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O-GalNAc type glycosylation is an abundant and complex protein modification. Recent developments in mass spectrometry resulted in significant success in quantitative analysis of O-GalNAc glycosylation. The analysis of released O-GalNAc type glycans expanded our horizons of understanding the glycome of various biological models. The site-specific analysis of glycosylation micro-heterogeneity of purified proteins opened perspectives for the improved design of glycoprotein therapeutics. Advanced gene editing and chemical technologies applied to O-glycoproteomics enabled to identify O-GalNAc glycosylation at unprecedented depth. Progress in the analysis of intact glycoproteins under native and reduced conditions enabled the monitoring of glycosylation proteoform variants. Despite of the astonishing results in quantitative O-GalNAc glycoproteomics, site-specific mapping of the full O-GalNAc structural repertoire in complex samples is yet a long way off. Here, we summarize the most common quantitative strategies in O-GalNAc glycoproteomics, review recent progress and discuss benefits and limitations of the various approaches in the field.

Gluten is a common dietary component with a complex protein structure. It forms incomplete products of digestion, which have the potential to mount an immune response in genetically predisposed individuals, resulting in celiac disease. It also has been linked with nonceliac gluten sensitivity and irritable bowel syndrome due to wheat allergy. A gluten-free diet is an effective treatment of these conditions; however, it can lead to micronutrient and mineral deficiencies and a macronutrient imbalance with higher sugar and lipid intake. Recent popularity has led to greater availability, but increasing cost, of commercially available gluten-free products.

Proteins in semen, either in spermatozoa (SPZ) or seminal plasma (SP), are directly involved in molecular processes and biological pathways regulating sperm function, including fertilizing ability. Therefore, semen proteins are candidates of choice for biomarkers discovery for fertility and for sperm (dys)function. Mass spectrometry (MS)-based proteomics has opened up a new era for characterizing and quantifying the protein profile of SP and SPZ, as well as for unveiling the complex protein interactions involved in the activation of sperm functionality. This article overviews existing literature on MS-based proteomics regarding porcine semen, with a specific focus on the potential practical application of the results achieved so far. The weaknesses of current studies and the perspectives for future research in MS-based pig semen proteomics are also addressed.

Two complex protein defense systems—complement and coagulation—are based on amplifying enzyme cascades triggered by specific local stimuli. Excess systemic activation of either system is pathologic and is normally prevented by a family of regulatory proteins. The 2 systems are ancient biological processes which share a common origin that predates vertebrate evolution. Recent research has uncovered multiple opportunities for cross talk between complement and coagulation including proteins traditionally viewed as coagulation factors that activate and regulate complement, and proteins traditionally seen as part of the complement system that participate in coagulation. Ten examples of cross talk between the 2 systems are described. The mutual engagement of both systems is increasingly recognized to occur in human diseases. Three conditions—paroxysmal nocturnal hemoglobinuria, atypical hemolytic uremic syndrome, and the antiphospholipid syndrome—provide examples of the importance of interactions between complement and coagulation in human biology. A better understanding of the mutual engagement of these 2 ancient defense systems is expected to result in improved diagnostics and new treatments for systemic diseases.

Understanding adsorption of important proteins as part of a complex protein mixture onto surfaces such as soil is critical for numerous environmental applications. In this study, we investigated the adsorption of urease as part of a total bacterial protein extract from Sporosarcina pasteurii onto soil mixtures, including sand and silt, and the resulting enzymatic activity. Proteomics analysis of the proteomes revealed that larger proteins were preferentially adsorbed onto the soil surfaces regardless of the type of soil; the median molecular weight of the proteins over-represented in the supernatant and soil fractions were 29.4 kDa and 36.6 kDa, respectively. In addition, the majority of total ureases (86.2–97.2%) was present in the soil fractions of soil mixtures containing silt. Adsorbed urease exhibited enzymatic activity up to 0.2 U/mg protein in the soil fractions at a substrate concentration of 1.67 mM. Additionally, urease activity in the soil correlated with the total amount of protein adsorbed and the amounts of adsorbed urease. Although the soil-adsorbed urease retained measurable activity, an overall loss of activity was observed in all samples. Understanding the dynamics of protein adsorption onto soil surfaces can aid in improved designs for engineering applications that utilize enzymatic activities.

Two-dimensional gel electrophoresis (2-DE) is a technique that has been widely applied in a variety of proteomics studies. It is capable of resolving complex protein mixtures into individual protein spots based on their isoelectric point and molecular weight, enabling large-scale analysis of protein expression patterns for deciphering their changes in different biological conditions. 2-DE is a powerful tool that empowers researchers to perform differential qualitative and quantitative proteome analysis and is particularly advantageous for characterizing protein isoforms and post-translationally modified proteins. Despite its popularity as the workhorse for proteomics in the past few decades, it has been gradually displaced by the more sophisticated and high-performance mass spectrometry-based methods. However, there are several variations of the 2-DE technique that have emerged as promising approaches that shine new light on specific niches that 2-DE could still contribute. In this review, we first provide an overview of the applications of 2-DE, its merits and pitfalls in the current proteomic research arena, followed by a discussion on several alternative approaches for potential future applications.

The solvent freeze out (SFO) technique is here the first time introduced and used to purify a realistic and complex protein mixture. Urease crystals were obtained from jack bean meal in the process and the purity of which were evaluated via both specific activity and SDS-PAGE. Compared to a conventional salting out crystallization, the use of SFO technology can provide a better control of the crystallization process. A detailed investigation into the crystallization process is presented by carrying out experiments with different parameters. Results showed that the quality of the ice layer is the key factor for the control of the crystallization process. The SFO technology can be considered a promising alternative in protein crystallization, because the process itself is efficient and reproducible. Even though not fully optimized, a satisfactory product purity and a decent yield of urease crystals were obtained using the SFO technology. The enzymatic activity was also preserved after the SFO process in the here carried out case study.

SummaryMega-hemocyanin is a 13.5 MDa oxygen transporter found in the hemolymph of some snails. Similar to typical gastropod hemocyanins, it is composed of 400 kDa building blocks but has additional 550 kDa subunits. Together, they form a large, completely filled cylinder. The structural basis for this highly complex protein packing is not known so far. Here, we report the electron cryomicroscopy (cryo-EM) structure of mega-hemocyanin complexes from two different snail species. The structures reveal that mega-hemocyanin is composed of flexible building blocks that differ in their conformation, but not in their primary structure. Like a protein origami, these flexible blocks are optimally packed, implementing different local symmetries and pseudosymmetries. A comparison between the two structures suggests a surprisingly simple evolutionary mechanism leading to these large oxygen transporters.

In vitro biocatalytic systems have moved far beyond established uses in food, diagnostic, and chemical applications. As new strategies to construct and manage multiple enzymes in ever more complex systems are developed, novel applications emerge. In the field of chemistry, complex protein networks are applied to enable the production of fine chemicals, such as dihydroxyacetone phosphate, and even bulk chemicals, such as biofuels, from cheap sugars. Cell-free protein synthesis is applied to expanding protein and nucleic acid biochemistry and enabling novel assay formats, while programmable DNA-circuits can be exploited to engineer sensitive detection methods. Novel developments in chemical analytics such as real-time mass spectrometry to follow the metabolism online, directed physical assembly of network members facilitating substrate channeling, and encapsulation forming biofunctional subunits enable a better control and potential for optimization.

This Feature describes the use of electron transfer dissociation (ETD) to analyze the hydrogen/deuterium exchange (HDX) of proteins at increased spatial resolution down to the level of individual residues. A practical overview of how to couple ETD to the classical bottom-up HDX-MS workflow is given and new options for method optimization are discussed and exemplified. In addition, the real-world applicability of the HDX-ETD method to pinpoint conformational changes in a large 75 kDa protein complex of therapeutic interest is demonstrated. This feature highlights how the conformation and interactions of complex protein systems of biological or pharmaceutical interest can now be analyzed at a hitherto unprecedented level of structural detail using an MS-based method.

We review new and established methods for the chemical modification of proteins in living cells and highlight recent applications. The review focuses on tag-mediated protein labeling methods, such as the tetracysteine tag and SNAP-tag, and new developments in this field such as intracellular labeling with lipoic acid ligase. Recent promising advances in the incorporation of unnatural amino acids into proteins are also briefly discussed. We describe new tools using tag-mediated labeling methods including the super-resolution microscopy of tagged proteins, the study of the interactions of proteins and protein domains, the subcellular targeting of synthetic ion sensors, and the generation of new semisynthetic metabolite sensors. We conclude with a view on necessary future developments, with one example being the selective labeling of non-tagged, native proteins in complex protein mixtures.

FeS cluster biogenesis is an essential process in virtually all forms of life. Complex protein machineries that are conserved from bacteria through higher eukaryotes facilitate assembly of the FeS cofactor in proteins. In the last several years, significant strides have been made in our understanding of FeS cluster assembly and the functional overlap of this process with cellular iron homeostasis. This minireview summarizes the present understanding of the cytosolic iron-sulfur cluster assembly (CIA) system in eukaryotes, with a focus on information gained from studies in budding yeast and mammalian systems.

A kaizen improvement effort was undertaken focusing on the workflows of an in-house workgroup whose aim was the rapid production of small amounts of protein reagents. The kaizen's goal was to reduce process lead times to accommodate more deliveries per year and more complex protein types. Business requirements were established, and baseline performance was evaluated against projected needs. Then potential areas for change were identified, selected, and implemented. Improvements were quantified based on established metrics as well as customer input. Overall in-house group capacity was raised 11% from 1.1 to 1.2 deliveries per person per week at the same time that the percentage of non-platform (more difficult) requests was increased to nearly 50% from under 10%. In-house group lead times from request to shipping for platform (less difficult) purification deliveries were improved by 30% from 11.1 to 7.7 days.

Purpose of Review: To describe progress in the application of proteomic approaches to advance our understanding of the biology of pancreatic cancer as well as contribute potential protein biomarkers for this disease. Recent Findings: Here we review proteomic studies relating to pancreatic cancer that have been published in the past 12 months. We describe novel techniques for the simplification of complex protein samples, focusing particularly on emerging methods for reducing the complexity of blood. We provide examples, where possible, of the application of these novel technologies to pancreatic cancer research. Summary: Both the range of proteomic-based approaches and their sensitivities for the detection of low-abundance proteins has increased. This provides promise that further research will yield insight into pancreatic cancer, including valuable information on proteins that may ultimately serve as biomarkers for pancreatic cancer.

Major advances in placental biology have been realized as new technologies have been developed and existing methods have been refined in many areas of biological research. Classical anatomy and whole-organ physiology tools once used to analyze placental structure and function have been supplanted by more sophisticated techniques adapted from molecular biology, proteomics, and computational biology and bioinformatics. In addition, significant refinements in morphological study of the placenta and its constituent cell types have improved our ability to assess form and function in highly integrated manner. To offer an overview of modern technologies used by investigators to study the placenta, this workshop: Advanced techniques in placental biology, assembled experts who discussed fundamental principles and real time examples of four separate methodologies. Y. Sadovsky presented the principles of microRNA function as an endogenous mechanism of gene regulation. J. Robinson demonstrated the utility of correlative microscopy in which light-level and transmission electron microscopy are combined to provide cellular and subcellular views of placental cells. A. Croy provided a lecture on the use of microdissection techniques which are invaluable for isolating very small subsets of cell types for molecular analysis. Finally, G. Rice presented an overview methods on profiling of complex protein mixtures within tissue and/or fluid samples that, when refined, will offer databases that will underpin a systems approach to modern trophoblast biology.

Our ability to alter and control the structure and function of biomolecules, and of proteins in particular, will be of utmost importance in order to understand their respective biological roles in complex systems such as living organisms. This challenge has prompted the development of powerful modern techniques in the fields of molecular biology, physical biochemistry and chemical biology. These fields complement each other and their successful combination has provided unique insights into protein structure and function at the level of isolated molecules, cells and organisms. Chemistry is without doubt most suited for introducing subtle changes into biomolecules down to the atomic level, but often struggles when it comes to large targets, such as proteins. In this review, we attempt to give an overview of modern and broadly applicable techniques that permit chemical synthesis to be applied to complex protein targets in order to gain control over their structure and function. As will be demonstrated, these approaches offer unique possibilities in our efforts to understand the molecular basis of protein functioning in vitro and in vivo. We will discuss modern synthetic reactions that can be applied to proteins and give examples of recent highlights. Another focus of this review will be the application of inteins as versatile protein engineering tools.

The success of genome sequencing projects has led to a shift from the description of single molecules to the characterisation of complex samples. At the same time, there is growing interest not only in studying organisms at the genomic level, but in the characterization of their proteome. Such a task would not be possible without the availability of appropriate technologies. Protein and antibody microarray technologies are, in addition to two-dimensional gel electrophoresis followed by mass spectrometry, two of the most propitious technologies for the screening of complex protein samples. Nevertheless, to succeed, protein and antibody microarrays have to overcome their current limitations. This review aims to introduce these new technologies and highlights their current prospects and limitations.

Mass spectrometry data generated in differential profiling of complex protein samples are classically exploited using database searches. In addition, quantitative profiling is performed by various methods, one of them using isotopically coded affinity tags, where one typically uses a light and a heavy tag. Here, we present a new algorithm, ICATcher, which detects pairs of light/heavy peptide MS/MS spectra independent of sequence databases. The method can be used for de novo sequencing and detection of posttranslational modifications. ICATcher is distributed as open source software.

Proteomics technology is progressing at an incredible rate. The latest generation of tandem mass spectrometers can now acquire tens of thousands of fragmentation spectra in a matter of hours. Furthermore, quantitative proteomics methods have been developed that incorporate a stable isotope-labeled internal standard for every peptide within a complex protein mixture for the measurement of relative protein abundances. These developments have opened the doors for 'shotgun' proteomics, yet have also placed a burden on the computational approaches that manage the data. With each new method that is developed, the quantity of data that can be derived from a single experiment increases. To deal with this increase, new computational approaches are being developed to manage the data and assess false positives. This review discusses current approaches for analyzing proteomics data by mass spectrometry and identifies present computational limitations and bottlenecks.

The objective of this presentation is to review the major proteomic technologies available to developmental toxicologists and, when possible, to provide examples of how various proteomic technologies have been used in developmental toxicology or toxicology in general. The field of proteomics is too broad for us to go into great depth about each technology, so we have attempted to provide brief overviews supplemented with many references that cover the subjects in more detail. Proteomics tools produce a global view of complex biological systems by examining complex protein mixtures using large-scale, high-throughput technologies. These technologies speed up the process of protein separation, quantification, and identification. As an important complement to genomics, proteomics allows for the examination of the entire complement of proteins in an organism, tissue, or cell-type. Current proteomics technologies not only identify protein expression, but also post-translational modifications and protein interactions. The field of proteomics is expanding rapidly to provide greater volume and quality of protein information to help understand the multifaceted nature of biological systems.

A major challenge in protein target discovery and validation is how to specifically dissect complex protein mixtures and measure trace targets. Immunoaffinity-based protein capture, separation and detection have proven to be one of the most effective approaches. Avian IgY antibody microbeads (Seppro™), representing a type of novel and specific protein sorbent, have several distinct advantages over IgG. Their utility and applications are compared with those of IgG and other affinity reagents.

Tandem mass spectrometry has been used increasingly for high-throughput analysis of complex protein samples. A major challenge lies in the consistent, objective and transparent analysis of the large amounts of data generated by such experiments and in their dissemination and publication. Here, we review currently available computational tools and discuss the need for statistical criteria in the analysis of large proteomics datasets.

The evidence and arguments for and against the occurrence of endocytosis in fungal hyphae are summarized. The balance of evidence is in favour of the existence of endocytosis. This is supported by an analysis of the recently sequenced Neurospora genome which strongly suggests that this fungus possesses the complex protein machinery required to conduct endocytosis.

This 93rd SMA workshop followed the European Neuromuscular Centre (ENMC) tradition to combine clinical and molecular topics with the aim of not only exchanging current knowledge but also initiating collaborative studies. Despite important milestones in research on autosomal recessive SMA with localisation on chromosome 5q (SMA 5q) in the past 10 years, we are just beginning to understand the molecular basis and phenotypic spectrum of non-5q-SMA entities. The possibility of analysing the SMN gene allowed the delineation of the diagnostic criteria of ‘classical’ proximal SMA and its clinical variability. On the other hand, different entities of SMA could be defined that show atypical features and proved to be unlinked to chromosome 5q. The field of interest has therefore been focussed on further genes responsible for anterior horn cell loss. This will contribute to further understand the underlying pathogenetic pathways, the complex protein interactions and genotype–phenotype correlations in various types of motor neuron disorders. The workshop was structured in a first part, briefly reviewing the current status of SMA 5q including animal models which have been generated. The second part included different sessions on non-5q-SMA forms; clinical and diagnostic criteria were discussed and adapted to current knowledge. These were summarized by invited chairpersons (named in brackets) and followed by contributions of the participants. The following short summaries cover the essentials of the reviews, the discussion and the consensus achieved. 1. Update on SMA 5q

Advances in molecular biology over the past decade have helped to enhance our understanding of the complex interplay between genetic, transcriptional and translational alterations in human cancers. These molecular changes are the basis for an evolving field of high-throughput cancer discovery techniques using microscopic amounts of patient-based materials. Laser capture microdissection allows pure populations of cells to be isolated from both the tumor and stroma in order to identify subtle differences in RNA and protein expression. Comparative analysis of these alterations between normal, pre-invasive, and invasive tissue using powerful bioinformatics programs has allowed us to identify novel tumor markers, profile complex protein pathways, and develop new molecular-based therapies. Continued refinement of such high-throughput microtechnologies will enable us to rapidly query patient specimens to identify novel methods for early detection, treatment, and follow-up of a wide array of human cancers.

ProtoPharm makes use of the ProtoChip™, a high-density immunoassay system, to construct epitope “fingerprints” of complex protein mixtures. Unlike all other protein biochip methods, the ProtoChip does not require the immobilization of proteins or antibodies on a solid support nor does the ProtoChip require the purification of large numbers of proteins. The ProtoChip may be used to profile complex protein mixtures, identify panels of diagnostic immunoassays, identify vaccine candidates, and provide leads for antibody therapeutics.

BRCA1 is a crucial human breast and ovarian cancer tumor suppressor gene. The article by Drost et al. in this issue of Cancer Cell together with a recent paper in Science now provide a clearer picture of how this large and complex protein suppresses tumorigenesis.

p97/Cdc48p/VCP is a highly conserved, essential member of the class of AAA+ ATPases present in both archaea and the eukaryotic cytosol. Like many of the AAA+ proteins, the functional state of p97 is a hexameric ring-shaped structure. However, the detailed relationship between monomer folding and assembly of the quaternary structure of p97, as well as other members of this class, has remained elusive. Here, we present a study of the structural changes of p97 during its folding and assembly, utilizing biophysical techniques including single-molecule Forster Resonance Energy Transfer (smFRET). p97 is large for using standard techniques to dual label with dyes for FRET studies. Therefore, this work aims to gain a deeper understanding about critical structural aspects of p97, while exploring advanced labeling methods that extend the scope of fluorescence studies to larger and more complex protein systems.

With whole genomes being sequenced almost routinely, the next logical step towards a better understanding of cellular mechanisms lies in studying the functional units of gene expression-proteins. One of the fundamental approaches in proteomics is the use of two-dimensional gel electrophoresis as a mode of separation and visualization of complex protein mixtures. Despite several limitations of the method, its ability to separate large numbers of proteins, including their post-translationally modified forms, ensures that it will continue to be popular in several well-defined areas of proteomics. In this article, we discuss the merits and drawbacks of two-dimensional gels and compare them with alternative systems such as one-dimensional gels and liquid chromatography-based separation methods. In the wake of recent advances in mass spectrometry and related areas, we outline areas where two-dimensional gels can best be utilized as the preferred separation method in proteomic strategies.

Centrioles are among the most beautiful and mysterious of all cell organelles. Although the ultrastructure of centrioles has been studied in great detail ever since the advent of electron microscopy, these studies raised as many questions as they answered, and for a long time both the function and mode of duplication of centrioles remained controversial. It is now clear that centrioles play an important role in cell division, although cells have backup mechanisms for dividing if centrioles are missing. The recent identification of proteins comprising the different ultrastructural features of centrioles has proven that these are not just figments of the imagination but distinct components of a large and complex protein machine. Finally, genetic and biochemical studies have begun to identify the signals that regulate centriole duplication and coordinate the centriole cycle with the cell cycle.

Biology ubiquitously uses molecular recognition and specificity to do its work. In contrast, the biomaterials widely used in medicine today non-specifically adsorb complex protein mixtures to their surfaces. These ill-defined protein layers are “read” by the cells (neutrophils, macrophages) that interrogate the implanted materials - the protein coat may be the trigger of subsequent biological reactions. Given the heterogeneity in composition (there are 200+ proteins in blood) and organization (proteins are adsorbed with no control of orientation or conformation) of adsorbed protein layers, it is no surprise that biological reactions, particularly in vivo, are poorly controlled. If fact, implanted synthetic materials are almost universally seen by the body as foreign objects and walled off into a tough, avascular, collagenous bag1.

General transcription factor TFIID consists of TATA box–binding protein (TBP) and TBP-associated factors (TAF II s), which together play a central role in both positive and negative regulation of transcription. The N-terminal region of the 230 kDa Drosophila TAF II (dTAF II 230) binds directly to TBP and inhibits TBP binding to the TATA box. We report here the solution structure of the complex formed by dTAF II 230 N-terminal region (residues 11–77) and TBP. dTAF II 230 11–77 comprises three α helices and a β hairpin, forming a core that occupies the concave DNA-binding surface of TBP. The TBP-binding surface of dTAF II 230 markedly resembles the minor groove surface of the partially unwound TATA box in the TBP–TATA complex. This protein mimicry of the TATA element surface provides the structural basis of the mechanism by which dTAF II 230 negatively controls the TATA box–binding activity within the TFIID complex.

Recently, large-scale experiments have provided new insights into the complex protein interaction network in yeast. However, previous analyses have shown that the number of interacting pairs that are common to different methods is extremely low and, therefore, less informative than expected. In this article, we show that comparing the connectivities of individual proteins can reveal that a common tendency between methods has been missed by the pairwise comparison of interactions. We found significant correlations between experimental methods and also between various in silico methods. Exceptionally, a computational method, gene neighbourhood, correlates with both in silico and experimental approaches.

A simple analytical method for characterization of food proteins by capillary electrophoresis (CE) has been developed. Major proteins in chicken eggs and cow's milk are characterized and can be quantitated by the CE technique. Egg white proteins are well resolved while the yolk shows a substantially more complex protein separation pattern than that in the egg white. Caseins and whey proteins in fresh milk were resolved by CE in a similar buffer system. Separation of both milk and egg proteins was performed reliably and reproducibly in an untreated fused-silica column, 25 cm × 20 μm I.D. Diluted egg or milk samples can be directly loaded on an automated instrument with on-line injection, detection and real-time data analysis in less than 10 min.

A method for reformulating the thermodynamic (delta G) description of complex equilibria is presented. The purpose of this reformulation is to take a system of N complexes which is completely defined by N delta Gs, and recast it in terms of a new set of N delta Gs. This reformulation is an extension of the concept of interaction energy (J. Wyman, Adv. Protein Chem. 19 (1964) 223-286). The new delta Gs obtained by this reformulation reflect the intrinsic properties of the binding sites and the hierarchical nature of potential interactions between them. A simple set of rules are developed which allow for the description of complex protein-ligand binding schemes and these rules are used to derive schemes for hemoglobin O2 binding. This reformulation represents the foundation for the theoretical description of the coupling of energy in protein-ligand systems as illustrated by the theoretical analysis of allosterism in a dimeric protein presented in the following paper. This reformulation also provides the foundation for the analysis of data pertaining to complex equilibria.

The anion-exchange separation of complex protein mixtures by displacement chromatography using spacer displacers driven by high-affinity final displacers is demonstrated. Guinea pig serum was separated on a medium-resolution adsorbent using a single heterogeneous mixture of carboxymethyldextran displacers to space the protein components. Mouse liver cytosol was separated on a low-resolution adsorbent using six carboxymethyldextran spacer displacers of increasing column affinity. The demonstration of the purification of alkaline phosphatase from E. coli periplasm by displacement chromatography on a high-performance liquid chromatography column is reviewed. The benefits of spacer displacers for separating minor components from complex biological protein mixtures is discussed. A simplified method for preparing carboxymethyldextran displacers is presented.

The targeting of cytosolically synthesized proteins into the thylakoid lumen is mediated by an aminoterminal pre-sequence consisting of an "envelope transit" and a "thylakoid transfer" signal in tandem. We have investigated the structural characteristics of several thylakoid transfer signals by determining the intermediate sites at which the stromal processing peptidase cleaves to remove the transit sequences. Using this approach we have found that the thylakoid transfer signals of Silene pratensis plastocyanin, 23-kDa oxygen-evolving complex protein from wheat, and 33-kDa oxygen-evolving complex protein from wheat, are 25, 39, and 48 residues in length, respectively. All of the transfer signals contain hydrophobic core sequences and a "-3,-1" motif reminiscent of those found in signal sequences, but the amino-terminal regions of the transfer signals of the 23- and 33-kDa proteins are both longer and more highly charged. The net charge of each amino-terminal region of the transfer sequences is +1, including the amino-terminal amino group. In each case, the stromal processing peptidase cleaves immediately after a positively charged residue, but otherwise the cleavage sites exhibit no common elements of either primary or secondary structure.

Current theraphy for hemophilia A requires frequent infusion of plasma-derived human factor VIII with the associated drawbacks of potential viral contaminamination, high cost and limited plasma availability. Factor VIII replacement theraphy has been improved through increased knowledge of molecular mechanisms regulating blood coagulation, derived largely from the isolation of the factor VIII gene and its expression in mammalian cells. Homogeneous pure preparations of factor VIII — the largest, most complex protein pharmaceutical produced to date through recombinant DNA technology — can now be produced for successful treatment of hemophilia A.

The development of new “pre-MS” methods for protein isolation/separation from complicated biological samples is a fundamental requirement for successful, MS-based approaches to proteomics. Flow field-flow fractionation (F4) has been applied as pre-MS step for proteomics. Hollow-fiber F4 (HF5) is the innovative, microcolumn version of F4. HF5 employs a piece of hollow fiber as separation channel and current HF5 shows performance comparable to commercial F4. The reduced channel volume and flowrates, the low dilution of fractionated analytes, and the potentially disposable usage to exclude contaminations or carryover then make HF5 ideally suited as online or offline pre-MS separation step for the characterization of complex protein samples in native form. We have developed different applications based on HF5 in combination with MS or LC-MS for the fractionation, purification and characterization of native proteins, and for proteomic analysis of complex protein samples.