An identification method for altered proteins in tissues utilizing fluorescence derivatization, liquid chromatography, tandem mass spectrometry, and a database-searching algorithm

Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) is now widely used as a tool for proteomic studies. For the sensitive determination of proteins in 2D-PAGE, fluorescence derivatization of primary amino moieties of proteins with cyanine dyes was recently developed. However, precipitation of the proteins could occur if completely derivatized because of the lower solubility of the resultant derivatives owing to the hydrophobicity of the reagents and the loss of the hydrophilic primary amino moieties. Thus, in this paper, a water-soluble and thiol-specific fluorogenic reagent, ammonium 7-fluoro-2,1,3-benzoxadiazole-4-sulfonate, was adopted for the derivatization of proteins in tissues either with and without stimulation. Then, the method follows a separation of the derivatives by liquid chromatography with fluorescence detection, an isolation of only the altered proteins, an enzymatic digestion of the isolated proteins, and an identification of the proteins by liquid chromatography/MS/MS with the database-searching algorithm. By using this method, we identified the altered expressions of five increased proteins (e.g., pancreatic polypeptide) as well as three decreased proteins (e.g., insulin 2) in the islets of Langerhans in Wistar rats 2 days after they were subcutaneously administered with dexamethasone.     

A Fluorogenic Reagent, 7-Phenylsulfonyl-4-(2,1,3-benzoxadiazolyl) Isocyanate for Alcohols, with Development Based on the Empirical Method for Prediction

During the course of our studies, we found the relationship between the fluorescence characteristics (the fluorescence intensity and the maximum excitation and emission wavelengths) of benzofurazan compounds and the sum and difference of Hammett substituent constants (σp) at the 4- and 7- positions. This prompted us to design a useful fluorogenic derivatization reagent having the benzofurazan skeleton for alcohols along this line of thought. Accordingly, the fluorogenic derivatization reagents, which have no fluorescence themselves, 7-N,N-dimethylaminosulfonyl-4-(2,1,3-benzoxadiazolyl) isocyanate (DBD-NCO), 7-phenylsulfonyl-4-(2,1,3-benzoxadiazolyl) isocyanate (PSBD-NCO), and 7-methylsulfonyl-4-(2,1,3-benzoxadiazolyl) isocyanate (MSBD-NCO), were synthesized. Among the derivatives derived from the three reagents, that from PSBD-NCO was most strongly fluorescent. PSBD-NCO reacted with 1-octanol within 4 h in acetonitrile solution in the absence of a catalyst at 60 °C. The derivatives with four alcohols (1-octanol, 1-nonanol, 1-decanol, and 1-undecanol) were separated on a reversed-phase column and detected fluorimetrically at 490 nm with the excitation at 368 nm. The detection limits were at the 10-femtomole level. PSBD-NCO was superior to other fluorescent-labeling reagents with regard to the avoidance of the interfering peaks derived from the reagents themselves and degradation products in the chromatogram. The effectiveness of our approach is disccussed in terms of the development of new fluorogenic reagents.     

Mass defect labeling of cysteine for improving peptide assignment in shotgun proteomic analyses

A method for improving the identification of peptides in a shotgun proteome analysis using accurate mass measurement has been developed. The improvement is based upon the derivatization of cysteine residues with a novel reagent, 2,4-dibromo-(2'-iodo)acetanilide. The derivitization changes the mass defect of cysteine-containing proteolytic peptides in a manner that increases their identification specificity. Peptide masses were measured using matrix-assisted laser desorption/ionization Fourier transform ion cyclotron mass spectrometry. Reactions with protein standards show that the derivatization of cysteine is rapid and quantitative, and the data suggest that the derivatized peptides are more easily ionized or detected than unlabeled cysteine-containing peptides. The reagent was tested on a 15N-metabolically labeled proteome from M. maripaludis. Proteins were identified by their accurate mass values and from their nitrogen stoichiometry. A total of 47% of the labeled peptides are identified versus 27% for the unlabeled peptides. This procedure permits the identification of proteins from the M. maripaludis proteome that are not usually observed by the standard protocol and shows that better protein coverage is obtained with this methodology.     

A fluorogenic reagent, 4-mercapto-7-methylthio-2,1,3-benzoxadiazole for carboxylic acids, designed by prediction of the fluorescence intensity

During the course of our studies of the development of fluorogenic reagents having a 4,7-disubstituted benzofurazan structure, we previously proposed 7-acetylamino-4-mercapto-2,1,3-benzoxadiazole (AABD-SH) as a fluorogenic reagent for carboxylic acids. Since then, progress has made it possible to estimate the fluorescence quantum yields of the 4,7-disubstituted benzofurazan compounds on the basis of the PM3 calculation of their S1-T2 energies. Subsequently, a new fluorogenic reagent, 4-mercapto-7-methylthio-2,1,3-benzoxadiazole (MTBDSH) was designed and synthesized. In the presence of condensation reagents, triphenylphosphine (TPP) and 2,2'-dipyridyl disulfide (DPDS), MTBD-SH readily reacted with n-caprylic acid within 1 min at room temperature. The derivatives of five carboxylic acids (n-caprylic acid, n-capric acid, lauric acid, myristic acid, and palmitic acid) were well-separated on a reversed-phase column and were fluorimetrically detected at 519 nm with excitation at 391 nm. The detection limits (S/N = 3) were 2.4-5.0 fmol. Thus, MTBD-SH had properties that were considered to be superior. For carboxylic acids, itwas superior not only to AABD-SH, but also to many other conventional reagents. The superiority was examined in terms of its reactivity and sensitivity and the avoidance of interfering peaks that were derived from the reagent itself or degradation products in the chromatogram.     

Determination of insulin in a single islet of Langerhans by high-performance liquid chromatography with fluorescence detection

Rodents (rat and mouse) have two types of insulin (insulin I and II; each contains a universal chain A and a different composition of each type BI chain or type BII chain). The physiological role for each isomer is not yet clarified because of the lack of an appropriate separative determination method for these isomers. Thus, in this paper, a sensitive and selective HPLC-fluorescence determination method for the isomers was developed, which includes derivatization with a fluorogenic reagent for thiols, 7-fluoro-2,1,3-benzoxadiazole-4-sulfonate, in the presence of a reducing agent, TCEP, a nonionic surfactant, n-dodecyl beta-D-maltopyranoside, and EDTA. The resultant chain A, BI, and BII derivatives were separated on a reversed-phase column (TSK gel ODS-120T, 250 x 4.6 mm i.d.) with a mobile phase containing 5 mM phosphate buffer (pH 7.0) and were detected at 505 nm with excitation at 380 nm. The detection limits for chain A, BI, and BII derivatives were 2.2, 3.4, and 3.7 fmol on column, respectively. The method was applicable to the determination of rodent insulin in a single islet of Langerhans, and the results indicated its feasibility for the investigation of the pathophysiological roles of the isomers in diabetes in the rodent.     

Enantiomeric Separation and Detection of 2-Arylpropionic Acids Derivatized with [(N,N-Dimethylamino)sulfonyl]benzofurazan Reagents on a Modified Cellulose Stationary Phase by High-Performance Liquid Chromatography

(RS)-2-Arylpropionic acids (2-APAs) were derivatized with the fluorogenic reagents, 4-[(N,N-dimethylamino)sulfonyl]-7-piperazino-2,1,3-benzoxadiazole (DBD-PZ) and 4-[[(N-hydrazinoformyl)methyl]-N-methyl]amino-7-[N,N-(dimethylamino)sulfonyl]-2,1,3-benzoxadiazole (DBD-COHz), and their enantiomeric separation by a chiral stationary phase high-performance liquid chromatography was investigated in the reversed-phase mode with H(2)O/CH(3)CN or H(2)O/MeOH as the mobile phase on a column of cellulose tris(3,5-dimethylphenyl carbamate) coated on a silica gel support (Chiralcel OD-R). The derivatives with DBD-PZ were enantiomerically separated well under the elution condition of H(2)O/MeOH, based on the π-π interaction between the derivatives and the stationary phase. The rigid and bulky structure of DBD-PZ was demonstrated to be more effective as compared to the less rigid ones. The derivatives with DBD-COHz were more efficiently separated into each enantiomer with H(2)O/CH(3)CN as the eluent. The effective separation was based on hydrogen-bonding interaction between the acid hydrazide of the derivatives and the carbamoyl moiety of the stationary phase. There was a reversal in the elution order of the enantiomers between the two fluorescent derivatives. The detection limits obtained for each enantiomer were approximately 10-30 fmol on column. The derivatization with the reagent and the concomitant use of the reversed-phase and chiral stationary-phase HPLC were demonstrated to be useful for the enantiomeric quantification in rat plasma after intravenous administration of flurbiprofen racemate, a representative of 2-APAs.     

Global amine and acid functional group modification of proteins

A sequential reaction methodology is employed for the complete derivatization of protein thiols, amines, and acids in high purity under denaturing conditions. Following standard thiol alkylation, protein amines are modified via reductive methylation with formaldehyde and pyridine-borane. Protein acids are subsequently amidated under buffered conditions in DMSO using the coupling reagent (7-azabenzotriazol-1-yloxy)tripyrrolidinophosphonium hexafluorophosphate. The generality of the approach is demonstrated with four proteins and with several amines yielding near-quantitative transformations as characterized by high-resolution Fourier transform mass spectrometry. The developed approach has numerous implications for protein characterization and general protein chemistry. Applications in mass spectrometry (MS) based proteomics of intact proteins (top-down MS) are explored, including the addition of stable isotopes for relative quantitation and protein identification through functional group counting. The methodology can be used for altering the physical and chemical properties of proteins, as demonstrated with amidation to modify protein isoelectric point and through derivatization with quaternary amines. Additionally, the chemistry has applications in the semisynthesis of monodisperse polymers based on protein scaffolds. We prepare proteins modified with azides and alkynes to enable further functionalization via copper(I)-catalyzed 1,3-dipolar Huisgen cycloaddition ("click") chemistry.     

Enhanced sample multiplexing for nitrotyrosine-modified proteins using combined precursor isotopic labeling and isobaric tagging

Current strategies for identification and quantification of 3-nitrotyrosine (3NT) post-translationally modified proteins (PTM) generally rely on biotin/avidin enrichment. Quantitative approaches have been demonstrated which employ isotopic labeling or isobaric tagging in order to quantify differences in the relative abundances of 3NT-modified proteins in two or potentially eight samples, respectively. Here, we present a novel strategy which uses combined precursor isotopic labeling and isobaric tagging (cPILOT) to increase the multiplexing capability of quantifying 3NT-modified proteins to 12 or 16 samples using commercially available tandem mass tags (TMT) or isobaric tags for relative and absolute quantification (iTRAQ), respectively. This strategy employs "light" and "heavy" labeled acetyl groups to block both N-termini and lysine residues of tryptic peptides. Next, 3NT is reduced to 3-aminotyrosine (3AT) using sodium dithionite followed by derivatization of light and heavy labeled 3AT-peptides with either TMT or iTRAQ multiplex reagents. We demonstrate the proof-of-principle utility of cPILOT with in vitro nitrated bovine serum albumin (BSA) and mouse splenic proteins using TMT(0), TMT(6), and iTRAQ(8) reagents and discuss limitations of the strategy.     

Chip-based on-line nanospray MS method enabling study of the kinetics of isocyanate derivatization reactions

The reaction of propyl isocyanate (2), benzyl isocyanate (3), and toluene-2,4-diisocyanate (4) with 4-nitro-7-piperazino-2,1,3-benzoxadiazole (1) to yield the corresponding urea derivatives 5 was carried out in a continuous flow glass microfluidics chip. Real-time monitoring of the derivatization reactions was done by electrospray ionization mass spectrometry, making use of a recently reported modular chip-MS interface. Rate constants of 1.5 x 10(4), 5.2 x 10(4), and 2.4 x 10(4) M(-1) min(-1) were determined for 2, 3, and 4, respectively. Using macroscale batch conditions, the rate constants are 3-4 times lower. The faster on-chip kinetics is attributed to the more efficient molecular diffusion in the micrometer-sized channel.     

Enrichment of carbonylated peptides using Girard P reagent and strong cation exchange chromatography

It has been shown that oxidatively modified forms of proteins accumulate during oxidative stress, aging, and in some age-related diseases. One of the unique features of protein oxidation by a wide variety of routes is the generation of carbonyl groups. Of major interest in the study of oxidative stress diseases is which proteins in a proteome are being oxidized and the site(s) of oxidation. Based on the fact that proteins are generally characterized through tryptic peptide fragments, this paper reports a method for the isolation of oxidized peptides, which involves (1) derivatization of oxidized proteins with Girard P reagent (GRP; 1-(2-hydrazino-2-oxoethyl)pyridinium chloride), (2) following proteolysis enrichment of the derivatized peptide using strong cation exchange (SCX) chromatography, and (3) identification of oxidation sites using tandem mass spectrometry. Derivatization of aldehydes and ketones in oxidized proteins was accomplished by reacting protein carbonyls with the hydrazide of GRP. The resulting hydrazone bond was reduced by sodium cyanoborohydride to further stabilize the labeling. Derivatization time and concentrations of the derivatizing agent were optimized with model peptides. Oxidized transferrin was used as model protein to study derivatization efficiency at the protein level. Following metal-catalyzed oxidation of transferrin, the protein was derivatized with GRP and trypsin digested. Positively charged peptides were then selected from the digest with SCX chromatography at pH 6.0. Seven GRP-derivatized peptides were found to be selected from transferrin by MALDI-TOF-TOF analysis. Fourteen underivatized native peptides were also captured by the SCX column at pH 6.0. Mapping of the derivatized peptides onto the primary structure of transferrin indicated that the oxidation sites were all on solvent-accessible regions at the protein surface. Efficiency of the method was further demonstrated in the identification of oxidized proteins from yeast.     

Quantitative proteomic analysis using a MALDI quadrupole time-of-flight mass spectrometer

We describe an approach to the quantitative analysis of complex protein mixtures using a MALDI quadrupole time-of-flight (MALDI QqTOF) mass spectrometer and isotope coded affinity tag reagents (Gygi, S. P.; et al. Nat. Biotechnol. 1999, 17, 994-9.). Proteins in mixtures are first labeled on cysteinyl residues using an isotope coded affinity tag reagent, the proteins are enzymatically digested, and the labeled peptides are purified using a multidimensional separation procedure, with the last step being the elution of the labeled peptides from a microcapillary reversed-phase liquid chromatography column directly onto a MALDI sample target. After addition of matrix, the sample spots are analyzed using a MALDI QqTOF mass spectrometer, by first obtaining a mass spectrum of the peptides in each sample spot in order to quantify the ratio of abundance of pairs of isotopically tagged peptides, followed by tandem mass spectrometric analysis to ascertain the sequence of selected peptides for protein identification. The effectiveness of this approach is demonstrated in the quantification and identification of peptides from a control mixture of proteins of known relative concentrations and also in the comparative analysis of protein expression in Saccharomyces cerevisiae grown on two different carbon sources.     

Microwave-assisted protein solubilization for mass spectrometry-based shotgun proteome analysis

Protein solubilization is a key step in mass spectrometry-based shotgun proteome analysis. We describe a microwave-assisted protein solubilization (MAPS) method to dissolve proteins in reagents, such as NH(4)HCO(3) and urea, with high efficiency and with an added benefit that the solubilized proteins are denatured to become more susceptible to trypsin digestion, compared to other conventional protein solubilization techniques. In this method, a sample vial containing proteins suspended in a solubilization reagent is placed inside a domestic microwave oven and subjected to microwave irradiation for 30 s, followed by cooling the sample on ice to room temperature (~40 s) and then intermittent homogenization by vortex for 2 min. This cycle of microwave irradiation, cooling, and homogenization is repeated six times. In this way, sample overheating can be avoided, and a maximum amount of protein can be dissolved. It was shown that in the case of trypsin digestion of bovine serum albumen (BSA) more peptides and higher sequence coverage could be obtained from the protein dissolved by the MAPS method than the conventional heating, sonication, or vortex method. Compared to the most commonly used vortex-assisted protein solubilization method, MAPS reduces the solubilization time significantly, increases the amount of protein dissolvable in a reagent, and increases the number of proteins and peptides identified from a proteome sample. For example, in the proteome analysis of an Escherichia coli K-12 integral membrane protein extract, the MAPS method in combination with sequential protein solubilization and shotgun two-dimensional liquid chromatography tandem mass spectrometry analysis identified a total of 1291 distinct proteins and 10363 peptides, compared to 1057 proteins and 6261 peptides identified using the vortex method. Because MAPS can be done using an inexpensive microwave oven, this method can be readily adopted.     

Peptide mapping of complex proteins at the low-picomole level with capillary electrophoretic separations.

A variety of different peptide-mapping schemes are presented, with emphasis on the development of procedures which can be done with limited quantities (i.e. 5 pmol) of protein. Results are obtained from model proteins which contain disulfide bonds, which must be broken prior to fragmentation of the protein. A reaction involving the simultaneous use of tributylphosphine and 2-methylaziridine to reduce and alkylate the disulfide bonds is employed, due to favorable attributes of these reagents for the scaled-down procedure. The traditional performic acid oxidation reaction to cleave cystine groups is also successfully used with low-picomole quantities of protein. Three different protein digestion reagents are used: trypsin, chymotrypsin, and cyanogen bromide. Each reagent produces a unique mixture of peptides. Capillary electrophoresis is used to separate the peptides, offering high separation efficiencies, short analysis times, and compatibility with small sample sizes. In addition to the conventional use of UV detection for underivatized peptides, laser-induced fluorescence detection is employed in conjunction with an arginine-selective derivatization reaction. This latter procedure for derivatization and detection offers an alternative peptide-mapping mode, in which only the arginine-containing peptides are detected, and is useful in simplifying the peptide maps of large proteins.     

Absolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags

The identification of proteins in complex mixtures is most useful when quantitative information is also obtained. We describe a new type of protein tagging reagent called the visible isotope-coded affinity tag (VICAT) which allows the absolute amount of a target protein or proteins to be quantified in a complex biological sample such as a eukaryotic cell lysate. VICAT reagents tag thiol groups of cysteines or thioacetylated amino groups and introduce into the tryptic peptide a biotin affinity handle, a visible moiety for tracking the chromatographic location of the target peptide by a method other than mass spectrometry, a photocleavable linker for removing a portion of the tag, and an isotope tag for distinguishing sample and internal standard peptides. We demonstrate the use of VICAT reagents together with isoelectric focusing of peptides on an immobilized gel strip followed by combined micro-liquid chromatography/electrospray ionization mass spectrometry operating in selected reaction monitoring mode to determine the absolute abundance of a specific protein, human group V phospholipase A(2), in eukaryotic cell lysates. It is found that human lung macrophages contain 66 fmol of this protein per 100 microg of cell protein. Western blot analysis of human group V phospholipase A(2) in macrophages gave inconclusive data. VICAT reagents should be useful for numerous applications including the analysis of candidate disease markers in complex mixtures such as serum.     

Development of an amino acid sequence and D/L-configuration determination method of peptide with a new fluorescence Edman reagent, 7-methylthio-4-(2,1,3-benzoxadiazolyl) isothiocyanate

On the basis of the relationship between the fluorescence characteristics of the benzofurazan compounds and the Hammett constants (sigma p), a new fluorescence Edman reagent, 7-methylthio-4-(2,1,3-benzoxadiazolyl) isothiocyanate (MTBD-NCS) was designed and synthesized. MTBD-thiohydantoin (TH)-amino acid derivatives produced by the Edman sequencing method gave fluorescence, whereas other degradation byproducts such as MTBD-thiocarbamoyl (TC)- or carbamoyl (CA)-amino acids did not fluoresce. MTBD-NCS was applicable as an Edman sequencing reagent to the simultaneous determination of both the sequence and D/L-configuration of amino acids in peptides. Boron trifluoride (BF3) and HC1/methanol were adopted as the cyclization/cleavage and conversion reagents to suppress the amino acid residue racemization. The MTBD-TH-amino acids were separated on a reversed-phase column for amino acid sequencing, and their enantiomers were resolved on two types of polysaccharide-based chiral stationary phases for D/L-configuration determination. The method was successfully applied to the sequence and D/L-configuration determination of D-amino acid-containing peptide [D-Ala2]-deltorphin II.     

Chemical suppression of contaminant metal ions using a metastable state in precolumn derivatizing HPLC: an ultratrace fluorometric detection of Al(III)

The contamination of metal ions from reagents used frequently restricts the practical detection limit of the metal ion, which itself is a source of contamination. We have found a novel solution to this problem, a chemical-suppressing method of contaminant metal ions on a reversed-phase HPLC for Al3+ with a detection limit of 7.6 x 10(-11) mol dm(-3) (2.1 ng dm(-3)) by only adding a certain agent into all stock solutions without any preconcentration or purification steps. This technique decreases the concentration of the contaminant Al3+ originating from the reagents by more than 1 order of magnitude using selective derivatization of sample Al3+ ions to a powerful fluorescent complex at a metastable state in the precolumn chelation processes. Meanwhile, the contaminant Al3+ remains as a nonfluorescent complex with a blocking reagent in order to suppress the contamination. This selective derivatization is achieved by the accumulation of several complexation processes based on the difference of formation, dissociation, and ligand-exchange kinetics and the thermodynamics between the derivatizing reagent, the 4',5'-geometorical isomer of calcein, and the blocking reagent, o,o'-dihydroxyazobenzene. This simple and smart HPLC system was validated through recovery tests of environmental and biological samples.     

In-spray supercharging of peptides and proteins in electrospray ionization mass spectrometry

Enhanced charging, or supercharging, of analytes in electrospray ionization mass spectrometry (ESI MS) facilitates high resolution MS by reducing an ion mass-to-charge (m/z) ratio, increasing tandem mass spectrometry (MS/MS) efficiency. ESI MS supercharging is usually achieved by adding a supercharging reagent to the electrospray solution. Addition of these supercharging reagents to the mobile phase in liquid chromatography (LC)-MS/MS increases the average charge of enzymatically derived peptides and improves peptide and protein identification in large-scale bottom-up proteomics applications but disrupts chromatographic separation. Here, we demonstrate the average charge state of selected peptides and proteins increases by introducing the supercharging reagents directly into the ESI Taylor cone (in-spray supercharging) using a dual-sprayer ESI microchip. The results are comparable to those obtained by the addition of supercharging reagents directly into the analyte solution or LC mobile phase. Therefore, supercharging reaction can be accomplished on a time-scale of ion liberation from a droplet in the ESI ion source.     

Mass spectrometric analysis of mercury incorporation into proteins for X-ray diffraction phase determination

Heavy-atom incorporation is an essential and often rate-limiting step in the determination of phases for X-ray diffraction studies of protein structures. Until the present, there has been no practical method (short of the X-ray diffraction experiment itself) to judge the success and extent of incorporation. Here we show that mass spectrometry is an effective tool for determining the extent of heavy-atom incorporation in proteins. In particular, we demonstrate the utility of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and electrospray ionization mass spectrometry (ESI-MS) for assaying mercury derivatization of cysteinyl thiol groups in proteins. Each of these mass spectrometric methods has advantages and drawbacks. ESI-MS provides a more accurate quantitative measurement of the extent of mercury incorporation, while MALDI-MS provides a useful lower limit to the level of mercury incorporation. Conversely, MALDI-MS does not require removal of excess derivatization reagents, salts and buffers, thus permitting facile analysis of single protein crystals as well as rapid, semiquantitative evaluation of the extent of protein mercuration. The approaches described in the present paper have contributed to the successful X-ray analyses of several noteworthy protein structures.     

Ion-molecule reactions for the characterization of polyols and polyol mixtures by ESI/FT-ICR mass spectrometry

A mass spectrometric method is described for the identification and counting of hydroxyl groups in an analyte. Analytes introduced into a FT-ICR mass spectrometer and ionized by positive mode ESI were allowed to react with the neutral reagent diethylmethoxyborane. This results in derivatization of the hydroxyl groups of the analytes by replacement of a proton with a diethylborenium ion. Protonated polyols react by consecutive derivatization reactions, wherein all, or nearly all, of the hydroxyls are derivatized. The polyol derivatization products are separated by 68 mass units in the mass spectrum. This 68 Da mass shift, along with 30 Da mass shifts arising from intramolecular derivatization of the primary derivatization products, makes it easy to count the number of functional groups present in the analyte. The utility of this method for the analysis of polyols as single-component solutions, as mixtures, or in HPLC effluent (LC-MS analysis) is demonstrated.     

C-terminal sequence analysis of peptides and proteins using carboxypeptidases and mass spectrometry after derivatization of Lys and Cys residues

C-Terminal sequence analysis of peptides and proteins using carboxypeptidase digestion in combination with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is convenient for protein and peptide characterization. After a short digestion, a sequence up to 20 residues can be identified, but the total number depends on the individual sequence. Due to the accuracy limits of the MALDI time-of-flight arrangement, the assignment of several residues with close mass values, including Lys/Glx, may remain ambiguous. We have used derivatization of lysine residues by guanidination to overcome the problem of Lys identification. The reaction is rapid and specific and results in full derivatization. In the case of Cys-containing peptides, problems arise from the fact that carboxypeptidases Y and P do not cleave peptides that contain nonderivatized cystine, cysteic acid, or (carboxymethyl)cysteine. Successful identification of Cys residues within the sequence is instead achieved by conversion of Cys to 4-thialaminine by (trimethylamino)-ethylation. The two derivatizations of Lys and Cys side chains provide opportunities for proton attachment and therefore facilitate the analysis by MALDI-MS. This C-terminal sequence analysis method is also useful for large proteins after fragmentation with specific enzymes.