Alkylated dihydroxybenzoic acid as a MALDI matrix additive for hydrophobic peptide analysis

Hydrophobic peptides are generally difficult to detect using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) because the majority of MALDI matrixes are hydrophilic and therefore have a low affinity for hydrophobic peptides. Here, we report on a novel matrix additive, o-alkylated dihydroxybenzoic acid (ADHB), which is a 2,5-dihydroxybenzoic acid (DHB) derivative incorporating a hydrophobic alkyl chain on a hydroxyl group to improve its affinity for hydrophobic peptides, thereby improving MALDI-MS sensitivity. The addition of ADHB to the conventional matrix α-cyano-4-hydroxycinnamic acid (CHCA) improved the sensitivity of hydrophobic peptides 10- to 100-fold. The sequence coverage of phosphorylase b digest was increased using ADHB. MS imaging indicated that hydrophobic peptides were enriched in the rim of a matrix/analyte dried spot when ADHB was used. In conclusion, the addition of ADHB to the standard matrix led to improved sensitivity of hydrophobic peptides by MALDI-MS.     

Enhanced detection of oligonucleotides in UV MALDI MS using the tetraamine spermine as a matrix additive.

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) has been used to analyze oligonucleotides. However, success has been limited by cation adduction and high detection limits. Both of these problems are due to the high net negative charge that oligonucleotides carry on the phosphodiester backbone. Comatrixes such as ammonium salts with UV absorbers such as 3-hydroxypicolinic acid, 2,4,6-trihydroxyacetophenone, and 6-aza-2-thiothymine have been used to improve the spectral quality for oligonucleotides in MALDI MS. Organic bases have also been used as co-matrixes; however, the most popular matrix, 3-hydroxypicolinic acid, is not compatible with these additives. We have found that the tetraamine spermine as a matrix additive can successfully eliminate cation adduction and lower the detection limits for DNA in the MALDI experiment, without having to resort to desalting steps. The results suggest that multiply protonated spermine molecules function better than ammonium ions in neutralizing oligonucleotides and displacing alkali cations. Protonated spermine is chemically similar to ammonium ions since it binds to the phosphate backbone and releases protons to the phosphate groups. Spermine can be used successfully with the matrixes 6-aza-2-thiothymine and 80% anthranilic acid/20% nicotinic acid but not with 3-hydroxypicolinic acid. The additive also works well for the analysis of metalated DNA.     

Gold nanoparticles as selective and concentrating probes for samples in MALDI MS analysis

MALDI mass spectrometry is used widely in various fields because it has the characteristics of speed, ease of use, high sensitivity, and wide detectable mass range, but suppression effects between analyte molecules and interference from the sample matrix frequently arise during MALDI analysis. The suppression effects can be avoided if target species are isolated from complicated matrix solutions in advance. Herein, we proposed a novel method for achieving such a goal. We describe a strategy that uses gold nanoparticles to capture charged species from a sample solution. Generally, ionic agents, such as anionic or cationic stabilizers, encapsulate gold nanoparticles to prevent their aggregation in solution. These charged stabilizers at the surface of the gold particles are capable of attracting oppositely charged species from a sample solution through electrostatic interactions. We have employed this concept to develop nanoparticle-based probes that selectively trap and concentrate target species in sample solutions. Additionally, to readily isolate them from solution after attracting their target species, we used gold nanoparticles that are adhered to the surface of magnetic particles through S-Au bonding. A magnet can then be employed to isolate the Au@magnetic particles from the solution. The species trapped by the isolated particles were then characterized by MALDI MS after a simple washing. We demonstrate that Au@magnetic particles having negatively charged surfaces are suitable probes for selectively trapping positively charged proteins from aqueous solutions. In addition, we have employed Au@magnetic particle-based probes successfully to concentrate low amounts of peptide residues from the tryptic digest products of cytochrome c (10(-7) M).     

Selective sampling of phosphopeptides for detection by MALDI mass spectrometry

The analysis of phosphopeptides by mass spectrometry (MS) is one of the most challenging tasks in proteomics. This is due to the lower isoelectric point (pI) of phosphopeptides, which leads to inefficient sample ionization in MS, particularly when competing with other peptides. The problem is compounded by the typical low abundance of phosphopeptides in biological samples. We describe here a simple nonsorptive method to isolate phosphopeptides based on their pI. A voltage is applied to selectively migrate the phosphopeptides into a capillary, which are negatively charged at acidic pH. The selectively sampled fraction is directly deposited onto MALDI sample target in nanoliter volumes (7-35 nL) for highly sensitive MS detection. No significant sample loss is evident in this procedure; hence, the MS was able to detect the isolated phosphopeptides at trace quantity. In this case, attomole-level detection limit is achieved for synthetic phosphopeptides (nM concentration and nL volume), from a mixture containing other peptides at up to 1 million times higher in concentration. Selective sampling was also applied to the tryptic digest of beta- and alpha-caseins to reveal the multiple phosphorylated peptides at the low-femtomole level using MALDI MS. Knowledge of pI based on the rejection/injection of peptides was found to be useful in peak assignment. To confirm the sequence of the selectively sampled peptides, fraction collection was performed for offline ESI MS/MS analysis.     

Comprehensive phosphorylation site analysis of individual phosphoproteins applying scoring schemes for MS/MS data

We have developed novel scoring schemes for the identification of (phospho)peptides (PeptideScore) and for pinpointing phosphorylation sites (PhosphoSiteScore) using MS/MS data. These scoring schemes have been developed for the in-depth analysis of individual phosphoproteins, not for large-scale phosphoproteomic-type data. The scoring schemes are implemented into the new software tool Phosm, which provides a concise and comprehensive presentation of the results. For development and evaluation of these schemes, we have analyzed approximately 500 phosphopeptide MS/MS spectra, most of them nontryptic peptides. The novel scoring schemes turned out to be very powerful, even with CID MS/MS spectra of very low quality. Many phosphopeptides and phosphorylation sites that remained unassigned in our LC-MS/MS data sets with Mascot could be identified with Phosm. Especially the number of identified multiply phosphorylated peptides could be significantly increased. The applied scoring parameters are described, and the scoring for several selected examples of phosphopeptides is discussed in detail. Furthermore, a new and simple nomenclature for all types of phosphorylated fragment ions is introduced in this publication.     

Tetraalkylphosphonium-based ionic liquids for a single-step dye extraction/MALDI MS analysis platform

Room temperature ionic liquids, or RTILs, based on tetraalkylphosphonium (PR(4)(+)) cations were used as the basis of a platform that enables separation of dyes from textiles, extraction of dyes from aqueous solution, and identification of the dyes by MALDI-MS in a single experimental step for forensic purposes. Ionic liquids were formed with PR(4)(+) cations and ferulate (FA), α-cyano-4-hydroxycinnamate (CHCA), and 2,5-dihydroxybenzoate (DHB) anions. The use of tetraalkylphosphonium-based ionic liquids in MALDI-MS allowed detection of small molecule dyes without addition of a traditional solid MALDI matrix.     

Analysis of lipids using 2,4,6-trihydroxyacetophenone as a matrix for MALDI mass spectrometry

Lipids exhibit a broad range of chemical properties that make their analysis quite demanding. Today, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) represents a versatile tool in the field of lipid analysis, also offering the possibility for molecular structural identification using novel MALDI tandem time-of-flight (TOF/TOF) instrumentation. In this study, we evaluated 2,4,6-trihydroxyacetophenone (THAP) for the analysis of various lipid classes including neutral storage lipids (triacylglycerols), polar membrane lipids (glycerophospho- and sphingolipids), and glycosphingolipids. THAP proved to be a versatile matrix for the routine analysis of various lipids from biological samples ("lipidomics"). A sample preparation methodology was established using selective alkali salt doping for subsequent MS/MS experiments. Sodiated and lithiated molecules provided superior structural information on lipids (i.e., acyl group identification); thus, following this approach, both selective peak detection with high sensitivity and more reliable structural information were obtained simultaneously.     

Photoimmobilization of proteins for affinity capture combined with MALDI TOF MS analysis

Affinity capture surfaces can be prepared in a number of ways. A method of obtaining such surfaces through UV-activated immobilization of binding proteins using a benzophenone derivative is reported. Photoimmobilized protein G was used to selectively capture and preconcentrate bovine IgG from a mixture with BSA, and the affinity of photoattached concanavalin A toward ovalbumin was compared with that of commercially available concanavalin A on agarose beads. The results of the capture after tryptic digestion were analyzed by MALDI TOF MS. Immobilized trypsin was also prepared through photoimmobilization and later used to digest hemoglobin. Immobilized enzyme digestion resulted in more partial cleavages than solution-phase digestion. More methionine and tryptophan oxidation was also observed. Photoimmobilization was shown to be a quick and easy way of immobilizing ligands on surfaces.     

Coumarin tags for improved analysis of peptides by MALDI-TOF MS and MS/MS. 1. Enhancement in MALDI MS signal intensities

The goal of this study was the development of N-terminal tags to improve peptide identification using high-throughput MALDI-TOF MS and MS/MS. The proposed tags, commercially available fluorescent derivatives of coumarin, can be advantageous for peptide analysis in both MS and MS/MS modes. This paper, part 1, will focus on the influence of derivatization on the intensities of MALDI-TOF MS signals of peptides. Labeling peptides with tags containing the coumarin core was found to enhance the intensities of peptide peaks (in some cases over 40-fold) in MALDI-TOF MS using CHCA and 2,5-DHAP matrixes. The signal enhancement was found to be peptide- and matrix-dependent, being the most pronounced for hydrophilic peptides. No correlation was found between the UV absorptivity of the tags at the excitation wavelengths typical for UV-MALDI and the magnitude of the signal enhancement. Interestingly, peptides labeled with Alexa Fluor 350, a coumarin derivative containing a sulfo group (i.e., bearing strong negative charge), showed a 5-15-fold increase in intensity of MALDI MS signal in the positive ion mode, relative to the underivatized peptides, when 2,5-DHAP was used as the matrix. The Alexa Fluor 350 tag yielded a significantly higher signal relative to that for the CAF tag, likely due to the increased hydrophobicity of the coumarin structure. With 2,5-DHB, a decrease of MALDI MS signal was observed for all coumarin-labeled peptides, again relative to the unlabeled species. These findings support the hypothesis that derivatization with coumarin, a relatively hydrophobic structure, improves incorporation of hydrophilic peptides into hydrophobic MALDI matrixes, such as CHCA and 2,5-DHAP.     

On-plate selective enrichment and self-desalting of peptides/proteins for direct MALDI MS analysis

In this paper, a new technique has been proposed to achieve simultaneous peptides/proteins enrichment and wash-free self-desalting on a novel sample support with a circle hydrophobic-hydrophilic-hydrophobic pattern. Upon deposition, the sample solution is first concentrated in a small area by repulsion of the hydrophobic outer layer, and then, the peptides/proteins and coexisting salt contaminants are selectively captured in different regions of the pattern through strong hydrophobic and hydrophilic attractions, respectively. As a result, the detection sensitivity is improved by 2 orders of magnitude better than the use of the traditional MALDI plate, and high-quality mass spectra are obtained even in the presence of NaCl (1 M), NH(4)HCO(3) (100 mM), or urea (1 M). The practical application of this method is further demonstrated by the successful analysis of myoglobin digests with high sequence coverage, demonstrating the great potential in proteomic research.     

Single-neuron analysis using CE combined with MALDI MS and radionuclide detection

Capillary electrophoresis (CE) has been combined with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) and radionuclide detection to assay mass-limited biological samples. Nanovial sampling techniques enable injections into the CE capillary from 50 to 150-nL volume samples; after the separation, nanoliter fraction collection combines the CE effluent with a MALDI matrix and minimizes sample spreading, thus allowing both MALDI MS and radionuclide detection on the CE fractions. MALDI MS complements the elution time information of CE by providing accurate molecular mass data, and radionuclide detection provides zeptomole limits of detection with quantitative information. While MALDI MS detects all fully processed peptides at sufficient concentration, culturing the neuron in media containing 35S-Met provides selective radionuclide detection of newly synthesized methionine-containing peptides. The analysis and detection of the expected neuropeptides and hormones in a single 40-microm bag cell neuron from Aplysia californica with CE/MALDI MS/radionuclide detection demonstrates the ability of this hyphenated approach to work with chemically complex mass-limited samples.     

Improved MALDI-MS analysis of oligonucleotides through the use of fucose as a matrix additive.

With the development of matrix additives, the MALDI-MS analysis of oligonucleotides has improved greatly. When the monosaccharide fucose is combined with the matrix, the homogeneity of the MALDI target, signal strength, and signal duration are increased. The sensitivity of the MALDI experiment increases, allowing for improved detection of components in a complex mixture of oligonucleotides, such as that encountered in sequencing experiments. The addition of fucose to the matrix also causes a reduction in the extent of fragmentation of oligonucleotides.     

Complementary use of MALDI and ESI for the HPLC-MS/MS analysis of DNA-binding proteins

Proteins from Escherichia coli were isolated based on their ability to bind DNA and digested in-solution with trypsin; the resulting peptides were separated using HPLC and subsequently analyzed using MALDI TOF/TOF and ESI Q-TOF instruments. Various properties of the peptides observed with the two ionization techniques were compared taking into account the differences between the mass analyzers. This empirical analysis of a data set containing hundreds of peptides and thousands of individual amino acids supports some of the currently held notions regarding the complementary nature of the two ionization processes. Specifically, ESI tends to favor the identification of hydrophobic peptides whereas MALDI tends to lead to the identification of basic and aromatic species. Findings from the present study suggest that ESI and MALDI may be complementary due to the biases of the two ionization techniques for certain classes of amino acids. From a practical standpoint, these biases indicate that, for the present at least, analyses must be performed on both types of instruments in order to gain the most information possible out of a given set of samples in a proteomics study.     

Disposable hydrophobic surface on MALDI targets for enhancing MS and MS/MS data of peptides

Automated analyses in MALDI MS are complicated by the uneven distribution of analyte over the sample spot, resulting in areas of analyte localization, or "sweet spots". Hence, the ability to concentrate and localize samples is advantageous, especially for automated studies involving low concentrations of analyte. A method for rapidly creating a removable and affordable hydrophobic surface that is free from memory effect is presented. The potential for such compounds to serve as a practical coating for MALDI targets is examined. An example compound with a complete methodology is shown to increase sample homogeneity, peak intensity, and resolution when used for peptide mixtures with CHCA and DHB.     

Detection of phosphopeptides using Fe(III)-nitrilotriacetate complexes immobilized on a MALDI plate

Metal affinity complexes were chemically grafted onto the surface of gold matrix-assisted laser desorption/ionization (MALDI) plates by coupling a derivative of nitrilotriacetate (NTA) to immobilized poly(acrylic acid) (PAA) and subsequently forming the Fe(III)-NTA complex. The immobilized complexes can adsorb phosphorylated peptides preferentially from protein digests; deposition of digests on these surface-modified plates, followed by rinsing with an acetic acid solution, addition of matrix, and subsequent analysis by MALDI MS, resulted in mass spectra dominated by peaks corresponding to phosphopeptides. In the case of analyzing a tryptic digest of beta-casein, conventional MALDI MS revealed only one monophosphopeptide, while use of the Fe(III)-NTA-PAA-modified plate resulted in strong signals due to two additional tetraphosphorylated species. The diminution or elimination of signals due to nonphosphorylated species also greatly simplified the identification of phosphopeptides during analysis of ovalbumin digests and myoglobin digests spiked with an equimolar mixture of angiotensin and phosphoangiotensin. The matrix 2',4',6'-trihydroxyacetophenone mixed with diammonium hydrogen citrate proved to be much better than alpha-cyano-4-hydroxycinnamic acid for the detection of phosphorylated peptides from digests of beta-casein and ovalbumin.     

Retrograde labeling of single neurons in conjunction with MALDI high-energy collision-induced dissociation MS/MS analysis for peptide profiling and structural characterization

To reveal the peptide contents of the visually nonidentifiable neurons from a neuronal circuit of interest, we combined retrograde labeling of neurons with mass spectrometric single cell analysis. We used the neuronal circuit involved in the copulation behavior of a freshwater snail, Lymnaea stagnalis, as a model. Central neurons that control this behavior are known to send their axons to the penis nerve and innervate the penis complex. By retrograde filling from the penis nerve with nickel-lysine, these neurons were selectively labeled darkish blue. Matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometric analyses of single stained neurons in the parietal ganglion from different animals reveal consistently the presence of several molecular ion species in the range of 800-1200 Da. From a single neuron, six molecular ion species were further characterized with MALDI time-of-flight/time-of-flight mass spectrometry, which demonstrates that the peptides are derived from a previously reported -FLRFamide precursor.     

Submicrosecond surface-induced dissociation of peptide ions in a MALDI TOF MS

Surface-induced dissociation (SID) has been implemented in a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI TOF MS), allowing production of tandem mass spectrometric information for peptide ions (MALDI TOF SID TOF). The instrument retains the standard operational modes such as the reflectron monitoring of the MALDI-generated intact ions and postsource decay. We show through ion trajectory simulations and experimental results that implementing SID in a commercial MALDI TOF spectrometer is feasible and that the SID products in this instrument fall in an observation time frame that allows the specific detection of fast-fragmentation channels. The instrument design, pulse timing sequence, and high-voltage electronics together with SID spectra of MALDI-generated peptide ions are presented. Standard peptides such as YGGFLR, angiotensin III, fibrinopeptide A, and des-Arg1-bradykinin were dissociated by means of hyperthermal collisions with a gold surface coated with a self-assembled monolayer of 2-(perfluorodecyl)ethanethiol. With the extraction fields and the short observation times used, the spectra obtained show intense low-mass ion signals such as immonium, b2, b3, and y2 ions. TOF data analysis involved matching simulated and experimental flight times and indicates that the observed fragments are produced at approximately 250 ns after the precursor ion collides with the surface. This submicrosecond gas-phase fragmentation time frame is complementary to the observation time frame of existing SID spectrometers, which are on the order of 10 micros for tandem quadrupoles and are larger than a few milliseconds for SID implemented in Fourier transform ion cyclotron resonance spectrometers.     

MALDI MS sample preparation by using paraffin wax film: systematic study and application for peptide analysis

Recently developed sample preparation techniques employing hydrophobic sample support have improved the detection sensitivity and mass spectral quality of matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). These methods concentrate the samples on target by minimizing the sample area via the solvent repellent effect of the target surface. In the current study, we employed the use of paraffin wax film (Parafilm M) for improved MALDI MS analysis of low-abundance peptide mixtures, including neuronal tissue releasate and protein tryptic digests. This thin film was found to strongly repel polar solvents including water, methanol, and acetonitrile, which enabled the application of a wide range of sample preparation protocols that involved the use of various organic solvents. A "nanoliter-volume deposition" technique employing a capillary column has been used to produce tiny ( approximately 400 microm) matrix spots of 2,5-dihydroxybenzoic acid on the film. By systematically optimizing the sample volume, solvent composition, and film treatment, the Parafilm M substrate in combination with the nanoliter-volume matrix deposition method allowed dilute sample to be concentrated on the film for MALDI MS analysis. Peptide mixtures with nanomolar concentrations have been detected by MALDI time-of-flight and MALDI Fourier transform ion cyclotron resonance mass spectrometers. Overall, the use of Parafilm M enabled improved sensitivity and spectral quality for the analysis of complex peptide mixtures.     

Deamidation as a consequence of beta-elimination of phosphopeptides

Beta-elimination procedures often precede mass spectrometric analyses of phosphorylated peptides. Unfortunately, the commonly employed reaction conditions facilitate the deamidation of amide-containing residues. In addition to being 1 Da heavier than their amide counterparts, the newly created acidic residues greatly influence peptide tandem mass spectra. The effects of deamidation are investigated for five different amide-containing synthetic peptides exposed to beta-elimination conditions. MALDI-generated ions are analyzed with a tandem TOF mass analyzer. Methodologies for estimating the degree of deamidation from peptide mass spectra are presented, the influence that adjacent residues exert on the rate of deamidation is catalogued, and the impact that deamidation can have on peptide tandem mass spectra is demonstrated. The complications this side reaction can cause for automated data interpretation are also noted.