The Rate of False Positive Sequence Matches of Peptides Profiled by MALDI MS and Identified by MS/MS

Proteomic signatures of extracellular vesicles secreted by nonmineralizing and mineralizing human osteoblasts and stimulation of tumor cell growth

Beyond forming bone, osteoblasts play pivotal roles in various biologic processes, including hematopoiesis and bone metastasis. Extracellular vesicles (EVs) have been implicated in intercellular communication via transfer of proteins and nucleic acids between cells. We focused on the proteomic characterization of nonmineralizing (NMOBs) and mineralizing (MOBs) human osteoblast (SV-HFOs) EVs and investigated their effect on human prostate cancer (PC3) cells by microscopic, proteomic, and gene expression analyses. Proteomic analysis showed that 97% of the proteins were shared among NMOB and MOB EVs, and 30% were novel osteoblast-specific EV proteins. Label-free quantification demonstrated mineralization stage-dependent 5-fold enrichment of 59 and 451 EV proteins in NMOBs and MOBs, respectively. Interestingly, bioinformatic analyses of the osteoblast EV proteomes and EV-regulated prostate cancer gene expression profiles showed that they converged on pathways involved in cell survival and growth. This was verified by in vitro proliferation assays where osteoblast EV uptake led to 2-fold increase in PC3 cell growth compared to cell-free culture medium-derived vesicle controls. Our findings elucidate the mineralization stage-specific protein content of osteoblast-secreted EVs, show a novel way by which osteoblasts communicate with prostate cancer, and open up innovative avenues for therapeutic intervention.

Conserved BK channel-protein interactions reveal signals relevant to cell death and survival

The large-conductance Ca²⁺-activated K⁺ (BK) channel and its β-subunit underlie tuning in non-mammalian sensory or hair cells, whereas in mammals its function is less clear. To gain insights into species differences and to reveal putative BK functions, we undertook a systems analysis of BK and BK-Associated Proteins (BKAPS) in the chicken cochlea and compared these results to other species. We identified 110 putative partners from cytoplasmic and membrane/cytoskeletal fractions, using a combination of coimmunoprecipitation, 2-D gel, and LC-MS/MS. Partners included 14-3-3γ, valosin-containing protein (VCP), stathmin (STMN), cortactin (CTTN), and prohibitin (PHB), of which 16 partners were verified by reciprocal coimmunoprecipitation. Bioinformatics revealed binary partners, the resultant interactome, subcellular localization, and cellular processes. The interactome contained 193 proteins involved in 190 binary interactions in subcellular compartments such as the ER, mitochondria, and nucleus. Comparisons with mice showed shared hub proteins that included N-methyl-D-aspartate receptor (NMDAR) and ATP-synthase. Ortholog analyses across six species revealed conserved interactions involving apoptosis, Ca²⁺ binding, and trafficking, in chicks, mice, and humans. Functional studies using recombinant BK and RNAi in a heterologous expression system revealed that proteins important to cell death/survival, such as annexinA5, γ-actin, lamin, superoxide dismutase, and VCP, caused a decrease in BK expression. This revelation led to an examination of specific kinases and their effectors relevant to cell viability. Sequence analyses of the BK C-terminus across 10 species showed putative binding sites for 14-3-3, RAC-α serine/threonine-protein kinase 1 (Akt), glycogen synthase kinase-3β (GSK3β) and phosphoinositide-dependent kinase-1 (PDK1). Knockdown of 14-3-3 and Akt caused an increase in BK expression, whereas silencing of GSK3β and PDK1 had the opposite effect. This comparative systems approach suggests conservation in BK function across different species in addition to novel functions that may include the initiation of signals relevant to cell death/survival.

Biomedical application of MALDI mass spectrometry for small-molecule analysis

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is an emerging analytical tool for the analysis of molecules with molar masses below 1,000 Da; that is, small molecules. This technique offers rapid analysis, high sensitivity, low sample consumption, a relative high tolerance towards salts and buffers, and the possibility to store sample on the target plate. The successful application of the technique is, however, hampered by low molecular weight (LMW) matrix-derived interference signals and by poor reproducibility of signal intensities during quantitative analyses. In this review, we focus on the biomedical application of MALDI-MS for the analysis of small molecules and discuss its favorable properties and its challenges as well as strategies to improve the performance of the technique. Furthermore, practical aspects and applications are presented.

Quantitative matrix-assisted laser desorption ionization-fourier transform ion cyclotron resonance (MALDI-FT-ICR) peptide profiling and identification of multiple-sclerosis-related proteins

We introduce a matrix-assisted laser desorption ionization-Fourier transform ion cyclotron resonance (MALDI-FT-ICR) method for quantitative peptide profiling, using peak height as a measure for abundance. Relative standard deviations in peak height of peptides spiked over 3 orders of magnitude in concentration were below 10% and allowed for accurate comparisons between multiple sclerosis and controls. Application on a set of 163 cerebrospinal fluid (CSF) samples showed significantly differential abundant peptides, which were subsequently identified into proteins (e.g., chromogranin A, clusterin, and complement C3).

Application of flavonoids - quercetin and rutin - as new matrices for matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of Pt(II) and Pd(II) complexes

Attempts are being made to overcome the resistance of tumour cells to platinum (Pt) drugs by the synthesis of new generations of Pt complexes, and it is important to find appropriate and simple methods for the characterization of those novel complexes. The additional applicability of such a method for the analysis of the interactions of metal complexes with biomolecules would be advantageous. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) seems to possess the capability to become this method of choice, since it could be applied to low-mass complexes as well as for the analysis of large biomolecules. In this work the applicability of flavonoids - quercetin and rutin - as matrices for MALDI-TOFMS analysis of dichlorido(ethylendiamine)platinum(II) ([PtCl(2)(en)]), dichlorido(diaminocyclohexane)platinum(II) ([PtCl(2)(dach)]) and chloride (diethylenetriamine) palladium(II) chloride ([PdCl(dien)]Cl) complexes is demonstrated. Spectra of Pt(II) and Pd(II) complexes recorded in the presence of quercetin and rutin are rather simple: Pt(II) complexes generate [M+Na](+) or [M+K](+)ions, whereas the investigated Pd(II) complex gives ions generated by the loss of one Cl(-) or HCl. Flavonoids give a relatively small number of well-defined ions in the low-mass region (at m/z 303.3 for quercetin and m/z 633.5 for rutin). Quercetin and rutin can be applied in much lower concentrations than other common MALDI matrices and require rather low laser intensity. We speculate that flavonoids stabilize the structures of the metal complexes and that they may be useful for the analysis of other biologically active metal complexes, thus implying their broader applicability.