[Show abstract][Hide abstract] ABSTRACT: Background: many full-time welders experience some sort of respiratory disorder e.g., asthma, bronchitis and metal fume fever. Thus, welding aerosols are thought to cause airway inflammation. There is a need for markers of welding aerosols in exposure assessments, and as most welding aerosols contain manganese and iron, these metals may possibly be used as an indicator. We have previously developed a novel non-invasive technique to collect endogenous particles in exhaled air (PEx). This study is designed to (i) develop a method for analysis of manganese and iron in PEx and (ii) investigate whether the manganese and/or iron content of PEx changes after exposure to welding aerosols. Methods: nine individuals were experimentally exposed to welding fumes. PEx was collected at three time points for each individual; before, after and 24 hours after exposure. Analyses of PEx samples were performed using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Results: four out of nine individuals showed an increase in manganese and iron levels after exposure to welding aerosols. The mean manganese and iron concentration increased from, <LOD to 82–84 pg L−1 (range from 0 to LOD for values <LOD) and 20–86 to 2600 pg L−1 of exhaled air respectively. Conclusions: an ICP-MS method for analysis of manganese and iron in PEx has been developed. The method could easily be expanded to include other trace metals of interest, such as cadmium, nickel or chromium. This first attempt to evaluate PEx as a tool for exposure assessments of airborne metals indicates that the method has potential.
[Show abstract][Hide abstract] ABSTRACT: We report on the analysis of endogenous peptides in cerebrospinal fluid (CSF) by mass spectrometry. A method was developed for preparation of peptide extracts from CSF. Analysis of the extracts by offline LC-MALDI MS resulted in the detection of 3,000-4,000 peptide-like features. Out of these, 730 peptides were identified by MS/MS. The majority of these peptides have not been previously reported in CSF. The identified peptides were found to originate from 104 proteins, of which several have been reported to be involved in different disorders of the central nervous system. These results support the notion that CSF peptidomics may be viable complement to proteomics in the search of biomarkers of CNS disorders.
PLoS ONE 08/2012; 7(8):e42555. DOI:10.1371/journal.pone.0042555 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Phosphorylation is one of the key mechanisms that regulate centrosome biogenesis, spindle assembly, and cell cycle progression. However, little is known about centrosome-specific phosphorylation sites and their functional relevance. Here, we identified phosphoproteins of intact Drosophila melanogaster centrosomes and found previously unknown phosphorylation sites in known and unexpected centrosomal components. We functionally characterized phosphoproteins and integrated them into regulatory signaling networks with the 3 important mitotic kinases, cdc2, polo, and aur, as well as the kinase CkIIβ. Using a combinatorial RNA interference (RNAi) strategy, we demonstrated novel functions for P granule, nuclear envelope (NE), and nuclear proteins in centrosome duplication, maturation, and separation. Peptide microarrays confirmed phosphorylation of identified residues by centrosome-associated kinases. For a subset of phosphoproteins, we identified previously unknown centrosome and/or spindle localization via expression of tagged fusion proteins in Drosophila SL2 cells. Among those was otefin (Ote), an NE protein that we found to localize to centrosomes. Furthermore, we provide evidence that it is phosphorylated in vitro at threonine 63 (T63) through Aurora-A kinase. We propose that phosphorylation of this site plays a dual role in controlling mitotic exit when phosphorylated while dephosphorylation promotes G(2)/M transition in Drosophila SL2 cells.
[Show abstract][Hide abstract] ABSTRACT: We recently developed a novel, noninvasive method for sampling nonvolatile material from the distal airways. The method is based on the collection of endogenous particles in exhaled air (PEx). The aim of this study was to characterize the protein composition of PEx and to verify that the origin of PEx is respiratory tract lining fluid (RTLF).
Healthy individuals exhaled into the sampling device, which collected PEx onto a silicon plate inside a 3-stage impactor. After their extraction from the plates, PEx proteins were separated by SDS-PAGE and then analyzed by LC-MS. Proteins were identified by searching the International Protein Index human database with the Mascot search engine.
Analysis of the pooled samples identified 124 proteins. A comparison of the identified PEx proteins with published bronchoalveolar lavage (BAL) proteomic data showed a high degree of overlap, with 103 (83%) of the PEx proteins having previously been detected in BAL. The relative abundances of the proteins were estimated according to the Mascot exponentially modified protein abundance index protocol and were in agreement with the expected protein composition of RTLF. No amylase was detected, indicating the absence of saliva protein contamination with our sampling technique.
Our data strongly support that PEx originate from RTLF and reflect the composition of undiluted RTLF.
[Show abstract][Hide abstract] ABSTRACT: In this study we test the hypothesis that endogenous particles in exhaled air (PEx), non-invasively sampled from lower airways, are well suited for the analysis of respiratory tract lining fluid (RTLF) proteins, i.e., surfactant protein A (SP-A) and albumin. Ten healthy volunteers were included in the study and participated in two sampling sessions. Blood, exhaled breath condensate (EBC) and PEx were collected at each session. 100 L of breath were collected for each exhaled sample. Serum and exhaled samples were analyzed for SP-A using an in-house ELISA. Albumin was analyzed in exhaled samples using a commercial ELISA kit. SP-A detection rates were 100%, 21%, and 89% for PEx, EBC and serum, respectively. Albumin was detected in PEx, but not in EBC. SP-A measurements in PEx showed good repeatability with an intra-individual coefficient of variation of 13%. Both SP-A and albumin showed significant correlation to mass of PEx (r(s) = 0.93, p < 0.001 and r(s) = 0.86, p = 0.003, respectively). Sampling and analysis of PEx is a valid non-invasive method to monitor RTLF proteins sampled from the lower respiratory tract, as demonstrated here by example of SP-A and albumin analysis.
Respiratory medicine 11/2011; 106(2):197-204. DOI:10.1016/j.rmed.2011.10.008 · 3.09 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Regulation of centrosome structure, duplication and segregation is integrated into cellular pathways that control cell cycle progression and growth. As part of these pathways, numerous proteins with well-established non-centrosomal localization and function associate with the centrosome to fulfill regulatory functions. In turn, classical centrosomal components take up functional and structural roles as part of other cellular organelles and compartments. Thus, although a comprehensive inventory of centrosome components is missing, emerging evidence indicates that its molecular composition reflects the complexity of its functions. We analysed the Drosophila embryonic centrosomal proteome using immunoisolation in combination with mass spectrometry. The 251 identified components were functionally characterized by RNA interference. Among those, a core group of 11 proteins was critical for centrosome structure maintenance. Depletion of any of these proteins in Drosophila SL2 cells resulted in centrosome disintegration, revealing a molecular dependency of centrosome structure on components of the protein translation machinery, actin- and RNA-binding proteins. In total, we assigned novel centrosome-related functions to 24 proteins and confirmed 13 of these in human cells.
The EMBO Journal 10/2010; 29(19):3344-57. DOI:10.1038/emboj.2010.210 · 10.43 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The technique of sampling exhaled air is attractive because it is noninvasive and so allows repeated sampling with ease and no risk for the patient. Knowledge of the biomarkers' origin is important to correctly understand and interpret the data. Endogenous particles, formed in the airways, are exhaled and reflect chemical composition of the respiratory tract lining fluid. However, the formation mechanisms and formation sites of these particles are unknown. We hypothesize that airway opening following airway closure causes production of airborne particles that are exhaled. The objective of this study was to examine production of exhaled particles following varying degrees of airway closure. Ten healthy volunteers performed three different breathing maneuvers in which the initial lung volume preceding an inspiration to total lung capacity was varied between functional residual capacity (FRC) and residual volume (RV). Exhaled particle number concentrations in the size interval 0.30-2.0 microm were recorded. Number concentrations of exhaled particles showed a 2- to 18-fold increase after exhalations to RV compared with exhalations where no airway closure was shown [8,500 (810-28,000) vs. 1,300 (330-13,000) particles/expired liter, P = 0.012]. The difference was most noticeable for the smaller size range of particles (<1 microm). There were significant correlations between particle concentrations for the different maneuvers. Our results show that airway reopening following airway closure is an important mechanism for formation of endogenous exhaled particles and that these particles originate from the terminal bronchioles.
[Show abstract][Hide abstract] ABSTRACT: Currently, the precursor ion selection strategies in LC-MS mainly choose the most prominent peptide signals for MS/MS analysis. Consequently, high-abundance proteins are identified by MS/MS of many peptides, whereas proteins of lower abundance might elude identification. We present a novel, iterative and result-driven approach for precursor ion selection that significantly increases the efficiency of an MS/MS analysis by decreasing data redundancy and analysis time. By simulating different strategies for precursor ion selection on an existing data set, we compare our method to existing result-driven strategies and evaluate its performance with regard to mass accuracy, database size, and sample complexity.
Journal of Proteome Research 05/2009; 8(7):3239-51. DOI:10.1021/pr800835x · 4.25 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: This study illustrates multifunctionality of proteins of honeybee royal jelly (RJ) and how their neofunctionalization result from various PTMs of maternal proteins. Major proteins of RJ, designated as apalbumins belong to a protein family consisting of nine members with M(r) of 49-87 kDa and they are accompanied by high number of minority homologs derived from maternal apalbumins. In spite of many data on diversity of apalbumins, the molecular study of their individual minority homologous is still missing. This work is a contribution to functional proteomics of second most abundant protein of RJ apalbumin2 (M(r) 52.7 kDa). We have purified a minority protein from RJ; named as apalbumin2a, differ from apalbumin2 in M(r) (48.6 kDa), in N-terminal amino acids sequences - ENSPRN and in N-linked glycans. Characterization of apalbumin2a by LC-MALDI TOF/TOF MS revealed that it is a minority homolog of the major basic royal jelly protein, apalbumin2, carrying two fully occupied N-glycosylation sites, one with high-mannose structure, HexNAc2Hex9, and another carrying complex type antennary structures, HexNAc4Hex3 and HexNAc5Hex4. We have found that apalbumin2a inhibit growth of Paenibacillus larvae. The obtained data call attention to functional plasticity of RJ proteins with potential impact on functional proteomics in medicine.
[Show abstract][Hide abstract] ABSTRACT: Determining which proteins are unique among one or several protein populations is an often-encountered task in proteomics. To this purpose, we present a new method based on trypsin-catalyzed incorporation of the stabile isotope (18)O in the C-termini of tryptic peptides, followed by LC-MALDI MS analysis. The analytical strategy was designed such that proteins unique to a given population out of several can be assigned in a single experiment by the isotopic signal intensity distributions of their tryptic peptides in the recorded mass spectra. The method is demonstrated for protein-protein interaction analysis, in which the differential isotope labeling was used to distinguish endogenous human brain proteins interacting with a recombinant bait protein from nonbiospecific background binders.
Journal of Proteome Research 12/2005; 4(6):2109-16. DOI:10.1021/pr050219i · 4.25 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The marine bacterium Rhodopirellula baltica, a member of the phylum Planctomycetes, has distinct morphological properties and contributes to remineralization of biomass in the natural environment. On the basis of its recently determined complete genome we investigated its proteome by 2-DE and established a reference 2-DE gel for the soluble protein fraction. Approximately 1000 protein spots were excised from a colloidal Coomassie-stained gel (pH 4-7), analyzed by MALDI-MS and identified by PMF. The non-redundant data set contained 626 distinct protein spots, corresponding to 558 different genes. The identified proteins were classified into role categories according to their predicted functions. The experimentally determined and the theoretically predicted proteomes were compared. Proteins, which were most abundant in 2-DE gels and the coding genes of which were also predicted to be highly expressed, could be linked mainly to housekeeping functions in glycolysis, tricarboxic acid cycle, amino acid biosynthesis, protein quality control and translation. Absence of predictable signal peptides indicated a localization of these proteins in the intracellular compartment, the pirellulosome. Among the identified proteins, 146 contained a predicted signal peptide suggesting their translocation. Some proteins were detected in more than one spot on the gel, indicating post-translational modification. In addition to identifying proteins present in the published sequence database for R. baltica, an alternative approach was used, in which the mass spectrometric data was searched against a maximal ORF set, allowing the identification of four previously unpredicted ORFs. The 2-DE reference map presented here will serve as framework for further experiments to study differential gene expression of R. baltica in response to external stimuli or cellular development and compartmentalization.
[Show abstract][Hide abstract] ABSTRACT: We report the development of a robust interface for off-line coupling of nano liquid chromatography (LC) to matrix-assisted laser desorption/ionisation-mass spectrometry (MALDI-MS) and its application to the analysis of proteolytic digests of proteins, both isolated and in mixtures. The interface makes use of prestructured MALDI sample supports to concentrate the effluent to a small sample plate area and localize the MALDI sample to a predefined array, thereby enriching the analyte molecules and facilitating automated MALDI-MS analysis. Parameters that influence the preparation of MALDI samples from the LC effluent were evaluated with regard to detection sensitivity, spectra quality, and reproducibility of the method. A procedure for data processing is described. The presented nano LC MALDI-MS system allowed the detection of several peptides from a tryptic digest of bovine serum albumin, at analyzed amounts corresponding to one femtomole of the digested protein. For the identification of native proteins isolated from mouse brain by two-dimensional gel electrophoresis, nano LC MALDI-MS increased the number of detected peptides, thereby allowing identification of proteins that could not be identified by direct MALDI-MS analysis. The ability to identify proteins in complex mixtures was evaluated for the analysis of Escherichia coli 50S ribosomal subunit. Out of the 33 expected proteins, 30 were identified by MALDI tandem time of flight fragment ion fingerprinting.
[Show abstract][Hide abstract] ABSTRACT: To gain insights into complex biological processes, such as transcription and replication, the analysis of protein-DNA interactions and the determination of their sequence requirements are of central importance. In this study, we probed protein microarray technology and ultraviolet crosslinking combined with mass spectrometry (MS) for their practicability to study protein-DNA interactions. We chose as a model system the well-characterized interaction of bacterial replication initiator DnaA with its cognate binding site, the DnaA box. Interactions of DnaA domain 4 with a high-affinity DnaA box (R4) and with a low-affinity DnaA box (R3) were compared. A mutant DnaA domain 4, A440V, was included in the study. DnaA domain 4, wt, spotted onto FAST slides, revealed a strong signal only with a Cy5-labeled, double-stranded, 21-mer oligonucleotide containing DnaA box R4. No signals were obtained when applying the mutant protein. Ultraviolet crosslinking combined with nanoLC/MALDI-TOF MS located the site of interaction to a peptide spanning amino acids 433- 442 of Escherichia coli DnaA. This fragment contains six residues that were identified as being involved in DNA binding by recently published crystal structure and nuclear magnetic resonance (NMR) analysis. In the future, the technologies applied in this study will become important tools for studying protein-DNA interactions.
[Show abstract][Hide abstract] ABSTRACT: Sustained off resonance irradiation (SORI) collision-induced dissociation (CID) is a commonly used method of collisionally activating ions for fragmentation in Fourier transform mass spectrometric experiments. To achieve the degree of fragmentation desired, both the irradiation frequency and amplitude must be optimized. This is a time-consuming procedure, particularly when the m/z values of the precursor ions vary over a broad range. We present an approach that simplifies this optimization by precalculating the irradiation frequency of the ions to be fragmented as a constant percentage of the reduced cyclotron frequency. Using this approach, the optimal amplitude was found to be significantly less dependent on the m/z value of the precursor ion, and therefore required little or no adjustment. This method considerably simplified optimization of SORI-CID for analysis of carbohydrates, glycoconjugates, and peptides over the mass range m/z 300-3500, requiring optimization of only a single experimental parameter, the irradiation amplitude, and only for the first MS/MS stage.
Journal of the American Society for Mass Spectrometry 05/2002; 13(4):318-24. DOI:10.1016/S1044-0305(02)00340-9 · 2.95 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Transiently elevating pressure in a matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS) source into the 1-10 mbar range during ionization decreases the metastable fragmentation of gangliosides. This allows detection of the molecular ion species without loss of the highly labile sialic acid residues. In these experiments, gangliosides with up to five sialic acids were ionized by MALDI and detected with the FTMS. In each case, when the high pressure collisional cooling was used, the singly charged molecular ion was the base peak in the spectra, both in the positive and negative ion modes, and minimal metastable fragmentation was observed. This result is promising, as the previously developed TLC separation methods can be coupled to MALDI-FTMS.
Journal of the American Society for Mass Spectrometry 05/2002; 13(4):402-7. DOI:10.1016/S1044-0305(02)00351-3 · 2.95 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Several variants of glucoamylase 1 (GA1) from Aspergillus niger were created in which the highly O-glycosylated peptide (aa 468--508) connecting the (alpha/alpha)(6)-barrel catalytic domain and the starch binding domain was substituted at the gene level by equivalent segments of glucoamylases from Hormoconis resinae, Humicola grisea, and Rhizopus oryzae encoding 5, 19, and 36 amino acid residues. Variants were constructed in which the H. resinae linker was elongated by proline-rich sequences as this linker itself apparently was too short to allow formation of the corresponding protein variant. Size and isoelectric point of GA1 variants reflected differences in linker length, posttranslational modification, and net charge. While calculated polypeptide chain molecular masses for wild-type GA1, a nonnatural proline-rich linker variant, H. grisea, and R. oryzae linker variants were 65,784, 63,777, 63,912, and 65,614 Da, respectively, MALDI-TOF-MS gave values of 82,042, 73,800, 73,413, and 90,793 Da, respectively, where the latter value could partly be explained by an N-glycosylation site introduced near the linker C-terminus. The k(cat) and K(m) for hydrolysis of maltooligodextrins and soluble starch, and the rate of hydrolysis of barley starch granules were essentially the same for the variants as for wild-type GA1. beta-Cyclodextrin, acarbose, and two heterobidentate inhibitors were found by isothermal titration calorimetry to bind to the catalytic and starch binding domains of the linker variants, indicating that the function of the active site and the starch binding site was maintained. The stability of GA1 linker variants toward GdnHCl and heat, however, was reduced compared to wild-type.
[Show abstract][Hide abstract] ABSTRACT: The present study demonstrates that treating O-glycosylated peptides with methylamine vapor followed by partial acid hydrolysis is an effective means for locating O-glycosylation site(s). The reaction with methylamine transforms the glycosylated Ser and Thr residues into stable methylamine derivatives with a mass increment of +13 Da relative to nonglycosylated Ser and Thr residues. Peptide sequencing based on partial acid hydrolysis followed by mass spectrometric analysis or in favorable cases by CID-MS/MS enables the determination of the formerly O-glycosylated sites.