The ABRF Proteomics Research Group studies: educational exercises for qualitative and quantitative proteomic analyses

Resource (core) facilities have played an ever-increasing role in furnishing the scientific community with specialized instrumentation and expertise for proteomics experiments in a cost-effective manner. The Proteomics Research Group (PRG) of the Association of Biomolecular Resource Facilities (ABRF) has sponsored a number of research studies designed to enable participants to try new techniques and assess their capabilities relative to other laboratories analyzing the same samples. Presented here are results from three PRG studies representing different samples that are typically analyzed in a core facility, ranging from simple protein identification to targeted analyses, and include intentional challenges to reflect realistic studies. The PRG2008 study compares different strategies for the qualitative characterization of proteins, particularly the utility of complementary methods for characterizing truncated protein forms. The use of different approaches for determining quantitative differences for several target proteins in human plasma was the focus of the PRG2009 study. The PRG2010 study explored different methods for determining specific constituents while identifying unforeseen problems that could account for unanticipated results associated with the different samples, and included (15) N-labeled proteins as an additional challenge. These studies provide a valuable educational resource to research laboratories and core facilities, as well as a mechanism for establishing good laboratory practices.     

Estimating the dynamic range of quantitative single-molecule localization microscopy

In recent years, there have been significant advances in quantifying molecule copy number and protein stoichiometry with single-molecule localization microscopy (SMLM). However, as the density of fluorophores per diffraction-limited spot increases, distinguishing between detection events from different fluorophores becomes progressively more difficult, affecting the accuracy of such measurements. Although essential to the design of quantitative experiments, the dynamic range of SMLM counting techniques has not yet been studied in detail. Here, we provide a working definition of the dynamic range for quantitative SMLM in terms of the relative number of missed localizations or blinks and explore the photophysical and experimental parameters that affect it. We begin with a simple two-state model of blinking fluorophores, then extend the model to incorporate photobleaching and temporal binning by the detection camera. From these models, we first show that our estimates of the dynamic range agree with realistic simulations of the photoswitching. We find that the dynamic range scales inversely with the duty cycle when counting both blinks and localizations. Finally, we validate our theoretical approach on direct stochastic optical reconstruction microscopy (dSTORM) data sets of photoswitching Alexa Fluor 647 dyes. Our results should help guide researchers in designing and implementing SMLM-based molecular counting experiments.     

Labeling of Bifidobacterium longum cells with 13C-substituted leucine for quantitative proteomic analyses

Stable isotope labeling of amino acids in cell culture was used for Bifidobacterium longum. A comprehensive proteomic strategy was developed and validated by designing an appropriate semidefined medium that allows stable replacement of natural leucine by [(13)C6]leucine. Using this strategy, proteins having variations of at least 50% in their expression rates can be quantified with great confidence.     

Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry

Stable isotope standards and capture by antipeptide antibodies (SISCAPA) couples affinity enrichment of peptides with stable isotope dilution and detection by multiple reaction monitoring mass spectrometry to provide quantitative measurement of peptides as surrogates for their respective proteins. In this report, we describe a feasibility study to determine the success rate for production of suitable antibodies for SISCAPA assays in order to inform strategies for large-scale assay development. A workflow was designed that included a multiplex immunization strategy in which up to five proteotypic peptides from a single protein target were used to immunize individual rabbits. A total of 403 proteotypic tryptic peptides representing 89 protein targets were used as immunogens. Antipeptide antibody titers were measured by ELISA and 220 antipeptide antibodies representing 89 proteins were chosen for affinity purification. These antibodies were characterized with respect to their performance in SISCAPA-multiple reaction monitoring assays using trypsin-digested human plasma matrix. More than half of the assays generated were capable of detecting the target peptide at concentrations of less than 0.5 fmol/μl in human plasma, corresponding to protein concentrations of less than 100 ng/ml. The strategy of multiplexing five peptide immunogens was successful in generating a working assay for 100% of the targeted proteins in this evaluation study. These results indicate it is feasible for a single laboratory to develop hundreds of assays per year and allow planning for cost-effective generation of SISCAPA assays.     

Comparative proteomic analyses of the nuclear envelope and pore complex suggests a wide range of heretofore unexpected functions

Since the discovery of several inherited diseases linked to the nuclear envelope the number of functions ascribed to this subcellular organelle has skyrocketed. However the molecular pathways underlying these functions are not clear in most cases, perhaps because of missing components. Several recent proteomic analyses of the nuclear envelope and nuclear pore complex proteomes have yielded not only enough missing components to potentially elucidate these pathways, but suggest an exponentially greater number of functions at the nuclear periphery than ever imagined. Many of these functions appear to derive from recapitulation of pathways utilized at the plasma membrane and from other membrane systems. Additionally, many proteins identified in the comparative nuclear envelope studies have sequence characteristics suggesting that they might also contribute to nuclear pore complex functions. In particular, the striking enrichment for proteins in the nuclear envelope fractions that carry phenylalanine-glycine (FG) repeats may be significant for the mechanism of nuclear transport. In retrospect, these findings are only surprising in context of the notion held for many years that the nuclear envelope was only a barrier protecting the genome. In fact, it is arguably the most complex membrane organelle in the cell.     

De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging

Proteomic studies require efficient, robust, and practical methods of characterizing proteins present in biological samples. Here we describe an integrated strategy for systematic proteome analysis based on differential guanidination of C-terminal lysine residues on tryptic peptides followed by capillary liquid chromatography-electrospray tandem mass spectrometry. The approach, termed mass-coded abundance tagging (MCAT), facilitates the automated, large-scale, and comprehensive de novo determination of peptide sequence and relative quantitation of proteins in biological samples in a single analysis. MCAT offers marked advantages as compared with previously described methods and is simple, economic, and effective when applied to complex proteomic mixtures. MCAT is used to identify proteins, including polymorphic variants, from complex mixtures and measure variation in protein levels from diverse cell types.     

Capture and analysis of quantitative proteomic data

Whilst the array of techniques available for quantitative proteomics continues to grow, the attendant bioinformatic software tools are similarly expanding in number. The data capture and analysis of such quantitative data is obviously crucial to the experiment and the methods used to process it will critically affect the quality of the data obtained. These tools must deal with a variety of issues, including identification of labelled and unlabelled peptide species, location of the corresponding MS scans in the experiment, construction of representative ion chromatograms, location of the true peptide ion chromatogram start and end, elimination of background signal in the mass spectrum and chromatogram and calculation of both peptide and protein ratios/abundances. A variety of tools and approaches are available, in part restricted by the nature of the experiment to be performed and available instrumentation. Currently, although there is no single consensus on precisely how to calculate protein and peptide abundances, many common themes have emerged which identify and reduce many of the key sources of error. These issues will be discussed, along with those relating to deposition of quantitative data. At present, mature data standards for quantitative proteomics are not yet available, although formats are beginning to emerge.     

Optimal isolation of mitochondria for proteomic analyses

Considering the key role of mitochondria in cellular (dys)functions, we compared a standard isolation protocol, followed by lysis in urea/detergent buffer, with a commercially available isolation buffer that rapidly yields a mitochondrial protein fraction. The standard protocol yielded significantly better overall resolution and coverage of both the soluble and membrane mitochondrial proteomes; although the kit was faster, it resulted in recovery of only approximately 56% of the detectable proteome. The quality of “omic” analysis depends on sample handling; for large-scale protein studies, well-resolved proteomes are highly dependent on the purity of starting material and the rigor of the extraction protocol.     

The impact of Zika virus exposure on the placental proteomic profile

Zika virus (ZIKV) infection has caused severe unexpected clinical outcomes in neonates and adults during the recent outbreak in Latin America, particularly in Brazil. Congenital malformations associated with ZIKV have been frequently reported; nevertheless, the mechanism of vertical transmission and the involvement of placental cells remains unclear. In this study, we applied quantitative proteomics analysis in a floating explant model of chorionic villi of human placental tissues incubated with ZIKV and with ZIKV pre-adsorbed with anti-ZIKV envelope protein. Proteomic data are available via ProteomeXchange with identifier PXD025764. Altered levels of proteins were involved in cell proliferation, apoptosis, inflammatory processes, and the integrin-cytoskeleton complex. Antibody-opsonized ZIKV particles differentially modulated the pattern of protein expression in placental cells; this phenomenon may play a pivotal role in determining the course of infection and the role of mixed infections. The expression of specific proteins was also evaluated by immunoperoxidase assays. These data fill gaps in our understanding of early events after ZIKV placental exposure and help identify infection control targets.     

The impact of Lake Victoria's lakefly abundance on Palearctic passerines

Wanink, J.H. & Goudswaard, K. 2000. The impact of Lake Victoria's lakefly abundance on Palearctic passerines. Ostrich 71 (1 & 2): 194–197.

In spite of an increase in lakeflies emerging from Lake Victoria, these periodically swarming insects remained an erratic food source for birds. However, even the relatively poor south-eastern shores were exploited by some Palearctic warblers on spring passage. Numbers and weights of Willow and Garden Warbler were correlated with lakefly abundance. The occurrence of lakefly swarms may trigger the birds' departure to the breeding areas, as the superabundance of food allows for rapid premigratory fattening.     

The impact of marine nutrient abundance on early eukaryotic ecosystems

The rise of eukaryotes to ecological prominence represents one of the most dramatic shifts in the history of Earth's biosphere. However, there is an enigmatic temporal lag between the emergence of eukaryotic organisms in the fossil record and their much later ecological expansion. In parallel, there is evidence for a secular increase in the availability of the key macronutrient phosphorus (P) in Earth's oceans. Here, we use an Earth system model equipped with a size‐structured marine ecosystem to explore relationships between plankton size, trophic complexity, and the availability of marine nutrients. We find a strong dependence of planktonic ecosystem structure on ocean nutrient abundance, with a larger ocean nutrient inventory leading to greater overall biomass, broader size spectra, and increasing abundance of large Zooplankton. If existing estimates of Proterozoic marine nutrient levels are correct, our results suggest that increases in the ecological impact of eukaryotic algae and trophic complexity in eukaryotic ecosystems were directly linked to restructuring of the global P cycle associated with the protracted rise of surface oxygen levels. Our results thus suggest an indirect but potentially important mechanism by which ocean oxygenation may have acted to shape marine ecological function during late Proterozoic time.     

Functional materials for microscale genomic and proteomic analyses

The design of functional materials for genomic and proteomic analyses in microscale systems has begun to mature, from materials designed for capillary-based electrophoresis systems to those tailored for microfluidic-based or 'chip-based' platforms. In particular, recent research has focused on evaluating different polymer chemistries for microchannel surface passivation and improved DNA separation matrix performance. Additionally, novel bioconjugate materials designed specifically for electrophoretic separations in microscale channels are facilitating new separation modalities.     

The impact of raptors on the abundance of upland passerines and waders

The issue of predator limitation of vertebrate prey populations is contentious, particularly when it involves species of economic or conservation value. In this paper, we examine the case of raptor predation on upland passerines and waders in Scotland. We analysed the abundance of five wader and passerine species on an upland sporting estate in southern Scotland during an eight-year period when hen harrier, peregrine and merlin numbers increased due to strict law enforcement. The abundance of meadow pipit and skylark declined significantly during this time. Golden plover also showed a declining trend, whereas curlew increased significantly and there was a near significant increase in lapwings. Contrasting the local population trends of these species with trends on nearby areas revealed higher rates of decline for meadow pipit and skylark at the site where raptors increased, but no differences in trends for any of the three wader species. There was a negative relationship between the number of breeding harriers and meadow pipit abundance the same year and between total annual raptor numbers and meadow pipit abundance. Predation rates of meadow pipit and skylark determined from observations at harrier nests suggested that predation in June was sufficient to remove up to 40% of the June meadow pipit population and up to 34% of the June skylark population. This 'quasi-natural' experiment suggests that harrier predation limited the abundance of their main prey, meadow pipit, and possibly the abundance of skylark. Thus, high densities of harriers may in theory reduce the abundance of the prey species which determine their breeding densities, potentially leading to lower harrier breeding densities in subsequent years. We found no evidence to suggest that raptor predation limited the populations of any of the three wader species. We infer that concerns over the impact of natural densities of hen harriers on vulnerable upland waders are unjustified.     

The impact of small chironomid grazers on epiphytic algal abundance and dispersion

• 1 A combination of field and laboratory experiments was used to assess the impact of chironomid grazers on taxonomic composition, abundance and dispersion of epiphytic algal assemblages.
• 2 In the laboratory, Psectrodadius sp. reduced the biovolume of algal species preferred as food and increased the degree of clumping of non-preferred species. Thienemanniella cf. fusca had both positive and negative effects (depending on the algal species) on the biovolumes of algal species preferred as food and increased the degree of clumping of non-preferred species.
• 3 In field exclosures, no effect of removal of chironomid larvae from the grazer assemblage could be detected in autumn or winter experiments. A third, longer removal experiment, conducted in summer, resulted in increased biovolumes of edible Cosmarium spp. and Aphanocapsa spp., preferred foods of chironomid larvae. Biovolumes of Lyngbya sp., Eulbochaete spp. and Oedogortium spp., filamentous taxa used extensively in larval case construction, also increased. Chironomid larvae had no effect on total algal biovolume or biovolume of large unicellular algae.
• 4 Chironomid larvae can influence epiphytic algal assemblages through selective grazing by reducing the biovolumes of preferred foods and through case-building activity by reducing the biovolumes of construction materials.

     

The dynamic range of human lightness perception

Natural viewing challenges the visual system with images that have a dynamic range of light intensity (luminance) that can approach 1,000,000:1 and that often exceeds 10,000:1 [1, 2]. The range of perceived surface reflectance (lightness), however, can be well approximated by the Munsell matte neutral scale (N 2.0/ to N 9.5/), consisting of surfaces whose reflectance varies by about 30:1. Thus, the visual system must map a large range of surface luminance onto a much smaller range of surface lightness. We measured this mapping in images with a dynamic range close to that of natural images. We studied simple images that lacked segmentation cues that would indicate multiple regions of illumination. We found a remarkable degree of compression: at a single image location, a stimulus luminance range of 5,905:1 can be mapped onto an extended lightness scale that has a reflectance range of 100:1. We characterized how the luminance-to-lightness mapping changes with stimulus context. Our data rule out theories that predict perceived lightness from luminance ratios or Weber contrast. A mechanistic model connects our data to theories of adaptation and provides insight about how the underlying visual response varies with context.