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1.  Accounting for population variation in targeted proteomics 
Journal of proteome research  2013;13(1):321-323.
Individual proteomes typically differ from the reference human proteome at ~10,000 single amino acid variants. When viewed at the population scale, this individual variation results in a wide variety of protein sequences. In targeted proteomics experiments, such variability can confound accurate protein quantification. To assist researchers in identifying target peptides with high variability within the human population we have created the Population Variation plug-in for Skyline, which provides easy access to the polymorphisms stored in dbSNP. Given a set of peptides, the tool reports minor allele frequency for common polymorphisms. We highlight the importance of considering genetic variation by applying the tool to public datasets.
doi:10.1021/pr4011052
PMCID: PMC3923399  PMID: 24320210
MRM/SRM; genetic variation; bioinformatics; dbSNP
2.  Proteogenomic database construction driven from large scale RNA-seq data 
Journal of proteome research  2013;13(1):21-28.
The advent of inexpensive RNA-Seq technologies and other deep sequencing technologies for RNA has the promise to radically improve genomic annotation, providing information on transcribed regions and splicing events in a variety of cellular conditions. Using MS based proteogenomics, many of these events can be confirmed directly at the protein level. However, the integration of large amounts of redundant RNA-seq data and mass spectrometry data poses a challenging problem. Our manuscript addresses this by construction of a compact database that contains all useful information expressed in RNA-seq reads. Applying our method to cumulative C. elegans data reduced 496.2GB of aligned RNA-seq SAM files to 410MB of splice graph database written in FASTA format. This corresponds to 1000× compression of data size, without loss of sensitivity. We performed a proteogenomics study using the custom dataset, using a completely automated pipeline and identified a total of 4044 novel events, including 215 novel genes, 808 novel exons, 12 alternative splicings, 618 gene-boundary corrections, 245 exon-boundary changes, 938 frame-shifts, 1166 reverse-strands, and 42 translated UTR. Our results highlight the usefulness of transcript+proteomic integration for improved genome annotations.
doi:10.1021/pr400294c
PMCID: PMC4034692  PMID: 23802565
3.  Molecular mechanisms underlying genotype-dependent responses to dietary restriction 
Aging cell  2013;12(6):10.1111/acel.12130.
Summary
Dietary restriction (DR) increases lifespan and attenuates age-related phenotypes in many organisms; however, the effect of DR on longevity of individuals in genetically heterogeneous populations is not well characterized. Here we describe a large-scale effort to define molecular mechanisms that underlie genotype-specific responses to DR. The effect of DR on lifespan was determined for 166 single-gene deletion strains in Saccharomyces cerevisiae. Resulting changes in mean lifespan ranged from a reduction of 79% to an increase of 103%. Vacuolar pH homeostasis, superoxide dismutase activity, and mitochondrial proteostasis were found to be strong determinants of the response to DR. Proteomic analysis of cells deficient in prohibitins revealed induction of a mitochondrial unfolded protein response (mtUPR) which has not previously been described in yeast. Mitochondrial proteotoxic stress in prohibitin mutants was suppressed by DR via reduced cytoplasmic mRNA translation. A similar relationship between prohibitins, the mtUPR, and longevity was also observed in Caenorhabditis elegans. These observations define conserved molecular processes that underlie genotype-dependent effects of DR that may be important modulators of DR in higher organisms.
doi:10.1111/acel.12130
PMCID: PMC3838465  PMID: 23837470
aging; replicative lifespan; longevity; yeast; dietary restriction; mitochondria; mitochondrial unfolded protein response
4.  Human Valacyclovir Hydrolase/Biphenyl Hydrolase-Like Protein Is a Highly Efficient Homocysteine Thiolactonase 
PLoS ONE  2014;9(10):e110054.
Homocysteinylation of lysine residues by homocysteine thiolactone (HCTL), a reactive homocysteine metabolite, results in protein aggregation and malfunction, and is a well-known risk factor for cardiovascular, autoimmune and neurological diseases. Human plasma paraoxonase-1 (PON1) and bleomycin hydrolase (Blmh) have been reported as the physiological HCTL detoxifying enzymes. However, the catalytic efficiency of HCTL hydrolysis by Blmh is low and not saturated at 20 mM HCTL. The catalytic efficiency of PON1 for HCTL hydrolysis is 100-fold lower than that of Blmh. A homocysteine thiolactonase (HCTLase) was purified from human liver and identified by mass spectrometry (MS) as the previously described human biphenyl hydrolase-like protein (BPHL). To further characterize this newly described HCTLase activity, BPHL was expressed in Escherichia coli and purified. The sequence of the recombinant BPHL (rBPHL) and hydrolytic products of the substrates HCTL and valacyclovir were verified by MS. We found that the catalytic efficiency (kcat/Km) of rBPHL for HCTL hydrolysis was 7.7 × 104 M−1s−1, orders of magnitude higher than that of PON1 or Blmh, indicating a more significant physiological role for BPHL in detoxifying HCTL.
doi:10.1371/journal.pone.0110054
PMCID: PMC4198189  PMID: 25333274
5.  Evidence for lysine acetylation in the coat protein of a polerovirus 
The Journal of General Virology  2014;95(Pt 10):2321-2327.
Virions of the RPV strain of Cereal yellow dwarf virus-RPV were purified from infected oat tissue and analysed by MS. Two conserved residues, K147 and K181, in the virus coat protein, were confidently identified to contain epsilon-N-acetyl groups. While no functional data are available for K147, K181 lies within an interfacial region critical for virion assembly and stability. The signature immonium ion at m/z 126.0919 demonstrated the presence of N-acetyllysine, and the sequence fragment ions enabled an unambiguous assignment of the epsilon-N-acetyl modification on K181. We hypothesize that selection favours acetylation of K181 in a fraction of coat protein monomers to stabilize the capsid by promoting intermonomer salt bridge formation.
doi:10.1099/vir.0.066514-0
PMCID: PMC4165934  PMID: 24939649
6.  Global Proteomics and Pathway Analysis of Pressure-overload Induced Heart Failure and Its Attenuation by Mitochondrial Targeted Peptides 
Circulation. Heart failure  2013;6(5):10.1161/CIRCHEARTFAILURE.113.000406.
Background
We investigated the protective effects of mitochondrial-targeted antioxidant and protective peptides, SS31 and SS20, on cardiac function, proteomic remodeling and signaling pathways.
Methods and Results
We applied an improved label-free shotgun proteomics approach to evaluate the global proteomics changes in transverse aortic constriction (TAC) induced heart failure, and the associated signaling pathway changes using Ingenuity Pathway Analysis (IPA). We found 538 proteins significantly changed after TAC, which mapped to 53 pathways. The top pathways were in the categories of actin cytoskeleton, mitochondrial function, intermediate metabolism, glycolysis / gluconeogenesis and citrate cycle. Concomitant treatment with SS31 ameliorated the congestive heart failure phenotypes and mitochondrial damage induced by TAC, in parallel with global attenuation of mitochondrial proteome changes, with an average of 84% protection of mitochondrial and 69% of non-mitochondrial protein changes. This included significant amelioration of All the IPA pathways noted above. SS20 had only modest effects on heart failure and this tracked with only partial attenuation of global proteomics changes; furthermore, while actin cytoskeleton pathways were significantly protected in SS20, mitochondrial and metabolic pathways essentially were not.
Conclusions
This study elucidates the signaling pathways significantly changed in pressure-overload induced heart failure. The global attenuation of TAC-induced proteomic alterations by the mitochondrial targeted peptide SS-31 suggests that perturbed mitochondrial function may be an upstream signal to many of pathway alterations in TAC and supports the potential clinical application of mitochondrial-targeted peptide drugs for the treatment heart failure.
doi:10.1161/CIRCHEARTFAILURE.113.000406
PMCID: PMC3856238  PMID: 23935006
heart failure; mitochondria; proteomics; signal transduction
7.  Proteomic analysis of adducted butyrylcholinesterase for biomonitoring organophosphorus exposures 
Chemico-biological interactions  2012;203(1):85-90.
Organophosphorus (OP) compounds include a broad group of toxic chemicals such as insecticides, chemical warfare agents and antiwear agents. The liver cytochromes P450 bioactivate many OPs to potent inhibitors of serine hydrolases. Cholinesterases were the first OP targets discovered and are the most studied. They are used to monitor human exposures to OP compounds. However, the assay that is currently used has limitations. The mechanism of action of OP compounds is the inhibition of serine hydrolases by covalently modifying their active-site serine. After structural rearrangement, the complex OP inhibitor-enzyme is irreversible and will remain in circulation until the modified enzyme is degraded. Mass spectrometry is a sensitive technology for analyzing protein modifications, such as OP-adducted enzymes. These analyses also provide some information about the nature of the OP adduct. Our aim is to develop high-throughput protocols for monitoring OP exposures using mass spectrometry.
doi:10.1016/j.cbi.2012.10.019
PMCID: PMC4108156  PMID: 23123252
Organophosphates; Mass spectrometry; Protein adducts; Butyrylcholinesterase
8.  Rapid assessment of RNAi-mediated protein depletion by selected reaction monitoring (SRM) mass spectrometry 
Journal of proteome research  2013;12(7):3246-3254.
We describe the use of a targeted proteomics approach, Selected Reaction Monitoring (SRM) mass spectrometry, to detect and assess RNAi-mediated depletion or ‘knockdown’ of specific proteins from human cells and from Drosophila flies. This label-free approach does not require any specific reagents to confirm the depletion of RNAi target protein(s) in unfractionated cell or whole organism extracts. The protocol described here is general, can be developed rapidly and can be multiplexed to detect and measure multiple proteins at once. Furthermore, the methodology can be extended to any tandem mass spectrometer - making it widely accessible. This methodology will be applicable to a wide range of basic science and clinical questions where RNAi-mediated protein depletion needs to be verified, or where differences in relative abundance of target proteins need to be rapidly assessed between samples.
doi:10.1021/pr400067k
PMCID: PMC3767422  PMID: 23713831
Mass spectrometry; selected reaction monitoring; RNAi
9.  Mass Spectrometry and Next-Generation Sequencing Reveal an Abundant and Rapidly Evolving Abalone Sperm Protein 
SUMMARY
Abalone, a broadcast spawning marine mollusk, is an important model for molecular interactions and positive selection in fertilization, but the focus has previously been on only two sperm proteins, lysin and sp18.We used genomic and proteomic techniques to bring new insights to this model by characterizing the testis transcriptome and sperm proteome of the Red abalone Haliotis rufescens. One pair of homologous, testis-specific proteins contains a secretion signal and is small, abundant, and associated with the acrosome. Comparative analysis revealed that homologs are extremely divergent between species, and show strong evidence for positive selection. The acrosomal localization and rapid evolution of these proteins indicates that they play an important role in fertilization, and could be involved in the species-specificity of sperm-egg interactions in abalone. Our genomic and proteomic characterization of abalone fertilization resulted in the identification of interesting, novel peptides that have eluded detection in this important model system for 20 years.
doi:10.1002/mrd.22182
PMCID: PMC4031754  PMID: 23585193
10.  Altered proteome turnover and remodeling by short-term caloric restriction or rapamycin rejuvenate the aging heart 
Aging Cell  2014;13(3):529-539.
Chronic caloric restriction (CR) and rapamycin inhibit the mechanistic target of rapamycin (mTOR) signaling, thereby regulating metabolism and suppressing protein synthesis. Caloric restriction or rapamycin extends murine lifespan and ameliorates many aging-associated disorders; however, the beneficial effects of shorter treatment on cardiac aging are not as well understood. Using a recently developed deuterated-leucine labeling method, we investigated the effect of short-term (10 weeks) CR or rapamycin on the proteomics turnover and remodeling of the aging mouse heart. Functionally, we observed that short-term CR and rapamycin both reversed the pre-existing age-dependent cardiac hypertrophy and diastolic dysfunction. There was no significant change in the cardiac global proteome (823 proteins) turnover with age, with a median half-life 9.1 days in the 5-month-old hearts and 8.8 days in the 27-month-old hearts. However, proteome half-lives of old hearts significantly increased after short-term CR (30%) or rapamycin (12%). This was accompanied by attenuation of age-dependent protein oxidative damage and ubiquitination. Quantitative proteomics and pathway analysis revealed an age-dependent decreased abundance of proteins involved in mitochondrial function, electron transport chain, citric acid cycle, and fatty acid metabolism as well as increased abundance of proteins involved in glycolysis and oxidative stress response. This age-dependent cardiac proteome remodeling was significantly reversed by short-term CR or rapamycin, demonstrating a concordance with the beneficial effect on cardiac physiology. The metabolic shift induced by rapamycin was confirmed by metabolomic analysis.
doi:10.1111/acel.12203
PMCID: PMC4040127  PMID: 24612461
caloric restriction; cardiac aging; dynamics; proteomics; rapamycin
11.  Implementation of Statistical Process Control for Proteomic Experiments via LC MS/MS 
Statistical process control (SPC) is a robust set of tools that aids in the visualization, detection, and identification of assignable causes of variation in any process that creates products, services, or information. A tool has been developed termed Statistical Process Control in Proteomics (SProCoP) which implements aspects of SPC (e.g., control charts and Pareto analysis) into the Skyline proteomics software. It monitors five quality control metrics in a shotgun or targeted proteomic workflow. None of these metrics require peptide identification. The source code, written in the R statistical language, runs directly from the Skyline interface which supports the use of raw data files from several of the mass spectrometry vendors. It provides real time evaluation of the chromatographic performance (e.g., retention time reproducibility, peak asymmetry, and resolution); and mass spectrometric performance (targeted peptide ion intensity and mass measurement accuracy for high resolving power instruments) via control charts. Thresholds are experiment- and instrument-specific and are determined empirically from user-defined quality control standards that enable the separation of random noise and systematic error. Finally, Pareto analysis provides a summary of performance metrics and guides the user to metrics with high variance. The utility of these charts to evaluate proteomic experiments is illustrated in two case studies.
doi:10.1007/s13361-013-0824-5
PMCID: PMC4020592  PMID: 24496601
Quality Control; Statistical Process Control; Proteomics; Mass Spectrometry; Shewhart Control Charts
12.  Using iRT, a normalized retention time for more targeted measurement of peptides 
Proteomics  2012;12(8):1111-1121.
Multiple reaction monitoring (MRM) has recently become the method of choice for targeted quantitative measurement of proteins using mass spectrometry. The method, however, is limited in the number of peptides that can be measured in one run. This number can be markedly increased by scheduling the acquisition if the accurate retention time (RT) of each peptide is known.
Here we present iRT, an empirically derived dimensionless peptide-specific value that allows for highly accurate RT prediction. The iRT of a peptide is a fixed number relative to a standard set of reference iRT-peptides that can be transferred across laboratories and chromatographic systems.
We show that iRT facilitates the setup of multiplexed experiments with acquisition windows more than 4 times smaller compared to in silico RT predictions resulting in improved quantification accuracy. iRTs can be determined by any laboratory and shared transparently. The iRT concept has been implemented in Skyline, the most widely used software for MRM experiments.
doi:10.1002/pmic.201100463
PMCID: PMC3918884  PMID: 22577012
Mass spectrometry; multiplexing; proteomics methods; optimization; quantitative analysis
13.  Multiplexed MS/MS for Improved Data Independent Acquisition 
Nature methods  2013;10(8):10.1038/nmeth.2528.
In mass spectrometry based proteomics, data-independent acquisition (DIA) strategies have the ability to acquire a single dataset useful for identification and quantification of detectable peptides in a complex mixture. Despite this, DIA is often overlooked due to noisier data resulting from a typical five to ten fold reduction in precursor selectivity compared to data dependent acquisition or selected reaction monitoring. We demonstrate a multiplexing technique which improves precursor selectivity five-fold.
doi:10.1038/nmeth.2528
PMCID: PMC3881977  PMID: 23793237
Data Independent Acquisition; Q-Exactive; Multiplexing; Targeted Proteomics; Shotgun Proteomics
14.  Identification of peptide features in precursor spectra using Hardklör and Krönik 
Hardklör and Krönik are software tools for feature detection and data reduction of high resolution mass spectra. Hardklör is used to reduce peptide isotope distributions to a single monoisotopic mass and charge state, and can deconvolve overlapping peptide isotope distributions. Krönik filters, validates, and summarizes peptide features identified with Hardklör from data obtained during liquid chromatography mass spectrometry (LC-MS). Both software tools contain a simple user interface and can be run from nearly any desktop computer. These tools are freely available from http://proteome.gs.washington.edu/software/hardklor.
doi:10.1002/0471250953.bi1318s37
PMCID: PMC3891918  PMID: 22389013
proteomics; mass spectrometry; liquid chromatography; high resolution; feature detection; deisotoping; peptide isotope distribution
15.  Effects of Column and Gradient Lengths on Peak Capacity and Peptide Identification in nanoflow LC-MS/MS of Complex Proteomic Samples 
Reversed-phase liquid chromatography is the most commonly used separation method for shotgun proteomics. Nanoflow chromatography has emerged as the preferred chromatography method for its increased sensitivity and separation. Despite its common use, there are a wide range of parameters and conditions used across research groups. These parameters have an effect on the quality of the chromatographic separation, which is critical to maximizing the number of peptide identifications and minimizing ion suppression. Here we examined the relationship between column lengths, gradient lengths, peptide identifications and peptide peak capacity. We found that while longer column and gradients lengths generally increase peptide identifications, the degree of improvement is dependent on both parameters and is diminished at longer column and gradients. Peak capacity, in comparison, showed a more linear increase with column and gradient lengths. We discuss the discrepancy between these two results and some of the considerations that should be taken into account when deciding on the chromatographic conditions for a proteomics experiment.
doi:10.1007/s13361-012-0508-6
PMCID: PMC3554873  PMID: 23197307
Shotgun proteomics; nanoflow liquid chromatography; peak capacity
16.  Selection on Plant Male Function Genes Identifies Candidates for Reproductive Isolation of Yellow Monkeyflowers 
PLoS Genetics  2013;9(12):e1003965.
Understanding the genetic basis of reproductive isolation promises insight into speciation and the origins of biological diversity. While progress has been made in identifying genes underlying barriers to reproduction that function after fertilization (post-zygotic isolation), we know much less about earlier acting pre-zygotic barriers. Of particular interest are barriers involved in mating and fertilization that can evolve extremely rapidly under sexual selection, suggesting they may play a prominent role in the initial stages of reproductive isolation. A significant challenge to the field of speciation genetics is developing new approaches for identification of candidate genes underlying these barriers, particularly among non-traditional model systems. We employ powerful proteomic and genomic strategies to study the genetic basis of conspecific pollen precedence, an important component of pre-zygotic reproductive isolation among yellow monkeyflowers (Mimulus spp.) resulting from male pollen competition. We use isotopic labeling in combination with shotgun proteomics to identify more than 2,000 male function (pollen tube) proteins within maternal reproductive structures (styles) of M. guttatus flowers where pollen competition occurs. We then sequence array-captured pollen tube exomes from a large outcrossing population of M. guttatus, and identify those genes with evidence of selective sweeps or balancing selection consistent with their role in pollen competition. We also test for evidence of positive selection on these genes more broadly across yellow monkeyflowers, because a signal of adaptive divergence is a common feature of genes causing reproductive isolation. Together the molecular evolution studies identify 159 pollen tube proteins that are candidate genes for conspecific pollen precedence. Our work demonstrates how powerful proteomic and genomic tools can be readily adapted to non-traditional model systems, allowing for genome-wide screens towards the goal of identifying the molecular basis of genetically complex traits.
Author Summary
Barriers to reproduction are necessary for generating new species. Little is known about the genes underlying reproductive barriers, particularly those that function prior to fertilization, but their identity is of great interest as they offer insight into the genetic mechanisms and evolutionary forces generating biological diversity. In this work, we use an emerging plant model system for speciation studies (yellow monkeyflowers, species of Mimulus) to identify genes that might influence the relative competitive abilities of male pollen from the same versus different species within the maternal flower's style. This is a common reproductive barrier among plant taxa known as conspecific pollen precedence (CPP), and is analogous to sperm competition during animal fertilization. We first identify the pollen proteins that are found within the style where pollen competition occurs, and then screen these for evidence that may indicate which genes have been targets of pollen competition (a form of sexual selection among individuals of a population) or adaptive diversification among species of yellow monkeyflowers (a common feature of genes underlying reproductive barriers). Our evolutionary analyses identify 159 candidates that may function in reproductive isolation of yellow monkeyflowers, and provide some of the first broad perspectives on evolution of plant reproductive genes.
doi:10.1371/journal.pgen.1003965
PMCID: PMC3854799  PMID: 24339787
17.  De novo Correction of Mass Measurement Error in Low Resolution Tandem MS Spectra for Shotgun Proteomics 
We report an algorithm designed for the calibration of low resolution peptide mass spectra. Our algorithm is implemented in a program called FineTune which corrects systematic mass measurement error in one minute, with no input required besides the mass spectra themselves. The mass measurement accuracy for a set of spectra collected on an LTQ-Velos improved 20-fold from −0.1776 ± 0.0010 m/z to 0.0078 ± 0.0006 m/z after calibration (avg +/− 95% confidence interval). The precision in mass measurement was improved due to the correction of non-linear variation in mass measurement accuracy across the m/z range.
doi:10.1007/s13361-012-0482-z
PMCID: PMC3515694  PMID: 23007965
Mass measurement accuracy; shotgun proteomics; linear ion trap
18.  Learning score function parameters for improved spectrum identification in tandem mass spectrometry experiments 
Journal of proteome research  2012;11(9):4499-4508.
The identification of proteins from spectra derived from a tandem mass spectrometry experiment involves several challenges: matching each observed spectrum to a peptide sequence, ranking the resulting collection of peptide-spectrum matches, assigning statistical confidence estimates to the matches, and identifying the proteins. The present work addresses algorithms to rank peptide-spectrum matches. Many of these algorithms, such as PeptideProphet, IDPicker, or Q-ranker, follow similar methodology that includes representing peptide-spectrum matches as feature vectors and using optimization techniques to rank them. We propose a richer and more flexible feature set representation that is based on the parametrization of the SEQUEST XCorr score and that can be used by all of these algorithms. This extended feature set allows a more effective ranking of the peptide-spectrum matches based on the target-decoy strategy, in comparison to a baseline feature set devoid of these XCorr-based features. Ranking using the extended feature set gives 10–40% improvement in the number of distinct peptide identifications relative to a range of q-value thresholds. While this work is inspired by the model of the theoretical spectrum and the similarity measure between spectra used specifically by SEQUEST, the method itself can be applied to the output of any database search. Further, our approach can be trivially extended beyond XCorr to any linear operator that can serve as similarity score between experimental spectra and peptide sequences.
doi:10.1021/pr300234m
PMCID: PMC3436966  PMID: 22866926
19.  Genomic and Proteomic Analysis of Schizaphis graminum Reveals Cyclophilin Proteins Are Involved in the Transmission of Cereal Yellow Dwarf Virus 
PLoS ONE  2013;8(8):e71620.
Yellow dwarf viruses cause the most economically important virus diseases of cereal crops worldwide and are transmitted by aphid vectors. The identification of aphid genes and proteins mediating virus transmission is critical to develop agriculturally sustainable virus management practices and to understand viral strategies for circulative movement in all insect vectors. Two cyclophilin B proteins, S28 and S29, were identified previously in populations of Schizaphisgraminum that differed in their ability to transmit the RPV strain of Cereal yellow dwarf virus (CYDV-RPV). The presence of S29 was correlated with F2 genotypes that were efficient virus transmitters. The present study revealed the two proteins were isoforms, and a single amino acid change distinguished S28 and S29. The distribution of the two alleles was determined in 12 F2 genotypes segregating for CYDV-RPV transmission capacity and in 11 genetically independent, field-collected S. graminum biotypes. Transmission efficiency for CYDV-RPV was determined in all genotypes and biotypes. The S29 isoform was present in all genotypes or biotypes that efficiently transmit CYDV-RPV and more specifically in genotypes that efficiently transport virus across the hindgut. We confirmed a direct interaction between CYDV-RPV and both S28 and S29 using purified virus and bacterially expressed, his-tagged S28 and S29 proteins. Importantly, S29 failed to interact with a closely related virus that is transported across the aphid midgut. We tested for in vivo interactions using an aphid-virus co-immunoprecipitation strategy coupled with a bottom-up LC-MS/MS analysis using a Q Exactive mass spectrometer. This analysis enabled us to identify a third cyclophilin protein, cyclophilin A, interacting directly or in complex with purified CYDV-RPV. Taken together, these data provide evidence that both cyclophilin A and B interact with CYDV-RPV, and these interactions may be important but not sufficient to mediate virus transport from the hindgut lumen into the hemocoel.
doi:10.1371/journal.pone.0071620
PMCID: PMC3739738  PMID: 23951206
20.  An expansive human regulatory lexicon encoded in transcription factor footprints 
Nature  2012;489(7414):83-90.
Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNaseI, leaving nucleotide-resolution footprints. Using genomic DNaseI footprinting across 41 diverse cell and tissue types, we detected 45 million factor occupancy events within regulatory regions, representing differential binding to 8.4 million distinct short sequence elements. Here we show that this small genomic sequence compartment, roughly twice the size of the exome, encodes an expansive repertoire of conserved recognition sequences for DNA-binding proteins that nearly doubles the size of the human cis-regulatory lexicon. We find that genetic variants affecting allelic chromatin states are concentrated in footprints, and that these elements are preferentially sheltered from DNA methylation. High-resolution DNaseI cleavage patterns mirror nucleotide-level evolutionary conservation and track the crystallographic topography of protein-DNA interfaces, indicating that transcription factor structure has been evolutionarily imprinted on the human genome sequence. We identify a stereotyped 50 base-pair footprint that precisely defines the site of transcript origination within thousands of human promoters. Finally, we describe a large collection of novel regulatory factor recognition motifs that are highly conserved in both sequence and function, and exhibit cell-selective occupancy patterns that closely parallel major regulators of development, differentiation, and pluripotency.
doi:10.1038/nature11212
PMCID: PMC3736582  PMID: 22955618
chromatin; protein occupancy; DNaseI footprinting; ENCODE; regulation
21.  A Method to Determine the Kinetics of Multiple Proteins in Human Infants with Respiratory Distress Syndrome 
Analytical and bioanalytical chemistry  2012;403(8):2397-2402.
We report a method to measure in vivo turnover of four proteins from sequential tracheal aspirates obtained from human newborn infants with respiratory distress syndrome using targeted proteomics. We detected enrichment for all targeted proteins approximately 3 hours from the start of infusion of [5,5,5-2H3] leucine, secretion times that varied from 1.2 to 2.5 hours, and half lives that ranged between 10 and 21 hours. Complement factor B, a component of the alternative pathway of complement activation, had an ~2-fold longer half life than the other three proteins. In addition, the kinetics of mature and carboxy-terminal tryptic peptides from the same protein (surfactant protein B) were not statistically different (p=0.49).
doi:10.1007/s00216-012-5953-3
PMCID: PMC3694176  PMID: 22526637
Protein Turnover; Respiratory Distress Syndrome; Selected Reaction Monitoring; SRM; Protein Kinetics; Protein Metabolism
22.  Determination of the Intra-individual Variability of Protein Expression in Benign/Cancerous Prostate Tissue via LC-MS – Efforts Towards Molecular Classification 
With a 1 in 6 lifetime risk and over 200,000 diagnoses per year in United States, prostate cancer is the most common noncutaneous cancer in men. The discrepancy between the number of diagnoses and the mortality risk (1 in 35) has led to scrutiny in the clinical management of the disease. The incidence of the disease has more than doubled since the FDA approval of prostate specific antigen test. Despite its low specificity, it has decreased the proportion of metastatic cancers at diagnosis. However, it has also increased the total number of cancers diagnosed with a majority of them having either indolent disease or completely benign conditions. This discrepancy between increased treatment and decreased disease aggressiveness has lead to much criticism that prostate cancer is “overdiagnosed” leading to unnecessary treatment. To this end, it is of interest to develop protein markers or panels of markers that are more indicative/specific of disease severity than currently available. Herein, we begin this endeavor by determining the precision of protein expression from different regions of benign tissue and Gleason 6 grade cancer tissue within the same individual using laser capture microdissection coupled to LC-MS.
After LCM, tissue were lysed and digested using established laboratory procedures. 500ng of protein was separated by LC and analyzed by a velos orbitrap mass spectrometer operating in a top 10 data dependent mode. Data was searched using Sequest and imported into skyline for differential abundance determination. Statistical design of experiments was used to optimized data dependent settings and afforded a 33% increase in unique peptide identifications from our current default DDA settings. 2000 proteins were identified including prostate specific antigen and prostatic acid phophatase. Label free methods will be used to develop an intra individual variability index of both benign and cancerous tissue which will aid in statistically identifying differences.
PMCID: PMC3635399
23.  A Cross-platform Toolkit for Mass Spectrometry and Proteomics 
Nature biotechnology  2012;30(10):918-920.
Mass-spectrometry-based proteomics has become an important component of biological research. Numerous proteomics methods have been developed to identify and quantify the proteins in biological and clinical samples1, identify pathways affected by endogenous and exogenous perturbations2, and characterize protein complexes3. Despite successes, the interpretation of vast proteomics datasets remains a challenge. There have been several calls for improvements and standardization of proteomics data analysis frameworks, as well as for an application-programming interface for proteomics data access4,5. In response, we have developed the ProteoWizard Toolkit, a robust set of open-source, software libraries and applications designed to facilitate proteomics research. The libraries implement the first-ever, non-commercial, unified data access interface for proteomics, bridging field-standard open formats and all common vendor formats. In addition, diverse software classes enable rapid development of vendor-agnostic proteomics software. Additionally, ProteoWizard projects and applications, building upon the core libraries, are becoming standard tools for enabling significant proteomics inquiries.
doi:10.1038/nbt.2377
PMCID: PMC3471674  PMID: 23051804
24.  Hematopoietic Protein-1 Regulates the Actin Membrane Skeleton and Membrane Stability in Murine Erythrocytes 
PLoS ONE  2013;8(2):e54902.
Hematopoietic protein-1 (Hem-1) is a hematopoietic cell specific member of the WAVE (Wiskott-Aldrich syndrome verprolin-homologous protein) complex, which regulates filamentous actin (F-actin) polymerization in many cell types including immune cells. However, the roles of Hem-1 and the WAVE complex in erythrocyte biology are not known. In this study, we utilized mice lacking Hem-1 expression due to a non-coding point mutation in the Hem1 gene to show that absence of Hem-1 results in microcytic, hypochromic anemia characterized by abnormally shaped erythrocytes with aberrant F-actin foci and decreased lifespan. We find that Hem-1 and members of the associated WAVE complex are normally expressed in wildtype erythrocyte progenitors and mature erythrocytes. Using mass spectrometry and global proteomics, Coomassie staining, and immunoblotting, we find that the absence of Hem-1 results in decreased representation of essential erythrocyte membrane skeletal proteins including α- and β- spectrin, dematin, p55, adducin, ankyrin, tropomodulin 1, band 3, and band 4.1. Hem1−/− erythrocytes exhibit increased protein kinase C-dependent phosphorylation of adducin at Ser724, which targets adducin family members for dissociation from spectrin and actin, and subsequent proteolysis. Increased adducin Ser724 phosphorylation in Hem1−/− erythrocytes correlates with decreased protein expression of the regulatory subunit of protein phosphatase 2A (PP2A), which is required for PP2A-dependent dephosphorylation of PKC targets. These results reveal a novel, critical role for Hem-1 in the homeostasis of structural proteins required for formation and stability of the actin membrane skeleton in erythrocytes.
doi:10.1371/journal.pone.0054902
PMCID: PMC3570531  PMID: 23424621
25.  Evaluation of Front-end Higher Energy Collision-Induced Dissociation on a Bench-top Dual Pressure Linear Ion Trap Mass Spectrometer for Shotgun Proteomics 
Analytical Chemistry  2012;84(3):1533-1539.
We report the implementation of front-end higher energy collision induced dissociation (fHCD) on a bench-top dual pressure linear ion trap. Software and hardware modifications were employed, described in detail vide-infra, to allow isolated ions to undergo collisions with ambient gas molecules in an intermediate multipole (q00) of the instrument. Results comparing the performance of fHCD and resonance excitation collision induced dissociation (RE-CID) in terms of injection time, total number of scans, efficiency, mass measurement accuracy (MMA), unique peptide identifications, and spectral quality of labile modified peptides are presented. fHCD is approximately 23% as efficient as RE-CID and, depending on the search algorithm, it identifies 6.6% more or 15% less peptides (q<0.01) from a soluble whole-cell lysate (Caenorhabditis elegans) than RE-CID using Mascot or Sequest search algorithms, respectively. fHCD offers a clear advantage for the analysis of phosphorylated and glycosylated (O-GlcNAc) peptides as the average cross-correlation score (XCorr) for spectra using fHCD was statistically greater (p<0.05) than for spectra collected using RE-CID.
doi:10.1021/ac203210a
PMCID: PMC3277647  PMID: 22192247

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