supercritical fluid and ethanol as the modifier before LC separation. The mobile phase used for LC separation consisted of acetic acid (1%, v/v), water (15%, v/v) and methanol (84%, v/v), and the elution was performed at a flow rate of 0.8 ml/min. The mass spectrometer was operated in APCI(+) mode with selected ion monitoring (SIM) to quantify OA and UA at m/z 439.4. Under optimum conditions, the linear responses of OA and UA were obtained in the concentration range of 0.5-80 (r = 0.9992) and 0.5-50 microg/ml (r = 0.9989) with the detection limits of 0.125 and 0.085 microg/ml, respectively. The proposed method has been used for the identification and quantitation of OA and UA in a real A. roxburghii sample.     

Matrix effects on accurate mass measurements of low-molecular weight compounds using liquid chromatography-electrospray-quadrupole time-of-flight mass spectrometry

Liquid chromatography (LC) with high-resolution mass spectrometry (HRMS) represents a powerful technique for the identification and/or confirmation of small molecules, i.e. drugs, metabolites or contaminants, in different matrices. However, reliability of analyte identification by HRMS is being challenged by the uncertainty that affects the exact mass measurement. This parameter, characterized by accuracy and precision, is influenced by sample matrix and interferent compounds so that questions about how to develop and validate reliable LC-HRMS-based methods are being raised. Experimental approaches for studying the effects of various key factors influencing mass accuracy on low-molecular weight compounds (MW < 150 Da) when using a quadrupole-time-of-flight (QTOF) mass analyzer were described. Biogenic amines in human plasma were considered for the purpose and the effects of peak shape, ion abundance, resolution and data processing on accurate mass measurements of the analytes were evaluated. In addition, the influence of the matrix on the uncertainty associated with their identification and quantitation is discussed. A critical evaluation on the calculation of the limits of detection was carried out, considering the uncertainty associated with exact mass measurement of HRMS-based methods. The minimum concentration level of the analytes that was able to provide a statistical error lower than 5 ppm in terms of precision was 10 times higher than those calculated with S/N = 3, thus suggesting the importance of considering both components of exact mass measurement uncertainty in the evaluation of the limit of detection.     

Simple fabrication of hydrophobic surface target for increased sensitivity and homogeneity in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis of peptides,phosphopeptides, carbohydrates and proteins

To enhance sample signals and improve homogeneity in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) analysis, a simple, rapid, and efficient sample preparation method was developed in this study. Polydimethylsiloxane (PDMS) was coated on a stainless steel MALDI plate, forming a transparent, hydrophobic surface that enhanced sample signals without producing observable background signals. Compared to the use of an unmodified commercial metal MALDI plate, peptide signals were enhanced by ~7.1–11.0-fold due to the reduced sample spot area of the PDMS-coated plate, and showed improved peptide mass fingerprinting (PMF) and MS/MS peptide sequencing results. In the analysis of phosphopeptides and carbohydrates with a 2,5-dihydroxybenzoic acid (DHB) matrix, the PDMS-coated plate showed improved sample homogeneity and signal enhancements of ~5.2–8.2-fold and ~2.8–3.2-fold, respectively. Improved sensitivity in the observation of more unique fragment ions by MS/MS analysis, to successfully distinguish isomeric carbohydrates, was also illustrated. In protein analysis with a sinapinic acid (SA) matrix, a ~3.4-fold signal enhancement was observed. The PDMS film coating was easily removed and refabricated to avoid sample carryover, and was applicable to diverse commercial MALDI plates. The PDMS-coated approach is a simple, practical, and attractive method for enhancing analyte signals and homogeneity.     

LC-MS-MS Method for the Determination of Protoveratrine A in Rat Plasma

The present experiments were designed for the development of a liquid chromatographic coupled with tandem mass spectrometric method for the quantitation of trace amount of protoveratrine A in rat plasma. A liquid-liquid extraction protocol was involved in sample preparation. Quantitation was achieved using multiple-reaction-monitoring (MRM) mode. The method was validated with the concentration range 0.02–40 ngmL^?1 in plasma. Intra-/inter-day accuracy and precision as well as the LOD and the lower limit of quantitation were acceptable. The method was further applied to analyze protoveratrine A in rat plasma samples.     

Closely spaced external standard: a universal method of achieving 5 ppm mass accuracy over the entire MALDI plate in axial matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Close deposition of the sample and external standard was used in axial matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) to achieve mass accuracy equivalent to that obtained with an internal standard across the entire MALDI plate. In this work, the sample and external standard were deposited by continuous deposition in separate traces, each approximately 200 micro m wide. The dependence of the mass accuracy on the distance between the sample and standard traces was determined across a MALDI target plate with dimensions of 57.5 mm x 57.0 mm by varying the gap between the traces from 100 micro m to 4 mm. During acquisition, two adjacent traces were alternately irradiated with a 200-Hz laser, such that the peaks in the resulting mass spectra combined the sample and external standard. Ion suppression was not observed even when the peptide concentrations in the two traces differed by more than two orders of magnitude. The five peaks from the external standard trace were used in a four-term mass calibration of the masses of the sample trace. The average accuracy across the whole plate with this method was 5 ppm when peaks of the sample trace had signal-to-noise ratios of at least 30 and the gap between the traces was approximately 100 micro m. This approach was applied to determining peptide masses of a reversed-phase liquid chromatographic (LC) separation of a tryptic digest of beta-galactosidase deposited as a long serpentine trace across the MALDI plate, with accuracy comparable to that obtainable using internal calibration. In addition, the eluent from reversed-phase LC separation of a strong cation-exchange fraction containing tryptic peptides from a yeast lysate along with the closely placed external standard was deposited on the MALDI plate. The data obtained in the MS and MS/MS modes on a MALDI-TOF/TOF mass spectrometer were combined and used in database searching with MASCOT. Since the significant score is a function of mass accuracy in the MS mode, database searching with high mass accuracy reduced the number of false positives and also added peptides which otherwise would have been eliminated at lower mass accuracy (false negatives).