Automated protein identification using atmospheric-pressure matrix-assisted laser desorption/ionization

Atmospheric-pressure matrix-assisted laser desorption/ionization (AP-MALDI) ion trap mass spectrometry (ITMS) has been evaluated for automated protein identification. By using signal averaging and long ion-injection times, protein identification limits in the 50-fmol range are achieved for standard protein digests. Data acquisition requires 7.5 min or less per sample and the MS/MS spectra files are automatically processed using the SEQUEST database searching algorithm. AP-MALDI-ITMS was compared with the widely used methods of microLC/MS/MS (ion trap) and automated MALDI-TOF peptide mass mapping. Sample throughput is 10-fold greater using AP-MALDI compared with microcapillary liquid chromatography/tandem mass spectrometry (microLC/MS/MS). The protein sequence coverage obtained from AP-MALDI-MS/MS spectra matched by SEQUEST is lower compared with microLC/MS/MS and MALDI-TOF mass mapping. However, by using the AP-MALDI full-scan peptide mass fingerprint spectrum, sequence coverage is increased. AP-MALDI-ITMS was applied for the analysis of Coomassie blue stained gels and was found to be a useful platform for rapid protein identification.     

Separation, determination and identification of the diastereoisomers of podophyllotoxin and its esters by high-performance liquid chromatography/tandem mass spectrometry

A rapid and stable high-performance liquid chromatography-diode array detection (HPLC-DAD) and a high-performance liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-ESI/MS/MS) method were developed and validated for the separation, determination, and identification of eight pairs of diastereoisomers of podophyllotoxin and its esters at C-2 position. The separation was carried out on BDS Hypersil C18 column with CH3OH-CH3CN-H2O as the mobile phase in a gradient program. Interestingly, every 2alpha-H compound migrated before its corresponding 2beta-H epimer under optimum conditions. Also, the [M+NH(4)](+) of all eight pairs of compounds was observed in the HPLC-ESI/MS spectra. The characteristic elimination from the precursor protonated ions and the product ions at m/z 397, 313, 282, and 229 were the common diagnostic masses. The ion ratios of relative abundance [M-ROH+H](+) (ion 397) to [M+NH(4)](+), [A+H](+) (ion 313) to [M-ROH+H](+), and [M-ROH-ArH+H](+) (ion 229) to [M-ROH+H](+) in the ESI/MS/MS spectra of each pair of diastereoisomers of the lignans specifically exhibited a stereochemical effect. Thus, by using identical sample solutions and chromatographic conditions (including the same columns and gradient programs), the combination of DAD and MS/MS data permitted the separation and identification of the eight pairs of diastereoisomers of the podophyllotoxin and its esters in the mixture. The method could be used in rapidly identifying the purity and monitoring of the epimerization of 2-H of podophyllotoxin and its analogues from natural products, chemical reactions, and pharmaceutical metabolism.     

Fourier-transform mass spectrometry for automated fragmentation and identification of 5-20 kDa proteins in mixtures

When presented with a mixture of intact proteins, electrospray ionization with Fourier-transform mass spectrometry (ESI-FTMS) has the capability to obtain direct fragmentation information from isolated ions. However, the automation of this capability has not been achieved to date. We have developed software for unattended acquisition of protein tandem mass spectrometry (MS/MS) data and batch processing of the resulting files for identification of whole proteins. Mixtures of both protein standards (8-29 kDa) and Methanococcus jannaschii cytosolic proteins (up to six components + 20 kDa) were infused via an autosampler, and MS/MS data were acquired without human intervention. The acquisition software recognizes ESI charge state patterns, generates protein-specific isolation waveforms on-the-fly, and fragments ions using two different infrared laser times. In addition to protein standards, five wild-type proteins (7-14 kDa) were identified automatically with 100% sequence coverage from the M. jannaschii database. The software underpins a measurement platform for sample-dependent acquisition of MS/MS data for whole proteins, a critical step to realize proteomics with 100% sequence coverage in a higher throughput setting.     

Fully automated chip-based nanoelectrospray combined with electron transfer dissociation for high throughput top-down proteomics

The conventional protocol for protein identification by electrospray ionization mass spectrometry (MS) is based on enzymatic digestion which renders peptides to be analyzed by liquid chromatography-MS and collision-induced dissociation (CID) multistage MS, in the so-called bottom-up approach. Though this method has brought a significant progress to the field, many limitations, among which, the low throughput and impossibility to characterize in detail posttranslational modifications in terms of site(s) and structure, were reported. Therefore, the research is presently focused on the development of procedures for efficient top-down fragmentation of intact protein ions. In this context, we developed here an approach combining fully automated chip-based-nanoelectrospray ionisation (nanoESI), performed on a NanoMate robot, with electron transfer dissociation (ETD) for peptide and top-down protein sequencing and identification. This advanced analytical platform, integrating robotics, microfluidics technology, ETD and alternate ETD/CID, was tested and found ideally suitable for structural investigation of peptides and modified/functionalized peptides as well as for top-down analysis of medium size proteins by tandem MS experiments of significantly increased throughput and sensitivity. The obtained results indicate that NanoMate-ETD and ETD/CID may represent a viable alternative to the current MS strategies, with potential to develop into a method of routine use for high throughput top-down proteomics.     

Disposable chromatography for a high-throughput nano-ESI/MS and nano-ESI/MS-MS platform

High-throughput proteomics has typically relied on protein identification based on MALDI-MS peptide maps of proteolytic digests of 2D-gel-separated proteins. This technique, however, requires significant sequence coverage in order to achieve a high level of confidence in the identification. Tandem MS data have the advantage of requiring fewer peptides (2) for high confidence identification, assuming adequate MS/MS sequence coverage. MALDI-MS/MS techniques are becoming available, but can still be problematic because of the difficulty of inducing fragment ions of a singly charged parent ion. Electrospray ionization, however, has the advantage of generating multiply charged species that are more readily fragmented during MS/MS analysis. Two electrospray/tandem mass spectrometry-based approaches, nanovial-ESI-MS/MS and LC-MS/MS, are used for high throughput proteomics, but much less often than MALDI-MS and peptide mass fingerprinting. Nanovial introduction entails extensive manual manipulation and often shows significant chemical background from the in-gel digest. LC-MS has the advantages that the chemical background can be removed prior to analysis and the analytes are concentrated during the separation, resulting in more abundant analyte signals. On the other hand, LC-MS can often be time intensive. Here, we report the incorporation of on-line sample clean-up and analyte concentration with a high-throughput, chip-based, robotic nano-ESI-MS platform for proteomics studies.     

A fully automated 2-D LC-MS method utilizing online continuous pH and RP gradients for global proteome analysis

The conventional 2-D LC-MS/MS setup for global proteome analysis was based on online and offline salt gradients (step and continuous) using strong-cation-exchange chromatography in conjunction with RP chromatography and MS. The use of the online system with step salt elution had the possibility of resulting in peptide overlapping across fractions. The offline mode had the option to operate with continuous salt gradient to decrease peak overlap, but exhibited decreased robustness, lower reproducibility, and sample loss during the process. Due to the extensive washing requirement between the chromatography steps, online continuous gradient was not an option for salt elution. In this report, a fully automated, online, and continuous gradient (pH continuous online gradient, pCOG) 2-D LC-MS/MS system is introduced that provided excellent separation and identification power. The pH gradient-based elution provided more basic peptides than that of salt-based elution. Fraction overlap was significantly minimized by combining pH and continuous gradient elutions. This latter approach also increased sequence coverage and the concomitant confidence level in protein identification. The salt and pH elution-based 2-D LC-MS/MS approaches were compared by analyzing the mouse liver proteome.     

Determination of polar pesticides in soil by solid phase microextraction coupled to high-performance liquid chromatography-electrospray/mass spectrometry

The determination of carbamate and triazine pesticides from soil leachates and slurries was investigated using solid phase microextraction (SPME) coupled to high-performance liquid chromatography-electrospray/ mass spectrometry (HPLC-ESI/MS). SPME was carried out using fibres with a newly developed 50 μm Carbowax/ template coating which are suitable for relatively polar analytes. These fibers exhibit precisions better than 10% RSD, and are resistant against high contents of organic solvents during desorption. The technique shows a high sampling frequency resulting in an increasing sample throughput.     

Development of a solvent-free method for the simultaneous identification/quantification of drugs of abuse and their metabolites in environmental water by LC-MS/MS

This work details a rapid analytical method using direct sample injection for the simultaneous identification/quantification of 22 drugs of abuse, including some of their major metabolites, in environmental samples. This has been developed using a hybrid triple quadrupole-linear ion trap-mass spectrometer (QqLIT). With the increasing sensitivity of today's tandem mass spectrometers, direct injection analysis of water samples has become an attractive alternative to traditional analytical protocols, which often include a preliminary pre-concentration step. What's more, this kind of analysis is in accordance with many of the main objectives of so-called green analytical chemistry, or environmentally friendly practice. The analytical performance of the LC-MS/MS method was evaluated in three different water matrices (surface water, influent and effluent wastewater). Data acquisition was carried out in selected reaction monitoring (SRM) mode under time-scheduled conditions, monitoring two SRM transitions for simultaneous identification/quantification of all target compounds in the samples. Additionally, an experiment was performed using the information-dependent acquisition (IDA) scan to carry out the identification of those analytes for which the second transition was present at a low intensity. Finally, the two methodologies developed were applied to real samples for evaluation.     

Determination of polar pesticides in soil by solid phase microextraction coupled to high-performance liquid chromatography-electrospray/mass spectrometry

The determination of carbamate and triazine pesticides from soil leachates and slurries was investigated using solid phase microextraction (SPME) coupled to high-performance liquid chromatography-electrospray/ mass spectrometry (HPLC-ESI/MS). SPME was carried out using fibres with a newly developed 50 μm Carbowax/ template coating which are suitable for relatively polar analytes. These fibers exhibit precisions better than 10% RSD, and are resistant against high contents of organic solvents during desorption. The technique shows a high sampling frequency resulting in an increasing sample throughput. Received: 17 December 1997 / Revised: 30 October 1998 / Accepted: 10 November 1998     

Fast on-column protein digestion with subsequent peptide mapping using tandem mass spectrometry with information dependent acquisition

A platform for rapid on-line protein digestion of protein mixtures for direct infusion to a mass spectrometer is presented. A mixture of protein A, staphylococcal enterotoxin B and cytochrome c was used as a model mixture injected on a gel filtration column and a trypsin reactor which were connected in series to a micro liquid chromatography (microLC) system. The peptides in the column eluate were analyzed with ESI tandem mass spectrometry, utilizing information dependent acquisition (IDA). In one step, the proteins in the mixture (microM concentrations) were concomitantly desalted, separated, digested and identified with an overall analysis time of less than 40 min. Protein sequence coverage of 78-95% for the involved substances was achieved.     

Optimized sample-processing time and peptide recovery for the mass spectrometric analysis of protein digests

Proteomics requires an optimized level of sample-processing, including a minimal sample-processing time and an optimal peptide recovery from protein digests, in order to maximize the percentage sequence coverage and to improve the accuracy of protein identification. The conventional methods of protein characterization from one-dimensional or two-dimensional gels include the destaining of an excised gel piece, followed by an overnight in-gel enzyme digestion. The aims of this study were to determine whether: (1) stained gels can be used without any destaining for trypsin digestion and mass spectrometry (MS); (2) tryptic peptides can be recovered from a matrix-assisted laser desorption/ionization (MALDI) target plate for a subsequent analysis with liquid chromatography (LC) coupled to an electrospray ionization (ESI) quadrupole ion trap MS; and (3) an overnight in-gel digestion is necessary for protein characterization with MS. These three strategies would significantly improve sample throughput. Cerebrospinal fluid (CSF) was the model biological fluid used to develop these methods. CSF was desalted by gel filtration, and CSF proteins were separated by two-dimensional gel electrophoresis (2DGE). Proteins were visualized with either silver, Coomassie, or Stains-All (counterstained with silver). None of the gels was destained. Protein spots were in-gel trypsin digested, the tryptic peptides were purified with ZipTip, and the peptides were analyzed with MALDI and ESI MS. Some of the samples that were spotted onto a wax-coated MALDI target plate were recovered and analyzed with ESI MS. All three types of stained gels were compatible with MALDI and ESI MS without any destaining. In-gel trypsin digestion can be performed in only 10-60 min for protein characterization with MS, the sample can be recovered from the MALDI target plate for use in ESI MS, and there was a 90% reduction in sample-processing time from overnight to ca. 3 h.     

Comparative evaluation of five protocols for protein extraction from stony corals (Scleractinia) for proteomics

Corals especially the reef‐building species are very important to marine ecosystems. Proteomics has been used for researches on coral diseases, bleaching and responses to the environment change. A robust and versatile protein extraction protocol is required for coral proteomics. However, a comparative evaluation of different protein extraction protocols is still not available for proteomic analysis of stony corals. In the present study, five protocols were compared for protein extraction from stony corals. The five protocols were TRIzol, phenol‐based extraction (PBE), trichloroacetic acid (TCA)‐acetone, glass bead‐assisted extraction (GBAE) and a commercially available kit. PBE, TRIzol and the commercial kit were more robust for extracting proteins from stony corals. The protein extraction efficiency and repeatability, two dimensional electrophoresis (2‐DE) and matrix‐assisted laser desorption/ionization time of flight mass spectrometry (MALDI TOF MS) were employed to evaluate the protocols. The results indicated that PBE protocol had the better protein extraction efficiency than the others. Protein extraction coverage varied among the procedures. Each protocol favored for certain proteins. Therefore, it is very important for coral proteomic analysis to select a suitable protein protocol upon the experimental design. In general, PBE protocol can be the first choice for extracting proteins from stony corals.     

Potential of long capillary monolithic columns for the analysis of protein digests

The gain in separation efficiency for protein digests using long monolithic columns has been evaluated for a LC‐MS system with capillary monolithic columns of different lengths (150 and 750 mm). A mixture of BSA, α‐casein and β‐casein tryptic digests was used as a test sample. Peak capacity and productivity (peak capacity per unit time) were determined from base peak chromatograms and MS/MS data were used for protein identification by MASCOT database searching. Peak capacity and protein identification scores were higher for the long column. Analyses with similar gradient slope for the two columns produced ratios of the peak capacities that were slightly higher than the expected value of the square root of the column length ratio. Peak capacity ratios varied from 2.7 to 4.0 for four different gradient slopes, while protein identification scores were 2–4 times higher for the long column. Similar values were obtained for the productivity of both columns and the highest productivity was obtained at gradient times of 45 and 75 min for the short and long column, respectively. The use of long monolithic columns improves peptide separation and increases reliability of protein identification for complex digests, especially if longer gradients are chosen.     

Staggered multistep elution solid-phase extraction capillary electrophoresis/tandem mass spectrometry: a high-throughput approach in protein analysis

An approach based on staggered multistep elution solid-phase extraction (SPE) capillary electrophoresis/tandem mass spectrometry (CE/MS/MS) was developed in the analysis of digested protein mixtures. On-line coupling of SPE with CE/MS was achieved using a two-leveled two-cross polydimethylsiloxane (PDMS)-based interface. Multistep elution SPE was used prior to CE to provide an additional dimension of separation, thus extending the separation capacity for the peptide mixture analysis. By decreasing in the number of co-eluting peptides, problems stemming from ionization suppression and finite MS/MS duty cycle were reduced. As a result, sequence coverage increased significantly using multistep elution SPE-CE/MS/MS compared to one-step elution SPE-CE/MS/MS in the analysis of a single protein tryptic digest (49% vs. 18%) and a six protein tryptic digest (22-71% vs. 10-44%). A staggered CE method was incorporated to increase the throughput. The electropherograms of consecutive CE runs were partially overlapped by injecting the sample plug at a fixed time interval. With the use of a 5 min injection interval, slightly poor results were obtained in comparison with the sequential CE method while the total analysis time was reduced to 28%.     

Flavonoid profile in soybeans by high-performance liquid chromatography/tandem mass spectrometry

Flavonoid profiling of a soybean sample has been performed by liquid chromatography/positive electrospray tandem mass spectrometry (LC/ESI(+)-MS/MS) using a quadrupole-linear ion trap (QLIT) instrument with an information-dependent data acquisition (IDA) protocol that looped, in a single run, an enhanced MS scan and an enhanced product ion scan. As compromise between time and obtainable information, spectra acquisition was split into two distinct runs: 220-450 Th and 400-800 Th, respectively. The isoflavones daidzein and genistein were identified as aglycones, monoglycosides, diglycosides, triglycosides, acetylglycosides, malonylglycosides, malonyl diglycosides, and dimalonyl diglycosides, whereas glycitein triglycosides, acetylglycosides, and dimalonyl diglycosides were not detected. Also kaempferol di- and triglycosides, malonylglycosides and malonyl diglycosides, previously reported in soy leaves and pods, and four naringenin malonylglycosides were identified.     

A comparison of preconcentration reagents for flow injection analysis flame atomic spectrometry

A small range of new commercially available chelating resins are compared with a resin prepared in-house in terms of their applicability for on-line preconcentration and matrix separation. The flow injection manifold was designed for rapid matrix separation and the resins were tested for the determination of Cull, ZnII, CdII, MnII and NiII. The resin based on controlled pore glass was found to be better for this rapid procedure because it did not require conditioning, although the polymer based resins had better capacities. The commercially available controlled pore glass based iminodiacetate (IDA) resin had a comparable performance to the in-house controlled pore glass 8-hydroxyquinoline (CPG-8-HQ) resin. The IDA resin had a much higher capacity than the 8-HQ, however as with all IDA based resins, some retention of Call was observed. The sample throughput was 12 h⁻¹.     

MALDI-target integrated platform for affinity-captured protein digestion

To address immunocapture of proteins in large cohorts of clinical samples high throughput sample processing is required. Here a method using the proteomic sample platform, ISET (integrated selective enrichment target) that integrates highly specific immunoaffinity capture of protein biomarker, digestion and sample cleanup with a direct interface to mass spectrometry is presented. The robustness of the on-ISET protein digestion protocol was validated by MALDI MS analysis of model proteins, ranging from 40 fmol to 1 pmol per nanovial. On-ISET digestion and MALDI MS/MS analysis of immunoaffinity captured disease-associated biomarker PSA (prostate specific antigen) from human seminal plasma are presented.     

Dansyl‐peptides matrix‐assisted laser desorption/ionization mass spectrometric (MALDI‐MS) and tandem mass spectrometric (MS/MS) features improve the liquid chromatography/MALDI‐MS/MS analysis of the proteome

Peptide tagging is a useful tool to improve matrix‐assisted laser desorption/ionization tandem mass spectrometric (MALDI‐MS/MS) analysis. We present a new application of the use of the dansyl chloride (DNS‐Cl). DNS‐Cl is a specific primary amine reagent widely used in protein biochemistry. It adds a fluorescent dimethylaminonaphthalene moiety to the molecule. The evaluation of MALDI‐MS and MS/MS analyses of dansylated peptides shows that dansylation raises the ionization efficiency of the most hydrophilic species compared with the most hydrophobic ones. Consequently, higher Mascot scores and protein sequence coverage are obtained by combining MS and MS/MS data of native and tagged samples. The N‐terminal DNS‐Cl sulfonation improves the peptide fragmentation and promotes the generation of b‐fragments allowing better peptide sequencing. In addition, we set up a labeling protocol based on the microwave chemistry. Peptide dansylation proved to be a rapid and cheap method to improve the performance of liquid chromatography (LC)/MALDI‐MS/MS analysis at the proteomic scale in terms of peptide detection and sequence coverage. Copyright © 2010 John Wiley & Sons, Ltd.     

High-performance liquid chromatography analysis of ten dyes for control of safety of commercial articles

Two high-performance liquid chromatographic methods, with ultraviolet-visible spectrophotometry detection (HPLC-UV/Vis) and with tandem mass spectrometry triple quadrupole interfaced with positive ion mode electrospray ionization detection (HPLC-ESI+-QqQ-MS/MS), for determination and quantification of ten commercial dyes are proposed for control in commercial products. Multiple peaks observed for some of the studied dyes in HPLC-UV/Vis chromatograms forced to obtain structural information by HPLC-ESI-MS/MS method with scan mode. The quality parameters of the two proposed chromatographic methods were evaluated for different requirements of normative, showing detection (LODs) and quantification (LOQs) limits around 60-890 and 200-2990 microg L(-1) for HPLC-UV/Vis, and 4.54-14.3 and 15.0-47.6 microg L(-1) for HPLC-ESI+-QqQ-MS/MS.     

Recent advances in capillary separations for proteomics

The sequencing of several organisms' genomes, including the human's one, has opened the way for the so-called postgenomic era, which is now routinely coined as "proteomics". The most basic task in proteomics remains the detection and identification of proteins from a biological sample, and the most traditional way to achieve this goal consists of protein separations performed by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). Still, the 2-D PAGE-mass spectrometry (MS) approach remains lacking in proteome coverage (for proteins having extreme isoelectric points or molecular masses as well as for membrane proteins), dynamic range, sensitivity, and throughput. Consequently, considerable efforts have been devoted to the development of non-gel-based proteome separation technologies in an effort to alleviate the shortcomings in 2-D PAGE while reserving the ability to resolve complex protein and peptide mixtures prior to MS analysis. This review focuses on the most recent advances in capillary-based separation techniques, including capillary liquid chromatography, capillary electrophoresis, and capillary electrokinetic chromatography, and combinations of multiples of these mechanisms, along with the coupling of these techniques to MS. Developments in capillary separations capable of providing extremely high resolving power and selective analyte enrichment are particularly highlighted for their roles within the broader context of a state-of-the-art integrated proteome effort. Miniaturized and integrated multidimensional peptide/protein separations using microfluidics are further summarized for their potential applications in high-throughput protein profiling toward biomarker discovery and clinical diagnosis.