Loss of BAP1 Results in Growth Inhibition and Enhances Mesenchymal-Epithelial Transition in Kidney Tumor Cells.
Abstract BRCA1-associated protein 1 (BAP1) is a member of the ubiquitin C‑terminal hydrolase family of deubiquitinating enzymes and is implicated in transcriptional regulation. The BAP1 gene is mutated in about 10% of patients with clear cell renal cell carcinoma (ccRCC), the most common form of renal cancer, suggesting that BAP1 is a tumor suppressor. However, whether BAP1 influences the progression of ccRCC tumors expressing WT BAP1 is unclear. Here, we assessed the expression and function of BAP1 using human ccRCC specimens and cell lines. Analysis of datasets in The Cancer Genome Atlas revealed that lower BA...
Source: Molecular and Cellular Proteomics : MCP - April 16, 2019 Category: Molecular Biology Authors: Chen P, Wang H, Zhang W, Chen Y, Lv Y, Wu D, Guo M, Deng H Tags: Mol Cell Proteomics Source Type: research

High-throughput exploration of the network dependent on AKT1 in mouse ovarian granulosa cells.
This study also allowed us to put forward new direct and indirect targets of the kinase. Indeed, a series of proteins involved in intracellular transport and mitochondrial physiology were significantly affected by Akt1depletion. Using in silicoanalyses, we also propose a set of kinases and transcription factors that can mediate the action of AKT1 on the deregulated transcripts and proteins. Taken altogether, our results provide a resource of direct and indirect AKT1 targets in granulosa cells and may help understand its roles in this ovarian cell type. PMID: 30992313 [PubMed - as supplied by publisher] (Source: Molecu...
Source: Molecular and Cellular Proteomics : MCP - April 16, 2019 Category: Molecular Biology Authors: Elzaiat M, Herman L, Legois B, Léger T, Todeschini AL, Veitia RA Tags: Mol Cell Proteomics Source Type: research

Integrated transcriptomic and proteomic analysis of human eccrine sweat glands identifies missing and novel proteins.
This study presents the first integrated analysis of the transcriptome and proteome of the human eccrine sweat gland and would become a valuable resource for studying sweat glands in physiology and disease. PMID: 30979791 [PubMed - as supplied by publisher] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - April 12, 2019 Category: Molecular Biology Authors: Na CH, Sharma N, Madugundu AK, Chen R, Atalar Aksit M, Rosson GD, Cutting GR, Pandey A Tags: Mol Cell Proteomics Source Type: research

Sensitive quantitative proteomics of human hematopoietic stem and progenitor cells by data-independent acquisition mass spectrometry.
Abstract Physiological processes in multicellular organisms depend on the function and interactions of specialized cell types operating in context. Some of these cell types are rare and thus obtainable only in minute quantities. For example, tissue-specific stem and progenitor cells are numerically scarce, but functionally highly relevant, and fulfill critical roles in development, tissue maintenance and disease. Whereas low numbers of cells are routinely analyzed by genomics and transcriptomics, corresponding proteomic analyses have so far not been possible due to methodological limitations. Here we describe a se...
Source: Molecular and Cellular Proteomics : MCP - April 11, 2019 Category: Molecular Biology Authors: Amon S, Meier-Abt F, Gillet LC, Dimitrieva S, Theocharides AP, Manz MG, Aebersold R Tags: Mol Cell Proteomics Source Type: research

TMT labeling for the masses: A robust and cost-efficient, in-solution labeling approach.
Abstract Isobaric stable isotope labeling using, for example, tandem mass tags (TMTs) is increasingly being applied for large-scale proteomic studies. Experiments focusing on proteoform analysis in drug time course or perturbation studies or in large patient cohorts greatly benefit from the reproducible quantification of single peptides across samples. However, such studies often require labeling of hundreds of micrograms of peptides such that the cost for labeling reagents represents a major contribution to the overall cost of an experiment. Here, we describe and evaluate a robust and cost-effective protocol for ...
Source: Molecular and Cellular Proteomics : MCP - April 9, 2019 Category: Molecular Biology Authors: Zecha J, Satpathy S, Kanashova T, Avanessian SC, Kane MH, Clauser KR, Mertins P, Carr SA, Kuster B Tags: Mol Cell Proteomics Source Type: research

Unravelling hidden components of the chloroplast envelope proteome: opportunities and limits of better MS sensitivity.
and N Abstract The chloroplast is a major plant cell organelle that fulfills essential metabolic and biosynthetic functions. Located at the interface between the chloroplast and other cell compartments, the chloroplast envelope system is a strategic barrier controlling the exchange of ions, metabolites and proteins, thus regulating essential metabolic functions (synthesis of hormones precursors, amino acids, pigments, sugars, vitamins, lipids, nucleotides…) of the plant cell. However, unraveling the contents of the chloroplast envelope proteome remains a difficult challenge; many proteins constituting this ...
Source: Molecular and Cellular Proteomics : MCP - April 8, 2019 Category: Molecular Biology Authors: Bouchnak I, Brugière S, Moyet L, Le Gall S, Salvi D, Kuntz M, Tardif M, Rolland N Tags: Mol Cell Proteomics Source Type: research

The mRNA-bound proteome of Leishmania mexicana: novel genetic insight into an ancient parasite.
Abstract Leishmania parasite infections, termed the leishmaniases, cause significant global infectious disease burden. The lifecycle of the parasite embodies three main stages that require precise coordination of gene regulation to survive environmental shifts between sandfly and mammalian hosts. Constitutive transcription in kinetoplastid parasites means that gene regulation is overwhelmingly reliant on post-transcriptional mechanisms, yet strikingly few Leishmania trans-regulators are known. Utilizing optimised crosslinking and deep, quantified mass spectrometry, we present a comprehensive analysis of 1,400 mRNA...
Source: Molecular and Cellular Proteomics : MCP - April 4, 2019 Category: Molecular Biology Authors: De Pablos LM, Ferreira TR, Dowle A, Forrester S, Parry E, Newling K, Walrad PB Tags: Mol Cell Proteomics Source Type: research

Analysis of 1508 plasma samples by capillary flow data-independent acquisition profiles proteomics of weight loss and maintenance.
In conclusion, we present herein the first large-scale plasma DIA study and one of the largest clinical research proteomic studies to date. Application of this fast and robust workflow has great potential to advance biomarker discovery in plasma. PMID: 30948622 [PubMed - as supplied by publisher] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - April 4, 2019 Category: Molecular Biology Authors: Bruderer R, Muntel J, Müller S, Bernhardt OM, Gandhi T, Cominetti O, Macron C, Carayol J, Rinner O, Astrup A, Saris WHM, Hager J, Valsesia A, Dayon L, Reiter L Tags: Mol Cell Proteomics Source Type: research

Phytoplasma-induced changes in the acetylome and succinylome of Paulownia tomentosa provide evidence for involvement of acetylated proteins in witches' broom disease.
Abstract Lysine acetylation and succinylation are post-translational modifications of proteins that have been shown to play roles in plants response to pathogen infection. Phytoplasma infection can directly alter multiple metabolic processes in the deciduous plant Paulownia and lead to Paulownia witches' broom (PaWB) disease, the major cause of Paulownia mortality worldwide. However, the extent and function of lysine aceylation and succinylation during phytoplasma infection have yet to be explored. Here, we investigated the changes in the proteome, acetylome, and succinylome of phytoplasma-infected Paulownia tomen...
Source: Molecular and Cellular Proteomics : MCP - April 1, 2019 Category: Molecular Biology Authors: Cao Y, Fan G, Wang Z, Gu Z Tags: Mol Cell Proteomics Source Type: research

Hypoxia-induced changes in SUMO conjugation affect transcriptional regulation under low oxygen.
Abstract Hypoxia occurs in pathological conditions, such as cancer, as a result of the imbalance between oxygen supply and consumption by proliferating cells. HIFs are critical molecular mediators of the physiological response to hypoxia but also regulate multiple steps of carcinogenesis including tumor progression and metastasis. Recent data support that sumoylation, the covalent attachment of the Small Ubiquitin-related MOdifier (SUMO) to proteins, is involved in the activation of the hypoxic response and the ensuing signaling cascade.  To gain insights into differences of the SUMO1 and SUMO2/3 proteome of ...
Source: Molecular and Cellular Proteomics : MCP - March 29, 2019 Category: Molecular Biology Authors: Chachami G, Stankovic-Valentin N, Karagiota A, Basagianni A, Plessmann U, Urlaub H, Melchior F, Simos G Tags: Mol Cell Proteomics Source Type: research

Quantitative Microproteomics Based Characterization of the Central and Peripheral Nervous System of a Mouse Model of Krabbe Disease.
Abstract Krabbe disease is a rare, childhood lysosomal storage disorder caused by a deficiency of galactosylceramide beta-galactosidase (GALC). The major effect of GALC deficiency is the accumulation of psychosine in the nervous system and widespread degeneration of oligodendrocytes and Schwann cells, causing rapid demyelination. The molecular mechanisms of Krabbe disease are not yet fully elucidated and a definite cure is still missing. Here we report the first in-depth characterization of the proteome of the Twitcher mouse, a spontaneous mouse model of Krabbe disease, to investigate the proteome changes in the C...
Source: Molecular and Cellular Proteomics : MCP - March 29, 2019 Category: Molecular Biology Authors: Pellegrini D, Del Grosso A, Angella L, Giordano N, Dilillo M, Tonazzini I, Caleo M, Cecchini M, McDonnell LA Tags: Mol Cell Proteomics Source Type: research

Proteomics of Asrij perturbation in Drosophila lymph glands for identification of new regulators of hematopoiesis.
Abstract Hematopoiesis is the process of differentiation of precursor blood cells into mature blood cells that is controlled by a complex set of molecular interactions. Understanding hematopoiesis is important for the study of hematological disorders. However, a comprehensive understanding of how physiological and genetic mechanisms regulate blood cell precursor maintenance and differentiation is lacking. Owing to simplicity and ease of genetic analysis, the Drosophila melanogaster lymph gland (LG) is an excellent model to study hematopoiesis. Here, we quantitatively analyzed the LG proteome under genetic conditio...
Source: Molecular and Cellular Proteomics : MCP - March 28, 2019 Category: Molecular Biology Authors: Sinha S, Ray A, Abhilash L, Kumar M, Sreenivasamurthy SK, Keshava Prasad TS, Inamdar MS Tags: Mol Cell Proteomics Source Type: research

Effects of size and geographical origin on Atlantic salmon, Salmo salar, mucin O-glycan repertoire.
Abstract Diseases cause ethical concerns and economic losses in the Salmonid industry. The mucus layer comprised of highly O-glycosylated mucins is the first contact between pathogens and fish. Mucin glycans govern pathogen adhesion, growth and virulence. The Atlantic salmon O-glycome from a single location has been characterized and the inter-individual variation was low. Since inter-individual variation is considered a population based defence, hindering the entire population from being wiped out by a single infection, low inter-individual variation among Atlantic salmon may be a concern. Here, we analysed the O...
Source: Molecular and Cellular Proteomics : MCP - March 28, 2019 Category: Molecular Biology Authors: Benktander J, Venkatakrishnan V, Padra JT, Sundh H, Sundell K, Murughan AVM, Maynard B, Linden SK Tags: Mol Cell Proteomics Source Type: research

Quantitative early auxin root proteomics identifies GAUT10, a galacturonosyltransferase, as a novel regulator of root meristem maintenance.
This report identifies early auxin responsive proteins in roots at 30 minutes and 2 hours after hormone treatment using a quantitative proteomics approach in which 3,514 proteins were reliably quantified. A comparison of the>100 differentially expressed proteins at each the time point showed limited overlap suggesting a dynamic and transient response to exogenous auxin. Several proteins with established roles in auxin mediated root development exhibited altered abundance, providing support for this approach. While novel targeted proteomics assays demonstrate that all six auxin receptors remain stable in response to...
Source: Molecular and Cellular Proteomics : MCP - March 27, 2019 Category: Molecular Biology Authors: Pu Y, Walley JW, Shen Z, Lang M, Briggs SP, Estelle M, Kelley D Tags: Mol Cell Proteomics Source Type: research

Salmonella effectors SseK1 and SseK3 target death domain proteins in the TNF and TRAIL signaling pathways.
Abstract Strains of Salmonella utilise two distinct type three secretion systems to deliver effector proteins directly into host cells. The Salmonella effectors SseK1 and SseK3 are arginine glycosyltransferases that modify mammalian death domain containing proteins with N-acetyl glucosamine (GlcNAc) when overexpressed ectopically or as recombinant protein fusions. Here, we combined Arg-GlcNAc glycopeptide immunoprecipitation and mass spectrometry to identify host proteins GlcNAcylated by endogenous levels of SseK1 and SseK3 during Salmonella infection. We observed that SseK1 modified the mammalian signaling protei...
Source: Molecular and Cellular Proteomics : MCP - March 22, 2019 Category: Molecular Biology Authors: Newson JP, Scott NE, Yeuk Wah Chung I, Wong Fok Lung T, Giogha C, Gan J, Wang N, Strugnell R, Brown NF, Cygler M, Pearson JS, Hartland EL Tags: Mol Cell Proteomics Source Type: research

Comprehensive analysis of individual variation in the urinary proteome revealed significant gender differences.
Abstract Disease biomarkers are the measurable changes associated with a pathophysiological process. Without homeostatic control, urine accumulates systematic changes in the body. Thus, urine is an attractive biological material for the discovery of disease biomarkers. One of the major bottlenecks in urinary biomarker discovery is that the concentration and composition of urinary proteins are influenced by many physiological factors. To elucidate the individual variation and related factors influencing the urinary proteome, we comprehensively analyzed the urine samples from healthy adult donors (aged 20-69 years)....
Source: Molecular and Cellular Proteomics : MCP - March 20, 2019 Category: Molecular Biology Authors: Shao C, Zhao M, Chen X, Sun H, Yang Y, Xiao X, Guo Z, Liu X, Lv Y, Chen X, Sun W, Wu D, Gao Y Tags: Mol Cell Proteomics Source Type: research

Reductive stress selectively disrupts collagen homeostasis and modifies growth factor-independent signalling through the MAPK/Akt pathway in human dermal fibroblasts.
, Benham AM Abstract Redox stress is a well-known contributor to ageing and diseases in skin. Reductants such as dithiothreitol (DTT) can trigger a stress response by disrupting disulfide bonds. However, the quantitative response of the cellular proteome to reductants has not been explored, particularly in cells such as fibroblasts that produce extracellular matrix proteins. Here, we have used a robust, unbiased, label-free SWATH-MS proteomic approach to quantitate the response of skin fibroblast cells to DTT in the presence or absence of the growth factor PDGF. Of the 4487 proteins identified, only 42 proteins sh...
Source: Molecular and Cellular Proteomics : MCP - March 19, 2019 Category: Molecular Biology Authors: Carne NA, Bell S, Brown AP, Määttä A, Flagler MJ, Benham AM Tags: Mol Cell Proteomics Source Type: research

Quantitative proteomics links the intermediate filament nestin to resistance to targeted BRAF inhibition in melanoma cells.
Abstract Targeted inhibition of mutated kinases using selective MAP kinase inhibitors in malignant melanoma often results in temporary improvement of clinical symptoms followed by rapid development of resistance. To gain insights in molecular processes that govern resistance, we performed SILAC-based quantitative proteomics profiling of vemurafenib-resistant and -sensitive melanoma cells. Among down-regulated proteins in vemurafenib-resistant cell lines we detected multiple proteins involved in cytoskeletal organization and signaling, including the intermediate filament nestin, which was one of the most down-regul...
Source: Molecular and Cellular Proteomics : MCP - March 19, 2019 Category: Molecular Biology Authors: Schmitt M, Sinnberg T, Nalpas NC, Maass A, Schittek B, Macek B Tags: Mol Cell Proteomics Source Type: research

Reproductive Proteomics Comes of Age.
PMID: 30889548 [PubMed - in process] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - March 15, 2019 Category: Molecular Biology Authors: Karr TL Tags: Mol Cell Proteomics Source Type: research

Integrated analyses of phenotype and quantitative proteome of CMTM4  deficient mice reveal its association with male fertility.
Integrated analyses of phenotype and quantitative proteome of CMTM4 deficient mice reveal its association with male fertility. Mol Cell Proteomics. 2019 Mar 13;: Authors: Liu F, Liu XX, Liu X, Li T, Zhu P, Liu Z, Xue H, Wang W, Yang X, Liu J, Han W Abstract The chemokine-like factor (CKLF)-like MARVEL transmembrane domain-containing family (CMTM) is a gene family that has been implicated in male reproduction. CMTM4 is an evolutionarily conserved member that is highly expressed in the testis. However, its function in male fertility remains unknown. Here, we demonstrate that CMTM4 is associated wit...
Source: Molecular and Cellular Proteomics : MCP - March 13, 2019 Category: Molecular Biology Authors: Liu F, Liu XX, Liu X, Li T, Zhu P, Liu Z, Xue H, Wang W, Yang X, Liu J, Han W Tags: Mol Cell Proteomics Source Type: research

Virulence factors produced by Staphylococcus  aureus biofilms have a moonlighting function contributing to biofilm integrity.
Virulence factors produced by Staphylococcus aureus biofilms have a moonlighting function contributing to biofilm integrity. Mol Cell Proteomics. 2019 Mar 08;: Authors: Graf AC, Leonard A, Schäuble M, Rieckmann LM, Hoyer J, Maaß S, Lalk M, Becher D, Pané-Farré J, Riedel K Abstract Staphylococcus aureus is the causative agent of various biofilm-associated infections in humans causing major healthcare problems worldwide. This type of infection is inherently difficult to treat due to a reduced metabolic activity of biofilm-embedded cells and the protective nature of a s...
Source: Molecular and Cellular Proteomics : MCP - March 8, 2019 Category: Molecular Biology Authors: Graf AC, Leonard A, Schäuble M, Rieckmann LM, Hoyer J, Maaß S, Lalk M, Becher D, Pané-Farré J, Riedel K Tags: Mol Cell Proteomics Source Type: research

Quantification of dynamic protein interactions and phosphorylation in LPS signaling pathway by SWATH-MS.
Abstract Lipopolysaccharide (LPS)-induced macrophage activation is a prototype of innate immune response. Although key effector proteins in LPS signaling pathway have been revealed, the map of dynamic protein interactions and phosphorylation as well as the stoichiometry of protein complexes are lacking. Here we present a dynamic map of protein interactions and phosphorylation in MyD88, TRAF6 and NEMO complexes obtained by SWATH-MS. The comprehensive MS measurement leads to quantification of up to about 3,000 proteins across about 21-40 IP samples. We detected and quantified almost all known interactors of MyD88, T...
Source: Molecular and Cellular Proteomics : MCP - March 8, 2019 Category: Molecular Biology Authors: Wu X, Yang D, Zhao F, Yang ZH, Wang D, Qiao M, Fang Y, Li W, Wu R, He P, Cong Y, Chen C, Hu L, Yan Y, Xie C, Wu Y, Han J, Zhong CQ Tags: Mol Cell Proteomics Source Type: research

Protein aggregation capture on microparticles enables multi-purpose proteomics sample preparation.
JV Abstract Universal proteomics sample preparation is challenging due to the high heterogeneity of biological samples. Here we describe a novel mechanism that exploits the inherent instability of denatured proteins for non-specific immobilization on microparticles by protein aggregation capture. To demonstrate the general applicability of this mechanism, we analyzed phosphoproteomes, tissue proteomes, and interaction proteomes as well as dilute secretomes. The findings presents a practical, sensitive and cost-effective proteomics sample preparation method. PMID: 30833379 [PubMed - as supplied by publisher] ...
Source: Molecular and Cellular Proteomics : MCP - March 4, 2019 Category: Molecular Biology Authors: Batth TS, Tollenaere MAX, Rüther PL, Gonzalez-Franquesa A, Prabhakar BS, Bekker-Jensen SH, Deshmukh AS, Olsen JV Tags: Mol Cell Proteomics Source Type: research

Spatiotemporal changes of the phagosomal proteome in dendritic cells in response to LPS stimulation.
In this study, we determined spatiotemporal changes of the proteome of DC phagosomes during their maturation and compared resting and lipopolysaccharide (LPS)-stimulated bone marrow-derived DCs by label-free, quantitative mass spectrometry. Ovalbumin-coupled latex beads were used as phagocytosis model system and revealed that LPS-treated DCs show decreased recruitment of proteins involved in phagosome maturation, such as subunits of the vacuolar proton ATPase, cathepsin B, D, S and RAB7. In contrast, those phagosomes were characterized by an increased recruitment of proteins involved in antigen cross-presentation, e.g. dif...
Source: Molecular and Cellular Proteomics : MCP - February 26, 2019 Category: Molecular Biology Authors: Pauwels AM, Härtlova A, Peltier J, Driege Y, Baudelet G, Brodin P, Trost M, Beyaert R, Hoffmann E Tags: Mol Cell Proteomics Source Type: research

Metabolic cross-talk between human bronchial epithelial cells and internalized Staphylococcus aureus as a driver for infection.
;lker U Abstract Staphylococcus aureus is infamous for causing recurrent infections of the human respiratory tract. This is a consequence of its ability to adapt to different niches, including the intracellular milieu of lung epithelial cells. To understand the dynamic interplay between epithelial cells and the intracellular pathogen, we dissected their interactions over four days by mass spectrometry. Additionally, we investigated the dynamics of infection through live cell imaging, immunofluorescence and electron microscopy. The results highlight a major role of often overlooked temporal changes in the bacterial...
Source: Molecular and Cellular Proteomics : MCP - February 26, 2019 Category: Molecular Biology Authors: Palma Medina LM, Becker AK, Michalik S, Yedavally H, Raineri EJM, Hildebrandt P, Gesell Salazar M, Surmann K, Pförtner H, Mekonnen SA, Salvati A, Kaderali L, van Dijl JM, Völker U Tags: Mol Cell Proteomics Source Type: research

An advanced strategy for comprehensive profiling of ADP-ribosylation sites using mass spectrometry-based proteomics.
Abstract ADP-ribosylation is a widespread post-translational modification (PTM) with crucial functions in many cellular processes. Here, we describe an in-depth ADP-ribosylome using our Af1521-based proteomics methodology for comprehensive profiling of ADP-ribosylation sites, by systematically assessing complementary proteolytic digestions and precursor fragmentation through application of electron-transfer higher-energy collisional dissociation (EThcD) and electron transfer dissociation (ETD), respectively. While ETD spectra yielded higher identification scores, EThcD generally proved superior to ETD in identific...
Source: Molecular and Cellular Proteomics : MCP - February 23, 2019 Category: Molecular Biology Authors: Hendriks IA, Larsen SC, Nielsen ML Tags: Mol Cell Proteomics Source Type: research

Metabolic, anti-apoptotic and immune evasion strategies of primary human myeloma cells indicate adaptations to hypoxia.
Abstract Multiple Myeloma (MM) is an incurable plasma cell malignancy primarily localized within the bone marrow (BM). It develops from a premalignant stage, monoclonal gammopathy of undetermined significance (MGUS), often via an intermediate stage, smoldering MM (SMM). The mechanisms of MM progression have not yet been fully understood, all the more because patients with MGUS and SMM already carry similar initial mutations as found in MM cells. Over the last years, increased importance has been attributed to the tumor microenvironment and its role in the pathophysiology of the disease. Adaptations of MM cells to ...
Source: Molecular and Cellular Proteomics : MCP - February 21, 2019 Category: Molecular Biology Authors: Janker L, Mayer RL, Bileck A, Kreutz D, Mader JC, Utpatel K, Heudobler D, Agis H, Gerner C, Slany A Tags: Mol Cell Proteomics Source Type: research

Streamlined protocol for deep proteomic profiling of FAC-sorted cells and its application to freshly isolated murine immune cells.
Abstract Proteomic profiling describes the molecular landscape of proteins in cells immediately available to sense, transduce, and enact the appropriate responses to extracellular queues. Transcriptional profiling has proven invaluable to our understanding of cellular responses, however, insights may be lost as mounting evidence suggests transcript levels only moderately correlate with protein levels in steady state cells. Mass spectrometry-based quantitative proteomics is a well-suited and widely used analytical tool for studying global protein abundances. Typical proteomic workflows are often limited by the amou...
Source: Molecular and Cellular Proteomics : MCP - February 21, 2019 Category: Molecular Biology Authors: Myers SA, Rhoads A, Cocco AR, Peckner R, Haber A, Schweitzer LD, Krug K, Mani DR, Clauser KR, Rozenblatt-Rosen O, Hacohen N, Regev A, Carr SA Tags: Mol Cell Proteomics Source Type: research

Conodipine-P1-3, the first phospholipases A2 characterized from injected cone snail-venom.
Abstract The phospholipase A2 (PLA2s) superfamily are ubiquitous small enzymes that catalyze the hydrolysis of phospholipids at the sn-2 ester bond. PLA2s in the venom of cone snails (conodipines, Cdpi) are composed of two chains termed as alpha and beta subunits. Conodipines are categorized within the group IX of PLA2s. Here we describe the purification and biochemical characterization of three conodipines (Cdpi-P1, -P2 and -P3) isolated from the injected venom of Conus purpurascens. Using proteomics methods, we determined the full sequences of all three conodipines. Conodipine-P1-3 have conserved consensus catal...
Source: Molecular and Cellular Proteomics : MCP - February 14, 2019 Category: Molecular Biology Authors: Moller C, Davis WC, Clark E, De Caprio A, Mari F Tags: Mol Cell Proteomics Source Type: research

For the sake of science.
PMID: 30760536 [PubMed - as supplied by publisher] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - February 13, 2019 Category: Molecular Biology Authors: Gierasch LM, Davidson NO, Rye KA, Burlingame AL Tags: Mol Cell Proteomics Source Type: research

The old and the new: discovery proteomics identifies putative novel seminal fluid proteins in Drosophila.
Abstract Seminal fluid proteins (SFPs), the non-sperm component of male ejaculates produced by male accessory glands, are viewed as central mediators of reproductive fitness. SFPs effect both male and female post-mating functions and show molecular signatures of rapid adaptive evolution. While Drosophila melanogaster is the dominant insect model for understanding SFP evolution, understanding of SFP evolutionary causes and consequences require additional comparative analyses of close and distantly-related taxa. While SFP identification was historically challenging, advances in label-free quantitative proteomics exp...
Source: Molecular and Cellular Proteomics : MCP - February 13, 2019 Category: Molecular Biology Authors: Karr TL, Southern H, Rosenow MA, Gossmann TI, Snook RR Tags: Mol Cell Proteomics Source Type: research

Microvesicle Proteomic profiling of Uterine Liquid Biopsy for Ovarian Cancer Early Detection.
anon K Abstract High-grade ovarian cancer (HGOC) is the leading cause of mortality from gynecological malignancies, due to diagnosis at a metastatic stage. Current screening options fail to improve mortality due to the absence of early-stage-specific biomarkers. We postulated that a liquid biopsy, such as utero-tubal lavage (UtL), may identify localized lesions better than systemic approaches of serum/plasma analysis. Furthermore, while mutation-based assays are challenged by the rarity of tumor DNA within non-mutated DNA, analyzing the proteomic profile, is expected to enable earlier detection, as it reveals pert...
Source: Molecular and Cellular Proteomics : MCP - February 13, 2019 Category: Molecular Biology Authors: Barnabas GD, Bahar-Shany K, Sapoznik S, Helpman L, Kadan Y, Beiner M, Weitzner O, Arbib N, Korach J, Perri T, Katz G, Blecher A, Brandt B, Friedman E, Stockheim D, Jakobson-Setton A, Eitan R, Armon S, Brand H, Zadok O, Aviel-Ronen S, Harel M, Geiger T, Le Tags: Mol Cell Proteomics Source Type: research

MaxQuant.Live enables global targeting of more than 25,000 peptides.
Abstract Mass spectrometry (MS)-based proteomics is often performed in a shotgun format, in which as many peptide precursors as possible are selected from full or MS1 scans so that their fragment spectra can be recorded in MS2 scans. While achieving great proteome depths, shotgun proteomics cannot guarantee that each precursor will be fragmented in each run. In contrast, targeted proteomics aims to reproducibly and sensitively record a restricted number of precursor/fragment combinations in each run, based on pre-scheduled mass-to-charge and retention time windows. Here we set out to unify these two concepts by a ...
Source: Molecular and Cellular Proteomics : MCP - February 12, 2019 Category: Molecular Biology Authors: Wichmann C, Meier F, Virreira Winter S, Brunner AD, Cox J, Mann M Tags: Mol Cell Proteomics Source Type: research

Probing H2O2-mediated Structural Dynamics of the Human 26S Proteasome Using Quantitative Cross-linking Mass Spectrometry (QXL-MS).
Abstract Cytotoxic protein aggregation-induced impairment of cell function and homeostasis are hallmarks of age-related neurodegenerative pathologies. As proteasomal degradation represents the major clearance pathway for oxidatively damaged proteins, a detailed understanding of the molecular events underlying its stress response is critical for developing strategies to maintain cell viability and function. Although the 26S proteasome has been shown to disassemble during oxidative stress, its conformational dynamics remains unclear. To this end, we have developed a new quantitative cross-linking mass spectrometry (...
Source: Molecular and Cellular Proteomics : MCP - February 5, 2019 Category: Molecular Biology Authors: Yu C, Wang X, Huszagh AS, Viner R, Novitsky EJ, Rychnovsky SD, Huang L Tags: Mol Cell Proteomics Source Type: research

Immunomic identification of malaria antigens associated with protection in mice.
Abstract Efforts to develop vaccines against malaria represent a major research target. The observations that 1) sterile protection can be obtained when the host is exposed to live parasites and 2) the immunity against blood stage parasite is principally mediated by protective antibodies suggest that a protective vaccine is feasible. However, only a small number of proteins have been investigated so far and most of the Plasmodium proteome has yet to be explored. To date, only few immunodominant antigens have emerged for testing in clinical trials but no formulation has led to substantial protection in humans. The ...
Source: Molecular and Cellular Proteomics : MCP - February 4, 2019 Category: Molecular Biology Authors: Siau A, Huang X, Loh HP, Zhang N, Meng W, Sze SK, Renia L, Preiser PR Tags: Mol Cell Proteomics Source Type: research

Integration of two in-depth quantitative proteomics approaches determines the kallikrein-related peptidase 7 (KLK7) degradome in ovarian cancer cell secretome.
Abstract Kallikrein-related peptidase 7 (KLK7) is a serine peptidase that is over expressed in ovarian cancer. In vitro functional analyses have suggested KLK7 to play a cancer progressive role, although monitoring of KLK7 expression has suggested a contradictory protective role for KLK7 in ovarian cancer patients. In order to help delineate its mechanism of action and thereby the functional roles, information on its substrate repertoire is crucial. Therefore, in this study a quantitative proteomics approach - PROtein TOpography and Migration Analysis Platform (PROTOMAP)-coupled with SILAC was used for in-depth an...
Source: Molecular and Cellular Proteomics : MCP - January 31, 2019 Category: Molecular Biology Authors: Munasinghage Silva L, Kryza T, Stoll T, Hoogland C, Dong Y, Stephens CR, Hastie ML, Magdolen V, Kleifeld O, Gorman JJ, Clements J Tags: Mol Cell Proteomics Source Type: research

DIAlignR provides precise retention time alignment across distant runs in DIA and targeted proteomics.
Abstract SWATH-MS has been widely used for proteomics analysis given its high-throughput and reproducibility but ensuring consistent quantification of analytes across large-scale studies of heterogeneous samples such as human-plasma remains challenging. Heterogeneity in large-scale studies can be caused by large time intervals between data-acquisition, acquisition by different operators or instruments, intermittent repair or replacement of parts, such as the liquid chromatography column, all of which affect retention time (RT) reproducibility and successively performance of SWATH-MS data analysis. Here, we present...
Source: Molecular and Cellular Proteomics : MCP - January 31, 2019 Category: Molecular Biology Authors: Gupta S, Ahadi S, Zhou W, Rost H Tags: Mol Cell Proteomics Source Type: research

Quantitative Multiplex Substrate Profiling of Peptidases by Mass Spectrometry.
Abstract Proteolysis is an integral component of life and has been implicated in many disease processes. To improve our understanding of peptidase function, it is imperative to develop tools to uncover substrate specificity and cleavage efficiency. Here, we combine the quantitative power of tandem mass tags (TMTs) with an established peptide cleavage assay to yield quantitative Multiplex Substrate Profiling by Mass Spectrometry (qMSP-MS). This assay was validated with papain, a well-characterized cysteine peptidase, to generate cleavage efficiency values for hydrolysis of 275 unique peptide bonds in parallel. To d...
Source: Molecular and Cellular Proteomics : MCP - January 31, 2019 Category: Molecular Biology Authors: Lapek JD, Jiang Z, Wozniak JM, Arutyunova E, Wang SC, Lemieux MJ, Gonzalez DJ, O'Donoghue AJ Tags: Mol Cell Proteomics Source Type: research

Mass spectrometry-based absolute quantification of 20S proteasome status for controlled ex-vivo expansion of Human Adipose-derived Mesenchymal Stromal/Stem Cells.
Abstract The proteasome controls a multitude of cellular processes through protein degradation and has been identified as a therapeutic target in oncology. However, our understanding of its function and the development of specific modulators are hampered by the lack of a straightforward method to determine the overall proteasome status in biological samples. Here, we present a method to determine the absolute quantity and stoichiometry of ubiquitous and tissue-specific human 20S proteasome subtypes based on a robust, absolute SILAC-based multiplexed LC-Selected Reaction Monitoring (SRM) quantitative mass spectrome...
Source: Molecular and Cellular Proteomics : MCP - January 30, 2019 Category: Molecular Biology Authors: Menneteau T, Fabre B, Garrigues L, Stella A, Zivkovic D, Roux-Dalvai F, Mouton-Barbosa E, Beau M, Renoud ML, Amalric F, Sensebe L, Gonzalez-de-Peredo A, Ader I, Burlet-Schiltz O, Bousquet MP Tags: Mol Cell Proteomics Source Type: research

Identification of candidate plasma protein biomarkers for cervical cancer using the multiplex proximity extension assay.
en U Abstract Human papillomavirus (HPV) is recommended as the primary test in cervical cancer screening, with co-testing by cytology for HPV-positive women to identify cervical lesions. Cytology has low sensitivity and there is a need to identify biomarkers that could identify dysplasia that are likely to progress to cancer. We searched for plasma proteins that could identify women with cervical cancer using the multiplex proximity extension assay (PEA). The abundance of 100 proteins were measured in plasma collected at the time of diagnosis of patients with invasive cervical cancer and in population controls usi...
Source: Molecular and Cellular Proteomics : MCP - January 28, 2019 Category: Molecular Biology Authors: Berggrund M, Enroth S, Lundberg M, Assarsson E, Stålberg K, Lindquist D, Hallmans G, Grankvist K, Olovsson M, Gyllensten U Tags: Mol Cell Proteomics Source Type: research

Human testis phosphoproteome reveals kinases as potential targets in spermatogenesis and testicular cancer.
Abstract Spermatogenesis is a complex cell differentiation process that includes marked genetic, cellular, functional and structural changes. It requires tight regulation, since disturbances in any of the spermatogenic processes would lead to fertility deficiencies as well as disorders in offspring. In order to increase our knowledge of signal transduction during sperm development, we carried out a large-scale identification of the phosphorylation events that occur in the human male gonad. Metal oxide affinity chromatography using TiO2combined with LC-MS/MS was conducted to profile the phosphoproteome of adult hum...
Source: Molecular and Cellular Proteomics : MCP - January 25, 2019 Category: Molecular Biology Authors: Castillo J, Knol JC, Korver CM, Piersma SR, Pham TV, Goeij de Haas RR, van Pelt AMM, Jimenez CR, Jansen BJH Tags: Mol Cell Proteomics Source Type: research

Investigating Lactococcus lactis MG1363 response to phage p2 infection  at the proteome level.
In this study, we used label-free quantitative proteomics to reveal the proteotypes of Lactococcus lactis MG1363 during infection by the virulent phage p2, a model for studying the biology of phages infecting Gram-positive bacteria. Our approach resulted in the high-confidence detection and quantification of 59% of the theoretical bacterial proteome, including 226 bacterial proteins detected only during phage infection and 6 proteins unique to uninfected bacteria. We also identified many bacterial proteins of differing abundance during the infection. Using this high-throughput proteomic datasets, we selected specific bacte...
Source: Molecular and Cellular Proteomics : MCP - January 24, 2019 Category: Molecular Biology Authors: Lemay ML, Otto A, Maaß S, Plate K, Becher D, Moineau S Tags: Mol Cell Proteomics Source Type: research

Apolipoprotein A1 forms 5/5 and 5/4 antiparallel dimers in human high-density lipoprotein.
Abstract Apolipoprotein A1 (APOA1), the major protein of high-density lipoprotein (HDL), contains 10 helical repeats that play key roles in protein-protein and protein-lipid interactions. The current structural model for HDL proposes that APOA1 forms an antiparallel dimer in which helix 5 in monomer 1 associates with helix 5 in monomer 2 along a left-left (LL5/5) interface, forming a protein complex with a two-fold axis of symmetry centered on helix 5. However, computational studies suggest that other orientations are possible. To test this idea, we used a zero-length chemical cross-linking reagent that forms cova...
Source: Molecular and Cellular Proteomics : MCP - January 18, 2019 Category: Molecular Biology Authors: He Y, Song HD, Anantharamaiah GM, Palgunachari MN, Bornfeldt K, Segrest JP, Heinecke J Tags: Mol Cell Proteomics Source Type: research

Multi-Isotype Glycoproteomic Characterization of Serum Antibody Heavy Chains Reveals Isotype- and Subclass-Specific N-Glycosylation Profiles.
Abstract Antibodies are critical glycoproteins that bridge the innate and adaptive immune systems to provide protection against infection. The isotype/subclass of the antibody, the co-translational N-glycosylation on the CH2 domain, and the remodeling of the N-linked glycans during passage through the ER and Golgi are the known variables within the Fc domain that program antibody effector function. Through investigations of monoclonal therapeutics, it has been observed that addition or removal of specific monosaccharide residues from antibody N-glycans can influence the potency of antibodies, highlighting the impo...
Source: Molecular and Cellular Proteomics : MCP - January 18, 2019 Category: Molecular Biology Authors: Chandler KB, Mehta N, Leon DR, Suscovich T, Alter G, Costello CE Tags: Mol Cell Proteomics Source Type: research

Data-independent acquisition improves quantitative cross-linking mass spectrometry.
In conclusion, the DIA software Spectronaut can now be used in cross-linking and DIA is indeed able to improve QCLMS. PMID: 30651306 [PubMed - as supplied by publisher] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - January 16, 2019 Category: Molecular Biology Authors: Müller F, Kolbowski L, Bernhardt OM, Reiter L, Rappsilber J Tags: Mol Cell Proteomics Source Type: research

Accurate Estimation of Context-Dependent False Discovery Rates in Top-Down Proteomics.
We present a new open-source tool, the TDCD_FDR_Calculator, which provides a scalable, context-dependent FDR calculation that can be applied post-search to enhance the quality of results in top-down proteomics from any search engine. PMID: 30647073 [PubMed - as supplied by publisher] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - January 15, 2019 Category: Molecular Biology Authors: LeDuc RD, Fellers RT, Early BP, Greer JB, Shams DP, Thomas P, Kelleher NL Tags: Mol Cell Proteomics Source Type: research

Macrophage phosphoproteome analysis reveals MINCLE-dependent and -independent mycobacterial cord factor signaling.
Lang R Abstract Immune sensing of Mycobacterium tuberculosis relies on recognition by macrophages. Mycobacterial cord factor, trehalose-6,6'-dimycolate (TDM), is the most abundant cell wall glycolipid and binds to the C-type lectin receptor (CLR) MINCLE. To explore the kinase signaling linking the TDM-MINCLE interaction to gene expression, we employed quantitative phosphoproteome analysis. TDM caused upregulation of 6.7% and suppressed 3.8% of the 14,000 phospho-sites identified on 3727 proteins. MINCLE-dependent phosphorylation was observed for canonical players of CLR signaling (e.g. PLCg, PKCd), and was enrich...
Source: Molecular and Cellular Proteomics : MCP - January 11, 2019 Category: Molecular Biology Authors: Hansen M, Peltier J, Killy B, Amin B, Bodendorfer B, Härtlova A, Uebel S, Bosmann M, Hofmann J, Büttner C, Ekici AB, Kuttke M, Franzyk H, Foged C, Beer-Hammer S, Schabbauer G, Trost M, Lang R Tags: Mol Cell Proteomics Source Type: research

High-density peptide arrays help to identify linear immunogenic B cell epitopes in individuals naturally exposed to malaria infection.
er FF Abstract High-density peptide arrays are an excellent means to profile anti-plasmodial antibody responses. Different protein intrinsic epitopes can be distinguished and additional insights are gained, when compared to assays involving the full-length protein. Distinct reactivities to specific epitopes within one protein may explain differences in published results, regarding immunity or susceptibility to malaria. We pursued three approaches to find specific epitopes within important plasmodial proteins, (1) twelve leading vaccine candidates were mapped as overlapping 15-mer peptides, (2) a bioinformatical ap...
Source: Molecular and Cellular Proteomics : MCP - January 10, 2019 Category: Molecular Biology Authors: Jaenisch T, Heiss K, Fischer N, Geiger C, Bischoff FR, Moldenhauer G, Rychlewski L, Sié A, Coulibaly B, Seeberger PH, Wyrwicz LS, Breitling F, Loeffler FF Tags: Mol Cell Proteomics Source Type: research

Proteome analysis of human neutrophil granulocytes from patients with monogenic disease using data-independent acquisition.
r J Abstract Neutrophil granulocytes are critical mediators of innate immunity and tissue regeneration. Rare diseases of neutrophil granulocytes may affect their differentiation and/or functions. However, there are very few validated diagnostic tests assessing the functions of neutrophil granulocytes in these diseases. Here, we set out to probe omics analysis as a novel diagnostic platform for patients with defective differentiation and function of neutrophil granulocytes. We analyzed highly purified neutrophil granulocytes from 68 healthy individuals and 16 patients with rare monogenic diseases. Cells were isolat...
Source: Molecular and Cellular Proteomics : MCP - January 10, 2019 Category: Molecular Biology Authors: Grabowski P, Hesse S, Hollizeck S, Rohlfs M, Behrends U, Sherkat R, Tamary H, Ünal E, Somech R, Patıroğlu T, Canzar S, van der Werff Ten Bosch J, Klein C, Rappsilber J Tags: Mol Cell Proteomics Source Type: research

Precision de novo peptide sequencing using mirror proteases of Ac-LysargiNase and trypsin for large-scale proteomics.
Abstract De novo peptide sequencing for large-scale proteomics remains challenging because of the lack of full coverage of ion series in tandem mass spectra. We developed a mirror protease of trypsin, acetylated LysargiNase (Ac-LysargiNase), with superior activity and stability. The mirror spectrum pairs derived from the Ac-LysargiNase and trypsin treated samples can generate full b and y ion series. The b and y ion series provide mutual complementarity and examination of each other, which allowed us to develop a novel algorithm, pNovoM, for de novo sequencing. Using pNovoM to sequence peptides of purified protein...
Source: Molecular and Cellular Proteomics : MCP - January 8, 2019 Category: Molecular Biology Authors: Yang H, Li Y, Zhao M, Wu F, Wang X, Xiao W, Wang Y, Zhang J, Wang F, Xu F, Zeng WF, Overall CM, He SM, Chi H, Xu P Tags: Mol Cell Proteomics Source Type: research