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High-throughput tissue proteomics has great potential in the advancement of precision medicine. Here, we investigated the combined sensitivity of trap-elute microflow liquid chromatography with a ZenoTOF for DIA proteomics and phosphoproteomics. Method optimization was conducted on HEK293T cell lines to determine the optimal variable window size, MS2 accumulation time and gradient length. The ZenoTOF 7600 was then compared to the previous generation TripleTOF 6600 using eight rat organs, finding up to 23% more proteins using a fifth of the sample load and a third of the instrument time. Spectral reference libraries generated from Zeno SWATH data in FragPipe (MSFragger-DIA/DIA-NN) contained 4 times more fragment ions than the DIA-NN only library and quantified more proteins. Replicate single-shot phosphopeptide enrichments of 50–100 μg of rat tryptic peptide were analyzed by microflow HPLC using Zeno SWATH without fractionation. Using Spectronaut we quantified a shallow phosphoproteome containing 1000–3000 phosphoprecursors per organ. Promisingly, clear hierarchical clustering of organs was observed with high Pearson correlation coefficients >0.95 between replicate enrichments and median CV of 20%. The combined sensitivity of microflow HPLC with Zeno SWATH allows for the high-throughput quantitation of an extensive proteome and shallow phosphoproteome from small tissue samples.

Proteomic analysis by mass spectrometry of small (≤2 mg) solid tissue samples from diverse formats requires high throughput and comprehensive proteome coverage. We developed a nearly universal, rapid, and robust protocol for sample preparation, suitable for high-throughput projects that encompass most cell or tissue types. This end-to-end workflow extends from original sample to loading the mass spectrometer and is centered on a one-tube homogenization and digestion method called Heat ‘n Beat (HnB). It is applicable to most tissues, regardless of how they were fixed or embedded. Sample preparation was divided into separate challenges. The initial sample washing and final peptide cleanup steps were adapted to three tissue sources: fresh frozen (FF), optimal cutting temperature (OCT) compound embedded (FF-OCT), and formalin-fixed paraffin embedded (FFPE). Third, for core processing, tissue disruption and lysis were decreased to a 7 min heat and homogenization treatment, and reduction, alkylation, and proteolysis were optimized into a single step. The refinements produced near doubled peptide yield when compared to our earlier method ABLE delivered a consistently high digestion efficiency of 85–90%, reported by ProteinPilot, and required only 38 min for core processing in a single tube, with the total processing time being 53–63 min. The robustness of HnB was demonstrated on six organ types, a cell line, and a cancer biopsy. Its suitability for high-throughput applications was demonstrated on a set of 1171 FF-OCT human cancer biopsies, which were processed for end-to-end completion in 92 h, producing highly consistent peptide yield and quality for over 3513 MS runs.

Myostatin, a highly conserved secretory protein, negatively regulates muscle development, affecting both the proliferation and differentiation of muscle cells. Proteolytic processing of the myostatin precursor protein generates a myostatin pro-peptide and mature protein. Dimerization of the mature myostatin protein creates the active form of myostatin. Myostatin dimer activity can be inhibited by noncovalent binding of two monomeric myostatin pro-peptides. This ability for myostatin to self-regulate as well as the altered expression of myostatin in states of abnormal health (e.g., muscle wasting) support the need for specific detection of myostatin forms. Current protein detection methods (e.g., Western blot) rely greatly on antibodies and are semiquantitative at best. Tandem mass spectometry (as in this study) provides a highly specific method of detection, enabling the characterization of myostatin protein forms through the analysis of discrete peptides fragments. Utilizing the scheduled high-resolution multiple reaction monitoring paradigm (sMRMHR; AB SCIEX 5600 TripleTOF) we identified the lower limit of quantitation (LLOQ) of both mature (DFGLDCDEHSTESR) and pro-peptide regions (ELIDQYDVQR) as 0.19 nmol/L. Furthermore, scheduled multiple reaction monitoring (sMRM; AB SCIEX QTRAP 5500) identified a LLOQ for a peptide of the pro-peptide region (LETAPNISK) as 0.16 nmol/L and a peptide of the mature region (EQIIYGK) as 0.25 nmol/L.

The combination of stable isotope labeling (SIL) with mass spectrometry (MS) allows comparison of the abundance of thousands of proteins in complex mixtures. However, interpretation of the large data sets generated by these techniques remains a challenge because appropriate statistical standards are lacking. Here, we present a generally applicable model that accurately explains the behavior of data obtained using current SIL approaches, including 18O, iTRAQ, and SILAC labeling, and different MS instruments. The model decomposes the total technical variance into the spectral, peptide, and protein variance components, and its general validity was demonstrated by confronting 48 experimental distributions against 18 different null hypotheses. In addition to its general applicability, the performance of the algorithm was at least similar than that of other existing methods. The model also provides a general framework to integrate quantitative and error information fully, allowing a comparative analysis of the results obtained from different SIL experiments. The model was applied to the global analysis of protein alterations induced by low H2O2concentrations in yeast, demonstrating the increased statistical power that may be achieved by rigorous data integration. Our results highlight the importance of establishing an adequate and validated statistical framework for the analysis of high-throughput data.

Liquid chromatography coupled with tandem mass spectrometry–based high‐throughput proteomics allows detection and characterization of thousands of peptides and their post‐translational modifications in a single sample. Protein phosphorylation affects most eukaryotic cellular processes, and its deregulation is considered a hallmark of cancer and other diseases. High‐throughput phosphoproteomics may enable monitoring of altered signaling pathways as a means of stratifying tumors and facilitating the discovery of new drugs. Unfortunately, the development of molecular tests for clinical use is constrained by the limited availability of fresh frozen, clinically annotated samples, and protocols that allow the use of human archival formalin‐fixed, paraffin‐embedded samples are required. The protocols in this article describe a global procedure for evaluating hundreds of protein phosphorylation sites in protein extracts obtained from formalin‐fixed, paraffin‐embedded tissues. Curr. Protoc. Chem. Biol. 4:161‐175 © 2012 by John Wiley & Sons, Inc.

The question of where the low-metallicity globular clusters in early-type galaxies came from has profound implications for the formation of those galaxies. Our work supports the idea that the metal-poor globular cluster systems of giant early-type galaxies formed in dwarf galaxies that have been subsumed by the giants. To support this hypothesis, two linear relations, one involving globular cluster metallicity versus host galaxy luminosity and one involving metallicity versus velocity dispersion were studied. Tentatively, these relations show that the bright ellipticals do not obey the same trend as the dwarfs, suggesting that the low-metallicity globular clusters did not form within their parent bright ellipticals.

KiSS-1is a metastasis suppressor gene reported to be involved in the progression of several solid neoplasias. The loss of KiSS-1gene expression has been shown to be inversely correlated with increasing tumor stage, distant metastases, and poor overall survival in bladder tumors. To identify the molecular pathways associated with the metastasis suppressor role of KiSS-1in bladder cancer, we carried out a proteomics analysis of bladder cancer cells (EJ138) transiently transfected with a vector encompassing the full-length KiSS-1gene using an iTRAQ (isobaric tags for relative and absolute quantitation) approach. Protein extracts collected after 24- and 48-h transfection were fractionated and cleaved with trypsin, and the resulting peptides were labeled with iTRAQ reagents. The labeled peptides were separated by strong cation exchange and reversed phase LC and analyzed by MALDI-TOF/TOF MS. Three software packages were utilized for data analysis: ProteinPilot for identification and quantification of differentially expressed proteins, Protein Center for gene ontology analysis, and Ingenuity Pathways Analysis to provide insight into biological networks. Comparative analysis among transfected, mock, and empty vector-exposed cells identified 1529 proteins with high confidence (>99%) showing high correlation rates among replicates (70%). The involvement of the identified proteins in biological networks served to characterize molecular pathways associated with KiSS-1expression and to select critical candidates for verification analyses by Western blot using independent transfected replicates. As part of complementary clinical validation strategies, immunohistochemical analyses of proteins regulated by KiSS-1, such as Filamin A, were performed on bladder tumors spotted onto tissue microarrays (n= 280). In summary, our study not only served to uncover molecular mechanisms associated with the metastasis suppressor role of KiSS-1in bladder cancer but also to reveal the biomarker role of Filamin A in bladder cancer progression and clinical outcome.

KiSS-1 is a metastasis suppressor gene reported to be involved in the progression of several solid neoplasias. The loss of KiSS-1 gene expression has been shown to be inversely correlated with increasing tumor stage, distant metastases, and poor overall survival in bladder tumors. To identify the molecular pathways associated with the metastasis suppressor role of KiSS-1 in bladder cancer, we carried out a proteomics analysis of bladder cancer cells (EJ138) transiently transfected with a vector encompassing the full-length KiSS-1 gene using an iTRAQ (isobaric tags for relative and absolute quantitation) approach. Protein extracts collected after 24- and 48-h transfection were fractionated and cleaved with trypsin, and the resulting peptides were labeled with iTRAQ reagents. The labeled peptides were separated by strong cation exchange and reversed phase LC and analyzed by MALDI-TOF/TOF MS. Three software packages were utilized for data analysis: ProteinPilot for identification and quantification of differentially expressed proteins, Protein Center for gene ontology analysis, and Ingenuity Pathways Analysis to provide insight into biological networks. Comparative analysis among transfected, mock, and empty vector-exposed cells identified 1529 proteins with high confidence (>99%) showing high correlation rates among replicates (70%). The involvement of the identified proteins in biological networks served to characterize molecular pathways associated with KiSS-1 expression and to select critical candidates for verification analyses by Western blot using independent transfected replicates. As part of complementary clinical validation strategies, immunohistochemical analyses of proteins regulated by KiSS-1, such as Filamin A, were performed on bladder tumors spotted onto tissue microarrays (n = 280). In summary, our study not only served to uncover molecular mechanisms associated with the metastasis suppressor role of KiSS-1 in bladder cancer but also to reveal the biomarker role of Filamin A in bladder cancer progression and clinical outcome.

The growing use of selected reaction monitoring (SRM) mass spectrometry in proteomic analyses led us to investigate how to identify peptides by SRM using only a minimal number of fragment ions. By using a computational model of the SRM work flow we computed the potential interferences from other peptides in a given proteome. From these results, we selected the deterministic SRM addresses that contained sufficient information to confer peptide and protein identity that we termed unique ion signatures (UIS). We computationally showed that UIS comprised of only two transitions are diagnostic for >99% of Escherichia coli proteins and >96% of human proteins that possess a sequence-unique peptide. We demonstrated an example of experimental use of UIS using a modified SRM methodology to profile the E. coli tricarboxylic acid cycle from a single injection of cell lysate. In addition, we showed the potential of UIS to form the first functionally orthogonal approach to validate peptide assignments obtained from conventional analyses of MS/MS spectra. The UIS methodology is a novel deterministic peptide identification method for MS/MS spectra based on information content. These robust theoretical assays will have widespread use when integrated with previously collected MS/MS data and conventional proteomics technologies.

The growing use of selected reaction monitoring (SRM) mass spectrometry in proteomic analyses led us to investigate how to identify peptides by SRM using only a minimal number of fragment ions. By using a computational model of the SRM work flow we computed the potential interferences from other peptides in a given proteome. From these results, we selected the deterministic SRM addresses that contained sufficient information to confer peptide and protein identity that we termed unique ion signatures (UIS). We computationally showed that UIS comprised of only two transitions are diagnostic for >99% of Escherichia coli proteins and >96% of human proteins that possess a sequence-unique peptide. We demonstrated an example of experimental use of UIS using a modified SRM methodology to profile the E. coli tricarboxylic acid cycle from a single injection of cell lysate. In addition, we showed the potential of UIS to form the first functionally orthogonal approach to validate peptide assignments obtained from conventional analyses of MS/MS spectra. The UIS methodology is a novel deterministic peptide identification method for MS/MS spectra based on information content. These robust theoretical assays will have widespread use when integrated with previously collected MS/MS data and conventional proteomics technologies.

Macrophage colony-stimulating factor (M-CSF or CSF-1) controls the development of macrophage lineage cells via activation of its tyrosine kinase receptor, c-Fms. After adding CSF-1 to M1 myeloid cells expressing CSF-1R (CSF-1 receptor), tyrosine phosphorylation of many cellular proteins occurs, which might be linked to subsequent macrophage differentiation. The biological significance and characterization of such proteins were explored by a dual strategy comprising two-dimensional SDS/PAGE analysis of cell lysates of CSF-1-treated M1 cells expressing the wild-type or a mutated receptor, together with an enrichment strategy involving a tyrosine-phosphorylated receptor construct. In the present study, we report the identification by MS of a novel, low-abundance, 110 kDa form of myosin XVIIIA (MysPDZ, myosin containing PDZ domain), which appears to be preferentially tyrosine-phosphorylated after CSF-1R activation when compared with other known isoforms. Receptor mutation studies indicate that CSF-1R-dependent tyrosine phosphorylation of p110myosin XVIIIA requires Tyr-559 in the cytoplasmic domain of the receptor and is therefore Src-family kinase-dependent. Gelsolin, Erp61 protein disulphide-isomerase and possibly non-muscle myosin IIA were also tyrosine-phosphorylated under similar conditions. Similar to the more abundant p190 isoform, p110 myosin XVIIIA lacks a PDZ domain and, in addition, it may lack motor activity. The phosphorylation of p110 myosin XVIIIA by CSF-1 may alter its cellular localization or target its association with other proteins.

Heteroglobin (HGB) is a 39-kDa heterodimeric protein detected under non-reducing conditions in harderian, parotid, and submaxillary glands and saliva of the Syrian hamster with antiserum raised against the carboxyl end deduced from the female harderian gland cDNA FHG22 (Domı́nguez, P. (1995) FEBS Lett.376, 257–261). After reduction, only one 5.6-kDa polypeptide, named HGB.A, was immunodetected and identified by sequencing as the mature FHG22 product. Tissue-specific expression of HGB.A and HGB mimics that of FHG22 mRNA, with sex differences in submaxillary and harderian glands. Purification of HGB revealed it consists of HGB.A disulfide bonded to HGB.B, a 33.5-kDa N-glycosylated subunit that yields a 9-kDa core polypeptide after deglycosylation. Two highly homologous (96.2%) cDNA clones (HGB.B1 and HGB.B2) encoding 94 amino acid-long isoforms were identified by screening a female harderian gland library with an HGB.B probe. The corresponding mature polypeptides are 78 amino acids long with 12 differences, but 3 putative N-glycosylation sites are maintained. The expression of HGB.B mRNAs is parallel to that of HGB and HGB.A, but no HGB.B2 mRNA was detected in submaxillary glands. Homology studies indicate that HGB.A and HGB.B1/HGB.B2 belong to different subfamilies of the secretoglobin-uteroglobin family and form heterodimers as previously described.

The role of rab33b, a Golgi-specific rab protein, was investigated. Microinjection of rab33b mutants stabilised in the GTP-specific state resulted in a marked inhibition of anterograde transport within the Golgi and in the recycling of glycosyltransferases from the Golgi to the ER, respectively. A GST-rab33b fusion protein stabilised in its GTP form was found to interact by Western blotting or mass spectroscopy with Golgi protein GM130 and rabaptin-5 and rabex-5, two rab effector molecules thought to function exclusively in the endocytic pathway. A similar binding was seen to rab1 but not to rab6, both Golgi rabs. In contrast, rab5 was as expected, shown to bind rabaptin-5 and rabex-5 as well as the endosomal effector protein EEA1 but not GM130. No binding of EEA1 was seen to any of the Golgi rabs.

The role of rab33b, a Golgi‐specific rab protein, was investigated. Microinjection of rab33b mutants stabilised in the GTP‐specific state resulted in a marked inhibition of anterograde transport within the Golgi and in the recycling of glycosyltransferases from the Golgi to the ER, respectively. A GST‐rab33b fusion protein stabilised in its GTP form was found to interact by Western blotting or mass spectroscopy with Golgi protein GM130 and rabaptin‐5 and rabex‐5, two rab effector molecules thought to function exclusively in the endocytic pathway. A similar binding was seen to rab1 but not to rab6, both Golgi rabs. In contrast, rab5 was as expected, shown to bind rabaptin‐5 and rabex‐5 as well as the endosomal effector protein EEA1 but not GM130. No binding of EEA1 was seen to any of the Golgi rabs.

AbstractIrreversible binding of Teven bacteriophages to Escherichia coli is mediated by the short tail fibres, which serve as inextensible stays during DNA injection. Short tail fibres are exceptionally stable elongated trimers of gene product 12 (gp12), a 56 kDa protein. The Nterminal region of gp12 is important for phage attachment, the central region forms a long shaft, while a Cterminal globular region is implicated in binding to the bacterial lipopolysaccharide core. When gp12 was treated with stoichiometric amounts of trypsin or chymotrypsin at 37 C, an Nterminally shortened fragment of 52 kDa resulted. If the protein was incubated at 56 C before trypsin treatment at 37 C, we obtained a stable trimeric fragment of 3 33 kDa lacking residues from both the N and Ctermini. Apparently, the protein unfolds partially at 56 C, thereby exposing proteasesensitive sites in the Cterminal region and extra sites in the Nterminal region. Welldiffracting crystals of this fragment could be grown. Our results indicate that gp12 carries a stable central region, consisting of the Cterminal part of the shaft and the attached Nterminal half of the globular region. Implications for structure determination of the gp12 protein and its folding are discussed.

We have identified 1057 globular cluster candidates in a WFPC2 image of the inner region of M87. The globular cluster luminosity function (GCLF) can be well fitted by a Gaussian profile with a mean value of m0V=23.67+-0.07 mag and s=1.39+-0.06 mag. The GCLF in five radial bins is found to be statistically the same at all points, showing no clear evidence of dynamical destruction processes based on the luminosity function (LF). Similarly, there is no obvious trend between the half-light radius of the clusters and the galactocentric distance. The core radius of the globular cluster density distribution is Rc=56'', considerably larger than the core of the stellar component (Rc=6.''8). The mean color of the cluster candidates is V-I=1.09 mag, which corresponds to an average metallicity of Fe/H=-0.74 dex. The color distribution is bimodal everywhere, with a blue peak at V-I=0.95 mag and a red peak at V-I=1.20 mag. The red population is only 0.1 mag bluer than the underlying galaxy, indicating that these clusters formed late in the metal-enrichment history of the galaxy and were possibly created in a burst of star/cluster formation 3-6 Gyr after the blue population. We also find that both the red and the blue cluster distributions have a more elliptical shape (Hubble type E3.5) than the nearly spherical galaxy. The average half-light radius of the clusters is [?]2.5 pc, which is comparable to the 3 pc average effective radius of the Milky Way clusters, although the red clusters are [?]20% smaller than the blue ones.

Current ideas on the amount, distribution, and nature of dark matter in galaxies are reviewed. Observations indicate that dark halos around most, if not all, galaxies. Recent evidence suggests that many dwarf galaxies have higher dark-matter fractions than normal galaxies as well as higher central dark-matter densities. Some spiral galaxy rotation curves are rising and others are falling at the optical radius, thereby weakening the "disk-halo conspiracy." Observational and theoretical techniques to probe the dark halos of ellipticals are becoming more refined, and various methods are being employed to investigate the shapes of halos. There are useful constraints on the extent of the dark matter around our own Galaxy, whereas in some other galaxies the edge of the halo may have been detected. Microlensing experiments have recently commenced which may soon uncover the nature of the Galactic dark matter. These and the other issues reviewed here have far-reaching implications for galaxy formation and evolution, and a variety of cosmological questions.

To achieve high throughput, protein microcharacterization sample preparation must be automated. We describe a cartesian robot capable of processing 32 protein samples in parallel. The system is based on specially designed flow-through reactors for contamination-free reagent delivery and removal. Washing of excised gel pieces, reduction and alkylation, proteolytic cleavage and peptide extraction are performed in these reactors. Compatibility of the system with HPLC peptide separation and Edman degradation as well as with laser desorption mass spectrometry of the unseparated mixture is demonstrated. This is the first report describing automated preparation and processing of multiple protein samples.

Since the introduction of fast analysis methods for peptide mixtures such as MALDI-MS, peptide micropreparation and digest methods have become an important bottleneck in the protein characterization process. We therefore developed and describe here a digest robot capable of processing 30 protein samples in parallel [Houthaeve el al.(1995), FEBS Lett.376, 91–94]. Briefly, after gel pieces or blots are cut out, they are loaded in flowthrough reactors and these are loaded in a thermocontrolled reactor block. The proteins are then washed, reduced, and alkylated, proteolytically or chemically cleaved, and resulting peptides extracted. The system allows the parallel use of different reagents and enzymes during the same run, and is compatible with RP-HPLC peptide separation and Edman degradation, MALDI-MS, and NanoES-MS/MS. The digest robot is now also commercially available from ABIMED. In an ongoing project aimed at elucidating proteinaceous structures involved in the functional and structural maintenance of the Golgi apparatus, we illustrate the strength of the digest robot for the fast analysis of several proteins. We conclude that the performance of the digest robot is comparable to currently used manual digestion methods. The approach outlined makes sample preparation procedures faster, simpler, and less labor-intensive.

The complete sequence determination of protein S1, the largest protein from the Escherichia coliribosome, revealed that it is composed of repeated internal duplications, mainly at the central region of the molecule which contains the mRNA-binding domain [Eur. J. Biochem. (1982) 123, 37–53]. With the aid of computer programs the statistical significance of the internal repeats in S1 was proven. Auto-comparison of the S1-sequence showed that it is composed of 87-residue strings with 44-residue subunits: 3 strings (residues 189–447) are highly related; 3 strings (residues 13–188 and 448–533) are less but significantly related. Statistical analysis revealed a more distant relatedness for the 44-residue subunits than for the 87-residue strings. Protein S1 was compared to all other E. coliribosomal proteins and to the 1100 primary structures listed in the last. Atlas of Protein Sequence and Structure (1978) showing parts of S1 distantly related with parts of several ribosomal proteins. However, distinct homologies between protein S1 and the other ribosomal proteins can be ruled out. The strongest repeats within the S1 sequence were mainly found corresponding to the mRNA-binding domain. Distantly related partial sequences were also found with ribosome-associated and nucleotide-binding proteins, with some enzymes, with several peptide hormones and with contractile proteins.

The described isocratic separation for phenylthiohydantoin (Pth) amino acid derivatives offers advantages over gradient systems: the baseline is more stable at high sensitivity, the resolution and reproducibility is excellent and the cost and consumption of solvent is very low. The separation of low picomolar quantities, on 2 different types of reverse phase columns, are presented. The method is used ‘off line’, i.e. as a separate analytical unit, or in an ‘on line’ mode, where it is directly connected to a protein sequencer for automatic identification of the released amino add derivatives.

The described isocratic separation for phenylthiohydantoin (Pth) amino acid derivatives offers advantages over gradient systems: the baseline is more stable at high sensitivity, the resolution and reproducibility is excellent and the cost and consumption of solvent is very low. The separation of low picomolar quantities, on 2 different types of reverse phase columns, are presented. The method is used ‘off line’, i.e. as a separate analytical unit, or in an ‘on line’ mode, where it is directly connected to a protein sequencer for automatic identification of the released amino add derivatives.

The rapid accumulation of sequence data generated by the various genome sequencingprojects and the generation of expressed sequence tag databases has resulted in the need forthe development of fast and sensitive methods for the identification and characterisation oflarge numbers of gel electrophoretically separated proteins to translate the sequence data intobiological function. To achieve this goal it has been necessary to devise new approaches toprotein analysis: matrix-assisted laser desorption and electrospray mass spectrometry havebecome important protein analytical tools which are both fast and sensitive. When combinedwith a robotic system for the in-gel digestion of electrophoretically separated proteins, itbecomes possible to rapidly identify many proteins by searching databases with MS data. Thepower of this combination of techniques is demonstrated by an analysis of the proteins presentin the myofibrillar lattice of the indirect flight muscle of Drosophila melanogaster. Theproteins were separated by SDS-PAGE and in-gel proteolysis was performed bothautomatically and manually. All 16 major proteins could quickly be identified by massspectrometry. Although most of the protein components were known to be present in theflight muscle, two new components were also identified. The combination of methodsdescribed offers a means for the rapid identification of large numbers of gel separatedproteins.

The complete sequence determination of protein S1, the largest protein from the Escherichia coliribosome, revealed that it is composed of repeated internal duplications, mainly at the central region of the molecule which contains the mRNA‐binding domain [Eur. J. Biochem. (1982) 123, 37–53]. With the aid of computer programs the statistical significance of the internal repeats in S1 was proven. Auto‐comparison of the S1‐sequence showed that it is composed of 87‐residue strings with 44‐residue subunits: 3 strings (residues 189–447) are highly related; 3 strings (residues 13–188 and 448–533) are less but significantly related. Statistical analysis revealed a more distant relatedness for the 44‐residue subunits than for the 87‐residue strings. Protein S1 was compared to all other E. coliribosomal proteins and to the 1100 primary structures listed in the last. Atlas of Protein Sequence and Structure (1978) showing parts of S1 distantly related with parts of several ribosomal proteins. However, distinct homologies between protein S1 and the other ribosomal proteins can be ruled out. The strongest repeats within the S1 sequence were mainly found corresponding to the mRNA‐binding domain. Distantly related partial sequences were also found with ribosome‐associated and nucleotide‐binding proteins, with some enzymes, with several peptide hormones and with contractile proteins.

To achieve high throughput, protein microcharacterization sample preparation must be automated. We describe a cartesian robot capable of processing 32 protein samples in parallel. The system is based on specially designed flow‐through reactors for contamination‐free reagent delivery and removal. Washing of excised gel pieces, reduction and alkylation, proteolytic cleavage and peptide extraction are performed in these reactors. Compatibility of the system with HPLC peptide separation and Edman degradation as well as with laser desorption mass spectrometry of the unseparated mixture is demonstrated. This is the first report describing automated preparation and processing of multiple protein samples.

Completion of the sequence determination of all 52 Escherichia coli ribosomal proteins enabled a final comparison of their sequences. Similarities in amino acid compositions were compared to the relatedness of the sequences, which was analyzed statistically with the aid of the computer programs RELATE and ALIGN.

The rapid accumulation of sequence data generated by the various genome sequencing projects and the generation of expressed sequence tag databases has resulted in the need for the development of fast and sensitive methods for the identification and characterisation of large numbers of gel electrophoretically separated proteins to translated the sequence data into biological function. To achieve this goal it has been necessary to devise new approaches to protein analysis: matrix-assisted laser desorption and electrospray mass spectrometry have become important protein analytical tools which are both fast and sensitive. When combined with a robotic system for the in-gel digestion of electrophoretically separated proteins, it becomes possible to rapidly identify many proteins by searching databases with MS data. The power of this combination of techniques is demonstrated by an analysis of the proteins present in the myofibrillar lattice of the indirect flight muscle ofDrosophila melanogaster. The proteins were separated by SDS-PAGE and in-gel proteolysis was performed both automatically and manually. All 16 major proteins could quickly be identified by mass spectrometry. Although most of the protein components were known to be present in the flight muscle, two new components were also identified. The combination of methods described offers a means for the rapid identification of large numbers of gel separated proteins.

We describe the construction of a laboratory workstation for the micromanipulation of liquids. The performance of the workstation is demonstrated by its use in a DNA sequencing protocol; although its operational units form the backbone of a robotic system with wide applications in molecular biology and biochemistry.

The article explores scientific research funding process in Australia. It notes that the Excellence in Research for Australia Initiative (ERA) of the Australian Research Council (ARC) seeks to determine and promote excellence in the research activity of the higher education institutions in the country. The funding application process is detailed in which the typical application can run to 40 to 50 pages while a rejected application can be resubmitted and funded the following year.

Inherent interindividual and intraindividual variation in the length of the menstrual cycle limits the accuracy of predicting days of peak fertility. To improve detection of days of peak fertility, a more detailed understanding of longitudinal changes in cervicovaginal fluid (CVF) biomarkers during the normal menstrual cycle is needed. The aim of this study, therefore, was to characterize longitudinal changes in CVF proteins during the menstrual cycle using a quantitative, data-independent acquisition mass spectrometry approach. Six serial samples were collected from women (n = 10) during the menstrual cycle. Samples were obtained at two time points for each phase of the cycle: early and late preovulatory, ovulatory, and postovulatory. Information-dependent acquisition (IDA) of mass spectra from all individual CVF samples was initially performed and identified 278 total proteins. Samples were then pooled by time of collection (n = 6 pools) and analyzed using IDA and information-independent acquisition (Sequential Windowed Acquisition of All Theoretical Mass Spectra [SWATH]). The IDA library generated contained 176 statistically significant protein identifications (P< 0.000158). The variation in the relative abundance of CVF proteins across the menstrual cycle was established by comparison with the SWATH profile against the IDA library. Using time-series, pooled samples obtained from 10 women, quantitative data were obtained by SWATH analysis for 43 CVF proteins. Of these proteins, 28 displayed significant variation in relative abundance during the menstrual cycle (assessed by ANOVA). Statistical significant changes in the relative expression of CVF proteins during preovulatory, ovulatory, and postovulatory phases of menstrual cycle were identified. The data obtained may be of utility not only in elucidating underlying physiological mechanisms but also as clinically useful biomarkers of fertility status.