Time Of Flight Tandem Mass Spectrometry Research Articles

Uncommon Modifications and Dehydration Reaction in the Analysis of Lysozyme by Matrix-assisted Laser Desorption Ionization Tandem Time of Flight-Mass Spectrometry

Tryptic digest of lysozyme was analyzed by MALDI-TOF/TOF mass spectrometry.Six unique peptides were identified with high confidence by database searching and the Mascot score was 420 with the protein coverage of 54%.Furthermore,several uncommon modifications including deamidation of asparagines(Asp) residue,deamidation of Asp plus oxidation of methionine(Met),deamidation of Asp plus oxidation of Met plus oxidation of Trp were observed for peptide 98IVSDGDGMNAWVAWR112.Furthermore,a dehydration reaction was observed in the process of MALDI for this peptide.All above results showed that the Asparagine at 103rd position had a highly chemical reactivity.In addition,the modification of propionamide(Cystine) was observed for another two peptides.This study indicated that,for those of unmatched data by database searching,the data utilization and the certainty of analysis result would be increased by using manual explantation and selecting very low abundant ions in primary spectrum and this method was also helpful for finding potential post-translational modifications.

Differential protein expression between EBV-positive and negative epithelial cells

Epstein Barr virus infection is believed to play a role in the development of nasopharyngeal carcinoma. In order to investigate the function of EBV in epithelial cell, proteomic methods were used to find and identify the differential proteins and expected to elucidate the mechanism of EBV. Altered protein expressions were found between 293 cell (HEK293) and EBV infected cell (293-EBV). In this study, we separated differential expressed proteins using 2D-DIGE method while matrix-assisted laser desorption/ionization tandem time of flight mass spectrometry (MALDI-TOF-MS) method was used to identify proteins. The results showed that 14 proteins were up regulated and 3 proteins were down regulated in 293-EBV cells. Bioinformatic analysis showed that these proteins are involved in cell proliferation, metastasis, apoptosis, metabolism, and signal transduction. Western blotting analysis was further carried out to verify the MS results. Thus, EBV may exert its functions by mediating differential expression of these proteins.

Modulation of mouse macrophage proteome induced by Toxoplasma gondii tachyzoites in vivo

Toxoplasma gondii is an obligate intracellular protozoan parasite, which can invade and multiply within the macrophages of humans and most warm-blooded animals. Macrophages are important effector cells for the control and killing of intracellular T. gondii, and they may also serve as long-term host cells for the replication and survival of the parasite. In the present study, we explored the proteomic profile of macrophages of the specific pathogen-free Kunming mice at 24 h after infection with tachyzoites of the virulent T. gondii RH strain using two-dimensional gel electrophoresis combined with matrix-assisted laser desorption ionization time-of-flight (TOF)/TOF tandem mass spectrometry. Totally, 60 differentially expressed protein spots were identified. Among them, 52 spots corresponded to 38 proteins matching to proteins of the mouse, including actin, enolase, calumenin, vimentin, plastin 2, annexin A1, cathepsin S, arginase-1, arachidonate 12-lipoxygenase, and aminoacylase-1. Functional prediction using Gene Ontology database showed that these proteins were mainly involved in metabolism, structure, protein fate, and immune responses. The findings provided an insight into the interactive relationship between T. gondii and the host macrophages, and will shed new lights on the understanding of molecular mechanisms of T. gondii pathogenesis.

Identification of differential hepatic proteins in rare minnow ( Gobiocypris rarus) exposed to pentachlorophenol (PCP) by proteomic analysis

Pentachlorophenol (PCP) is a ubiquitous contaminant that has been shown to lead to hepatoxicity and is implicated in the incidence of liver tumors in human. A number of previous studies have described the toxic effects of PCP based on conventional toxicological indices. However, little evidence on protein levels is available at present. For further understanding of mechanisms of action and identifying the potential protein biomarkers for PCP exposure, two-dimensional electrophoresis coupled with mass spectrometry has been used to identify proteins differentially expressed in the livers of rare minnow ( Gobiocypris rarus) following PCP exposure of 0.5, 5, 50 μg/L. After comparison of the protein profiles from treated and control groups, 39 protein spots were found altered in abundance (>2-fold) from male and female PCP-treated groups. Matrix-assisted laser desorption/ionization (MALDI) tandem time-of-flight mass spectrometry (TOF/MS) analysis allowed the unambiguous identification, and 18 protein spots were identified successfully, 12 proteins in females and 6 proteins in males, respectively. These proteins were involved in transport, metabolism, response to oxidative stress and other biological processes. Of these proteins, four differentially expressed mRNA encoding proteins underwent quantitative analysis by quantitative real-time PCR (QRT-PCR). The consistent and discrepant results between mRNA and protein levels suggested that complicated regulatory mechanisms of gene expression were implicated in the response to PCP exposure. In addition, marked gender differences in response to PCP have been described from the comparison of the male and female liver protein profiles.

Fraction collection in capillary electrophoresis for various stand-alone mass spectrometers

A procedure for collecting fractions during capillary electrophoresis for their analysis using various stand-alone instruments is described. The results of a systematic study of the optimization and application of capillary electrophoresis (CE) in conjunction with a reverse-phase high-performance liquid chromatography electrospray ionization quadrupole time of flight-tandem mass spectrometry (RP-HPLC-ESI-Q-TOF-MS/MS) and inductively-coupled mass spectrometry (ICP-MS) to the analysis of the seed extract of the Japanese Pagoda Tree ( Sophora japonica) are presented. The off-line coupling of CE to the matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS) for the proteins mixture was applied. The cathode end of the capillary was placed inside a stainless steel needle using a coaxial liquid-sheath-flow configuration. The optimization of experimental parameters resulted in an efficient methodology for MS analysis of fractions. Several components contained in the extract of S. japonica were identified, some not previously known. It was demonstrated that low sensitivity, which is a real problem in off-line CE–MS analysis, could be tolerated because of a more flexible optimization of the CE separation conditions and the choice of independent stand-alone instruments for analysis of separated fractions. The estimated limit of detection for CE-RP-HPLC-ESI-Q-TOF-MS was 50 μM of polyphenols and for CE-ICP-MS, 1–100 μg/l.

Affinity labeling coupled with matrix assistant laser desorption tandem time of flight mass spectrometry for quantitative proteomics research

A relative quantitative method for differential proteomics by cleavable isotope-coded affinity tag (cICAT) and matrix-assisted laser desorption/ionization tandem timeof-flight mass spectrometry (MALDI-TOF-MS) was established. The accuracy and reproducibility of the method were evaluated by bovine serum albumin (BSA) digest as having a relative standard deviation of less than 30% and good reproducibility. The dynamic range was also evaluated by analyzing two mixtures of several standard proteins with different concentration. The experimental results showed that in the dynamic range of 1:30, the quantitation error of the method was less than 30%. Although the quantitation error becomes very large when used beyond this range, it does not affect the derivation of information on the differential proteins. All the work provides an alternative method for differential proteomics analysis in biological samples from different origins.

Enhancement of matrix‐assisted laser desorption/ionization photodissociation tandem time‐of‐flight mass spectra; spectral reduction and cleanup of isotopomeric contamination

Weak signal intensity and poor precursor ion selection are the major difficulties in tandem time-of-flight (TOF) mass spectrometry of ions generated by matrix-assisted laser desorption/ionization (MALDI). Even though the latter can be overcome in photodissociation (PD) tandem TOF mass spectrometry via ion pulse-PD laser pulse synchronization, clean monoisotopic selection of precursor ions of high m/z can often be difficult for various reasons. A considerable enhancement of post-source decay (PSD) and PD tandem mass spectra has been achieved in this work via single-ion detection and post-acquisition reduction of the spectra. Also, an algorithm has been developed to clean up isotopomeric contamination when the resolution for precursor ion selection is less than adequate. A high-quality tandem TOF mass spectrum which results from PD of virtually monoisotopic precursor ions has been obtained.

Comparison of protein and peptide prefractionation methods for the shotgun proteomic analysis of Synechocystis sp. PCC 6803

Proteome analysis by gel-free "shotgun" proteomics relies on the simplification of a peptide mixture before it is analyzed in a mass spectrometer. While separation on a reverse-phase (RP) liquid chromatographic column is widely employed, a variety of other methods have been used to fractionate both proteins and peptides before this step. We compared six different protein and peptide fractionation workflows, using Synechocystis sp. PCC 6803, a useful model cyanobacterium for potential exploitation to improve its production of hydrogen and other secondary metabolites. Pre-digestion protein separation was performed by strip-based isoelectric focusing, one-dimensional polyacrylamide gel electrophoresis, or weak anion exchange chromatography, while pre-RP peptide separation was accomplished by isoelectric focusing (IEF) or strong cation exchange chromatography. Peptides were identified using electrospray ionization quadrupole time of flight-tandem mass spectrometry. Mass spectrometry (MS) and tandem mass spectra were analyzed using ProID software employing both a single organism database and the entire NCBI non-redundant database, and a total of 776 proteins were identified using a stringent set of selection criteria. Method comparisons were made on the basis of the results obtained (number and types of proteins identified), as well as ease of use and other practical aspects. IEF-IEF protein and peptide fractionation prior to RP gave the best overall performance.

Comprehensive proteome analysis of ovarian cancers using liquid phase separation, mass mapping and tandem mass spectrometry: a strategy for identification of candidate cancer biomarkers.

A two-dimensional (2-D) liquid phase separation method, liquid isoelectric focusing followed by nonporous reversed-phase high performance liquid chromatography (HPLC), was used to separate proteins from human ovarian epithelial whole cell lysates. HPLC eluent was interfaced on-line to an electrospray ionization (ESI) time of flight (TOF) mass spectrometer to obtain accurate intact protein molecular weights (Mr). 2-D protein expression maps were generated displaying protein isoelectric point (pI) versus intact protein Mr. Resulting 2-D images effectively displayed quantitative differential protein expression in ovarian cancer cells versus non-neoplastic ovarian epithelial cells. Protein peak fractions were collected from the HPLC eluent, enzymatically digested, and analyzed by matrix-assisted laser desorption/ionization (MALDI) TOF-mass spectrometry (MS) peptide mass fingerprinting and by MALDI-quadrupole TOF tandem mass spectrometry peptide sequencing. Interlysate comparisons of differential protein expression between two ovarian adenocarcinoma cell lines, ES2 and MDAH-2774, and ovarian surface epithelial cells was performed. Five pI fractions from each sample were selected for comparative study and over 300 unique proteins were positively identified from the 2-D liquid expression maps using MS, which covered around 60% of proteins detected by on-line ESI-TOF-MS. This represents one of the most comprehensive proteomic analyses of ovarian cancer samples to date. Protein bands with significant up- or down-regulation in one cell line versus another as viewed in the 2-D expression maps were identified. This strategy may prove useful in identifying novel ovarian cancer marker proteins.

Sequencing of oligosaccharides derivatized with benzylamine using electrospray ionization-quadrupole time of flight-tandem mass spectrometry.

Oligosaccharides were derivatized by reductive amination using benzylamine and analyzed by nanoelectrospray ionization-quadrupole time of flight-tandem mass spectrometry (nanoESI-QTOF-MS/MS) in the positive ion mode. The major signals were obtained under these conditions from the [M+H]+ ions for all benzylamine-derivatized oligosaccharides. To obtain structural information from these derivatized oligosaccharides, MS/MS was applied. Protonated molecular ions underwent extensive fragmentation, even under low-energy collision-induced dissociation. MS/MS spectra of [M+H]+ ions are characterized by simple fragmentation patterns which result from cleavage of the glycosidic bonds and thus allow a straightforward interpretation. Fragmentation of the [M+H]+ ions gave predominantly B- and Y-type glycosidic fragments. A systematic study of various oligosaccharides showed that information on sugar sequence and branching could easily be obtained. Predictable and reproducible fragmentation patterns could be obtained in all cases. This derivatization procedure and mass spectrometric methodology were applied successfully to neutral and acidic glycans released from 10 microg of glycoproteins separated by gel electrophoresis. Moreover, the derivatives retain their sensitivity to exoglycosidases. Thus a series of sequential on-target exoglycosidase treatments combined with matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) was found to be useful for the determination of structural features of the glycans released from proteins separated by gel electrophoresis such as the monosaccharide sequence, branching pattern, and anomeric configurations of the corresponding glycosidic linkages. Our strategy can be used successfully to assign the major glycans released from proteins separated by gel electrophoresis.

Intact protein analysis by matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry.

Direct tandem mass spectrometric (MS/MS) analysis of small, singly charged protein ions by tandem time-of-flight mass spectrometry (TOFMS) is demonstrated for proteins up to a molecular mass of 12 kDa. The MALDI-generated singly charged precursor ions predominantly yield product ions resulting from metastable fragmentation at aspartyl and prolyl residues. Additional series of C-terminal sequence ions provide in some cases sufficient information for protein identification. The amount of sample required to obtain good quality spectra is in the high femtomolar to low picomolar range. Within this range, MALDI-MS/MS using TOF/TOF trade mark ion optics now provides the opportunity for direct protein identification and partial characterization without prior enzymatic hydrolysis.

A capillary electrophoresis and off-line capillary electrophoresis/electrospray ionization-quadrupole time of flight-tandem mass spectrometry approach for ganglioside analysis.

A systematic study for the optimization and implementation of high-performance capillary electrophoresis (HPCE) in conjunction with negative ion electrospray ionization-quadrupole time of flight-tandem mass spectrometry (ESI-QTOF-MS/MS) for the analysis of complex glycolipids is described. The performance of the capillary electrophoresis (CE) and off-line CE/ESI-QTOF-MS approach has been explored for screening a complex ganglioside mixture from bovine brain. All instrumental and solution parameters demonstrated to require special adjustment and to have the most substantial effect on the CE separation, abundance of product ions produced in a low-energy collision-induced dissociation (CID) process and their detection by MS/MS, when attempting to identify and sequence single ganglioside molecular species from CE eluted fractions. Upon optimization of the experimental parameters, an efficient methodology emerged providing the general basic requirements for combined CE/ESI-MS analysis of this type of complex glycoconjugate.

Surface induced dissociation for tandem time-of-flight mass spectrometry

We have investigated surface induced dissociation (SID) in a reflectron time-of-flight (TOF) mass spectrometer using an “in-line” collision device in the reflectron mirror. Ions are created by multiphoton ionization, mass selected by pulsed deflection, and impinge on the collision device with collision energy that can be raised from 0 to 2.6 keV. The present apparatus achieves unit mass resolution at m/z 200 for the precursor ion selection and a product ion mass resolution of 70 at m/z 100. We find that high internal excitation of ions results for collision energies in excess of 150 eV, as determined from the fragmentation of phenanthrene molecular ions, (C 14H 10) + . The SID process is shown to cause efficient ion dissociation; for example, the sum of the abundance of all daughter ions, relative to the initial parent ion abundance of 4-methylanisole, (C 8H 10O) + , is 0.15 ± 0.03 at a collision energy of 30 eV. In addition to SID, we observe sputtering of hydrocarbon molecules on the collision device surface as well as reaction with these adsorbate species. Thus, SID appears to be an attractive technique for TOF tandem mass spectrometry, particularly for the dissociation of large singly-charged ions.