We describe an integrated workstation for the automated, high-throughput, and conclusive identification of proteins by reverse-phase chromatography electrospray ionization tandem mass spectrometry. The instrumentation consists of a refrigerated autosampler, a submicrobore reverse-phase liquid chromatograph, and an electrospray triple quadrupole mass spectrometer. For protein identification, enzymatic digests of either homogeneous polypeptides or simple protein mixtures were generated and loaded into the autosampler. Samples were sequentially injected every 32 min. Ions of eluting peptides were automatically selected by the mass spectrometer and subjected to collision-induced dissociation. Following each run, the resulting tandem mass spectra were automatically analyzed by SEQUEST, a program that correlates uninterpreted peptide fragmentation patterns with amino acid sequences contained in databases. Protein identification was established by SEQUEST-SUMMARY a program that combines the SEQUEST scores of peptides originating from the same protein and ranks the cumulative results in a short summary.The workstation's performance was demonstrated by the unattended identification of 90 proteins from the yeast Saccharomyces cerevisiae, which were separated by high-resolution two-dimensional PAGE. The system was found to be very robust and identification was reliably and conclusively established for proteins if quantities exceeding 1-5 pmol were applied to the gel. The level of automation, the throughput, and the reliability of the results suggest that this system will be useful for the many projects that require the characterization of large numbers of proteins.Keywords: electrospray ionization mass spectrometry; protein identification; proteome; Saccharomyces cerevisiae; sequence database; two-dimensional gel electrophoresis The identification of proteins by their amino acid sequence has been a common and important process in diverse areas of biological research. Traditionally, proteins of a particular function were purified to homogeneity and then sequenced. The recent dramatic growth of large-scale genomic and expressed sequence tag sequence databases and their ease of accessibility through the Internet have created new challenges and opportunities for protein Reprint requests to: Ruedi

The prochlorophytes are oxygenic prokaryotes differing from other cyanobacteria by the presence of a light-harvesting system containing both chlorophylls (Chls) a and b and by the absence of phycobilins. We demonstrate here that the Chl a/b binding proteins from all three known prochlorophyte genera are closely related to IsiA, a cyanobacterial Chl a-binding protein induced by iron starvation, and to CP43, a constitutively expressed Chl a antenna protein of photosystem II. The prochlorophyte Chl a/b protein (pcb) genes do not belong to the extended gene family encoding eukaryotic Chl a/b and Chl a/c light-harvesting proteins. Although higher plants and prochlorophytes share common pigment complements, their light-harvesting systems have evolved independently.

BAP31 is a 28-kDa integral membrane protein of the endoplasmic reticulum whose cytosolic domain contains two identical caspase recognition sites (AAVD.G) that are preferentially cleaved by initiator caspases, including caspase 8. Cleavage of BAP31 during apoptosis generates a p20 fragment that remains integrated in the membrane and, when expressed ectopically, is a potent inducer of cell death. To examine the consequences of maintaining the structural integrity of BAP31 during apoptosis, the caspase recognition aspartate residues were mutated to alanine residues, and Fas-mediated activation of caspase 8 and cell death were examined in human KB epithelial cells stably expressing the caspase-resistant mutant crBAP31. crBAP31 only modestly slowed the time course for activation of caspases, as assayed by the processing of procaspases 8 and 3 and the measurement of total DEVDase activity. As a result, cleavage of the caspase targets poly(ADP-ribosyl) polymerase and endogenous BAP31, as well as the redistribution of phosphatidylserine and fragmentation of DNA, was observed. In contrast, cytoplasmic membrane blebbing and fragmentation and apoptotic redistribution of actin were strongly inhibited, cell morphology was retained near normal, and the irreversible loss of cell growth potential following removal of the Fas stimulus was delayed. Of note, crBAP31-expressing cells also resisted Fas-mediated release of cytochrome c from mitochondria, and the mitochondrial electrochemical potential was only partly reduced. These results argue that BAP31 cleavage is important for manifesting cytoplasmic apoptotic events associated with membrane fragmentation and reveal an unexpected cross talk between mitochondria and the endoplasmic reticulum during Fas-mediated apoptosis in vivo.Programmed cell death is characterized by a series of morphological and structural changes culminating in the coordinated packaging of cellular contents into apoptotic bodies, which are ultimately eliminated via phagocytosis by neighboring cells. Early events in this process typically include cell rounding, loss of phospholipid asymmetry in the cell membrane, extensive cytoplasmic membrane blebbing and fragmentation, nuclear pyknosis, and internucleosomal DNA cleavage (26). Although much remains to be learned about the mechanisms underlying these events, programmed cell death is achieved in most cell death pathways as a consequence of the proteolytic cleavage of a diverse array of structural and regulatory proteins by the executors of apoptosis, the caspase family of cysteine proteases (33,46,48). Several of the caspase targets are known to have critical roles in at least some of the apoptotic processes. These targets include the DFF40/CAD inhibitor, DFF45/ICAD, which plays a role in the fragmentation of DNA (23, 36), and the actin-associated capping protein gelsolin, which plays a role in cytoplasmic membrane blebbing (17). In addition, the activation of several kinases by caspase cleavage, including PAK2 (20, 34) and the Ste20-related kinases MST1 (14,1...

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We describe an analytical system for the rapid identification of proteins by correlation of tandem mass spectra with protein sequence databases. The system consists of an integrated solid phase microextraction/capillary zone electrophoresis peptide separation device that is connected through a microelectrospray ion source to a tandem mass spectrometer. The limits of detection are 660 amol of sample at a concentration limit of < 33 amol/microliters for peptide mass measurement, and < 10 fmol of sample, at a concentration limit of < 300 amol/microliters for peptide analysis by collision-induced dissociation. Using this system, we have identified low nanogram amounts of yeast proteins separated by high-resolution two-dimensional gel electrophoresis.

A method for the identification of proteins by their amino acid sequence at the low-femtomole to subfemtomole sensitivity level is described. It is based on an integrated system consisting of a capillary zone electrophoresis (CZE) instrument coupled to an electrospray ionization triple- quadrupole tandem mass spectrometer (ESI-MS/MS) via a microspray interface. The method consists of proteolytic fragmentation of a protein, peptide separation by CZE, analysis of separated peptides by ESI-MS/MS, and identification of the protein by correlation of the collision-induced dissociation (CID) patterns of selected peptides with the CID patterns predicted from all the isobaric peptides in a sequence database. Using standard peptides applied to a 20-microns-i.d. capillary, we demonstrate an ESI-MS limit of detection of less than 300 amol and CID spectra suitable for searching sequence databases obtained with 600 amol of sample applied to the capillary. Successful protein identification by the method was demonstrated by applying 50 and 38 fmol of a tryptic digest of the proteins beta-lactoglobulin and bovine serum albumin, respectively, to the system.

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A 97-kDa protein present in the glucose transporter (GLUT4 isotype)-containing vesicles from rat adipocytes has been isolated, the sequences of two tryptic peptides were obtained, and on the basis of these its cDNA partially cloned. The 97-kDa protein is almost certainly identical to a major integral glycoprotein of this size in the rat adipocyte plasma membrane, since its predicted N-terminal sequence is the same as that recently determined for this glycoprotein by amino acid sequencing. Moreover, the predicted partial sequence (322 amino acids) of the 97-kDa protein is highly homologous to the corresponding region of a human placental amine oxidase, which was cloned simultaneously and proposed to be a secreted protein. The amino acid sequence of the 97-kDa rat/human amine oxidase indicates that the protein consists of a very short N-terminal cytoplasmic domain followed by a single transmembrane segment and a large extracellular domain containing the catalytic site. Thus this study establishes the 97-kDa rat/human amine oxidase as the first integral membrane amine oxidase to be cloned. The membrane amine oxidase was more abundant in the plasma membranes than the low density microsomes of the adipocyte, and in contrast to some other proteins found in GLUT4 vesicles, it did not redistribute to the plasma membrane in response to treatment of the cells with insulin.