Cell cycle profiling reveals protein oscillation, phosphorylation, and localization dynamics.
Altun M Abstract The cell cycle is a highly conserved process involving the coordinated separation of a single cell into two daughter cells. To relate transcriptional regulation across the cell cycle with oscillatory changes in protein abundance and activity, we carried out a proteome- and phospho-proteome-wide mass spectrometry profiling. We compared protein dynamics with gene transcription, revealing a large number of transcriptionally regulated G2 mRNAs that only produce a protein shift after mitosis. Integration of CRISPR/Cas9 survivability studies further highlighted proteins essential for cell viability. Ana...
Source: Molecular and Cellular Proteomics : MCP - February 12, 2020 Category: Molecular Biology Authors: Herr P, Boström J, Rullman E, Rudd SG, Vesterlund M, Lehtiö J, Helleday T, Maddalo G, Altun M Tags: Mol Cell Proteomics Source Type: research

Improving identification of in-organello protein-protein interactions using an affinity-enrichable, isotopically-coded, and mass spectrometry-cleavable chemical crosslinker.
Abstract An experimental and computational approach for identification of protein-protein interactions by ex-vivo chemical crosslinking and mass spectrometry (CLMS) has been developed that takes advantage of the specific characteristics of cyanurbiotindipropionylsuccinimide (CBDPS), an affinity-tagged isotopically-coded mass spectrometry (MS)-cleavable crosslinking reagent. Utilizing this reagent in combination with a crosslinker-specific data-dependent acquisition strategy based on MS2 scans, and a software pipeline designed for integrating crosslinker-specific mass spectral information led to demonstrated improv...
Source: Molecular and Cellular Proteomics : MCP - February 12, 2020 Category: Molecular Biology Authors: Makepeace KAT, Mohammed Y, Rudashevskaya EL, Petrotchenko EV, Voegtle FN, Meisinger C, Sickmann A, Borchers CH Tags: Mol Cell Proteomics Source Type: research

A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients.
JV Abstract State-of-the-art proteomics-grade mass spectrometers can measure peptide precursors and their fragments with ppm mass accuracy at sequencing speeds of tens of peptides per second with attomolar sensitivity. Here we describe a compact and robust quadrupole-orbitrap mass spectrometer equipped with a front-end High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Interface. The performance of the Orbitrap Exploris 480 mass spectrometer is evaluated in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes in combination with FAIMS. We demonstrate that different compensat...
Source: Molecular and Cellular Proteomics : MCP - February 12, 2020 Category: Molecular Biology Authors: Bekker-Jensen DB, Martinez-Val A, Steigerwald S, Rüther PL, Fort KL, Arrey TN, Harder A, Makarov AA, Olsen JV Tags: Mol Cell Proteomics Source Type: research

Decreased immunoglobulin G core fucosylation, a player in antibody-dependent cell-mediated cytotoxicity, is associated with autoimmune thyroid diseases.
Lin EM, Walsh JP, Pocheć E, Spector TD, Wilson SG, Lauc G Abstract Autoimmune thyroid diseases (AITD) are the most common group of autoimmune diseases, associated with lymphocyte infiltration and the production of thyroid autoantibodies, like thyroid peroxidase antibodies (TPOAb), in the thyroid gland. Immunoglobulins and cell-surface receptors are glycoproteins with distinctive glycosylation patterns that play a structural role in maintaining and modulating their functions. We investigated associations of total circulating IgG and peripheral blood mononuclear cells glycosylation with AITD and the influence of ge...
Source: Molecular and Cellular Proteomics : MCP - February 5, 2020 Category: Molecular Biology Authors: Martin TC, Šimurina M, Ząbczyńska M, Martinic Kavur M, Rydlewska M, Pezer M, Kozłowska K, Burri A, Vilaj M, Turek-Jabrocka R, Krnjajić-Tadijanović M, Trofimiuk-Müldner M, Ugrina I, Lityńska A, Hubalewska-Dydejczyk A, Trbojevic-Akmacic I, Lin EM, W Tags: Mol Cell Proteomics Source Type: research

Phenotypic adaption of Pseudomonas aeruginosa by hacking siderophores produced by other microorganisms.
Abstract Bacteria secrete siderophores to access iron, a key nutrient poorly bioavailable and the source of strong competition between microorganisms in most biotopes. Many bacteria also use siderophores produced by other microorganisms (exosiderophores) in a piracy strategy. Pseudomonas aeruginosa, an opportunistic pathogen, produces two siderophores, pyoverdine and pyochelin, and is also able to use a panel of exosiderophores. We first investigated expression of the various iron-uptake pathways of P. aeruginosa in three different growth media using proteomic and RT-qPCR approaches and observed three different ph...
Source: Molecular and Cellular Proteomics : MCP - February 5, 2020 Category: Molecular Biology Authors: Perraud Q, Cantero P, Roche B, Gasser V, Normant VP, Kuhn L, Hammann P, Mislin GLA, Ehret-Sabatier L, Schalk IJ Tags: Mol Cell Proteomics Source Type: research

A quantitative tri-fluorescent yeast two-hybrid system: from flow cytometry to in-cellula affinities.
We present a technological advancement for the estimation of the affinities of Protein-Protein Interactions (PPIs) in living cells. A novel set of vectors is introduced that enables a quantitative yeast two-hybrid system based on fluorescent fusion proteins. The vectors allow simultaneous quantification of the reaction partners (Bait and Prey) and the reporter at the single-cell level by flow cytometry. We validate the applicability of this system on a small but diverse set of PPIs (eleven protein families from six organisms) with different affinities; the dissociation constants range from 117 pM to 17 µM. After only...
Source: Molecular and Cellular Proteomics : MCP - February 3, 2020 Category: Molecular Biology Authors: Cluet D, Amri I, Vergier B, Léault J, Audibert A, Grosjean C, Calabrési D, Spichty M Tags: Mol Cell Proteomics Source Type: research

Correction: Graph Algorithms for Condensing and Consolidating Gene Set Analysis Results.
PMID: 32007940 [PubMed - in process] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - February 1, 2020 Category: Molecular Biology Authors: Savage SR, Shi Z, Liao Y, Zhang B Tags: Mol Cell Proteomics Source Type: research

Integrative metabolic pathway analysis reveals novel therapeutic targets in osteoarthritis.
Abstract In osteoarthritis (OA), impairment of cartilage regeneration can be related to a defective chondrogenic differentiation of mesenchymal stromal cells (MSCs). Therefore, understanding the proteomic- and metabolomic-associated molecular events during the chondrogenesis of MSCs could provide alternative targets for therapeutic intervention. Here, a SILAC-based proteomic analysis identified 43 proteins related with metabolic pathways whose abundance was significantly altered during the chondrogenesis of OA human bone marrow MSCs (hBMSCs). Then, the level and distribution of metabolites was analyzed in these ce...
Source: Molecular and Cellular Proteomics : MCP - January 24, 2020 Category: Molecular Biology Authors: Rocha B, Cillero-Pastor B, Eijkel G, Fernandez-Puente P, Paine MRL, Ruiz-Romero C, Heeren RMA, Calamia V, Blanco FJ Tags: Mol Cell Proteomics Source Type: research

Discovery of species-unique peptide biomarkers of bacterial pathogens by tandem mass spectrometry-based proteotyping.
This study applied nano-liquid chromatography (LC) coupled with tandem MS, with a bioinformatics pipeline and an in-house database of curated high-quality reference genome sequences to identify species-unique peptides as potential biomarkers for four bacterial pathogens commonly found in respiratory tract infections (RTIs): Staphylococcus aureus; Moraxella catarrhalis; Haemophilus influenzae and Streptococcus pneumoniae. The species-unique peptides were initially identified in pure cultures of bacterial reference strains, reflecting the genomic variation in the four species and, furthermore, in clinical respiratory tract s...
Source: Molecular and Cellular Proteomics : MCP - January 15, 2020 Category: Molecular Biology Authors: Karlsson R, Thorsell A, Gomila M, Salvà-Serra F, Jakobsson HE, Gonzales-Siles L, Jaén-Luchoro D, Skovbjerg S, Fuchs J, Karlsson A, Boulund F, Johnning A, Kristiansson E, Moore E Tags: Mol Cell Proteomics Source Type: research

Guidance document: validation of a high-performance liquid chromatography-tandem mass spectrometry immunopeptidomics assay for the identification of HLA class I ligands suitable for pharmaceutical therapies.
Abstract For more than two decades naturally presented, human leukocyte antigen (HLA)-restricted peptides (immunopeptidome) have been eluted and sequenced using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Since, identified disease-associated HLA ligands have been characterized and evaluated as potential active substances. Treatments based on HLA-presented peptides have shown promising results in clinical application as personalized T cell-based immunotherapy. Peptide vaccination cocktails are produced as investigational medicinal products under GMP conditions. In order to support clinical trials bas...
Source: Molecular and Cellular Proteomics : MCP - January 14, 2020 Category: Molecular Biology Authors: Ghosh M, Gauger M, Marcu A, Nelde A, Denk M, Schuster H, Rammensee HG, Stevanovic S Tags: Mol Cell Proteomics Source Type: research

Integration Of IgA and IgG Autoantigens Improves Performance Of Biomarker Panels For Early Diagnosis Of Lung Cancer.
Abstract Lung cancer (LC) remains the leading cause of mortality from malignant tumors worldwide. In our previous study, we surveyed both IgG and IgM-bound serological biomarkers and validated a panel of IgG-bound autoantigens for early LC diagnosis with 50% sensitivity at 90% specificity. To further improve the performance of these serological biomarkers, we surveyed HuProt arrays, comprised of 20, 240 human proteins, for IgA-bound autoantigens since IgAs are a major immunoglobulin isotype in the lung. Integrating with IgG-bound autoantigens, we discovered and validated a combined biomarker panel using ELISA-form...
Source: Molecular and Cellular Proteomics : MCP - January 10, 2020 Category: Molecular Biology Authors: Pan J, Yu L, Wu Q, Lin X, Liu S, Hu S, Rosa C, Eichinger DJ, Pino I, Zhu H, Qian J, Huang Y Tags: Mol Cell Proteomics Source Type: research

N-glycosylation site analysis reveals sex-related differences in protein N-glycosylation in the rice brown planthopper (Nilaparvata lugens).
In conclusion, this study provides further evidence for protein N-glycosylation to be sex-related in insects. Furthermore, original data on N-glycosylation sites of N. lugens adults are presented, providing novel insights into planthopper's biology and information for future biological pest control strategies. PMID: 31924694 [PubMed - as supplied by publisher] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - January 10, 2020 Category: Molecular Biology Authors: Scheys F, Van Damme EJ, Pauwels J, Staes A, Gevaert K, Smagghe G Tags: Mol Cell Proteomics Source Type: research

AMPK interactome reveals its new function in non-homologous end joining DNA repair.
Abstract Adenosine monophosphate-activated protein kinase (AMPK) is an obligate heterotrimer that consists of a catalytic subunit (α) and two regulatory subunits (β and γ). AMPK is a key enzyme in the regulation of cellular energy homeostasis. It has been well studied and is known to function in many cellular pathways. However, the interactome of AMPK has not yet been systematically established, although protein-protein interaction is critically important for protein function and regulation. Here, we used tandem-affinity purification, coupled with mass spectrometry (TAP-MS) analysis, to determine ...
Source: Molecular and Cellular Proteomics : MCP - January 3, 2020 Category: Molecular Biology Authors: Chen Z, Wang C, Jain A, Srivastava M, Tang M, Zhang H, Feng X, Nie L, Su D, Xiong Y, Jung SY, Qin J, Chen J Tags: Mol Cell Proteomics Source Type: research

Characterizing Patients with Recurrent Urinary Tract Infections in Vesicoureteral Reflux: A Pilot Study of the Urinary Proteome.
Abstract Recurrent urinary tract infections (UTIs) pose a significant burden on the health care system. Underlying mechanisms predisposing children to UTIs and associated changes in the urinary proteome are not well understood. We aimed to investigate the urinary proteome of a subset of children who have vesicoureteral reflux (VUR) and recurrent UTIs because of their risk of developing infection-related renal damage. Improving diagnostic modalities to identify UTI risk factors would significantly alter the clinical management of children with VUR. We profiled the urinary proteomes of 22 VUR patients with low grade...
Source: Molecular and Cellular Proteomics : MCP - January 2, 2020 Category: Molecular Biology Authors: Vitko D, Cho P, Kostel SA, DiMartino SE, Cabour LD, Migliozzi MA, Logvinenko T, Warren PG, Froehlich JW, Lee RS Tags: Mol Cell Proteomics Source Type: research

Concentration determination of > 200 proteins in dried blood spots for biomarker discovery and validation.
Concentration determination of>200 proteins in dried blood spots for biomarker discovery and validation. Mol Cell Proteomics. 2020 Jan 02;: Authors: Eshghi A, Pistawka AJ, Liu J, Chen M, Sinclair NJT, Hardie DB, Elliott M, Chen L, Newman R, Mohammed Y, Borchers CH Abstract The use of protein biomarkers as surrogates for clinical endpoints requires extensive multilevel validation including development of robust and sensitive assays for precise measurement of protein concentration.  Multiple reaction monitoring (MRM) is a well-established mass-spectrometric method that can be used for reproducib...
Source: Molecular and Cellular Proteomics : MCP - January 2, 2020 Category: Molecular Biology Authors: Eshghi A, Pistawka AJ, Liu J, Chen M, Sinclair NJT, Hardie DB, Elliott M, Chen L, Newman R, Mohammed Y, Borchers CH Tags: Mol Cell Proteomics Source Type: research

Correction: Alternative mammalian target of rapamycin (mTOR) signal activation in sorafenib-resistant hepatocellular carcinoma cells revealed by array-based pathway profiling.
PMID: 31894100 [PubMed - in process] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - January 1, 2020 Category: Molecular Biology Authors: Masuda M, Chen WY, Miyanaga A, Nakamura Y, Kawasaki K, Sakuma T, Ono M, Chen CL, Honda K, Yamada T Tags: Mol Cell Proteomics Source Type: research

The challenge of classifying metastatic cell properties by molecular profiling exemplified with cutaneous melanoma cells and their cerebral metastasis from patient derived mouse xenografts.
Abstract The prediction of metastatic properties from molecular analyses still poses a major challenge. Here we aimed at the classification of metastasis-related cell properties by proteome profiling making use of cutaneous and brain-metastasizing variants from single melanomas sharing the same genetic ancestry. Previous experiments demonstrated that cultured cells derived from these xenografted variants maintain a stable phenotype associated with a differential metastatic behavior: The brain metastasizing variants produce more spontaneous micro-metastases than the corresponding cutaneous variants. Four correspond...
Source: Molecular and Cellular Proteomics : MCP - December 31, 2019 Category: Molecular Biology Authors: Neuditschko B, Janker L, Niederstaetter L, Brunmair J, Krivanek K, Izraely S, Sagi-Assif O, Meshel T, Keppler B, Del Favero G, Witz IP, Gerner C Tags: Mol Cell Proteomics Source Type: research

Site-specific N-glycan analysis of antibody-binding Fc γ receptors from primary human monocytes.
Site-specific N-glycan analysis of antibody-binding Fc γ receptors from primary human monocytes. Mol Cell Proteomics. 2019 Dec 30;: Authors: Roberts JT, Patel KR, Barb AW Abstract FcγRIIIa (CD16a) and FcγRIIa (CD32a) on monocytes are essential for proper effector functions including antibody dependent cellular cytotoxicity (ADCC) and phagocytosis (ADCP). Indeed, therapeutic monoclonal antibodies (mAbs) that bind FcγRs with greater affinity exhibit greater efficacy. Furthermore, post-translational modification impacts antibody binding affinity, most notably the composition of th...
Source: Molecular and Cellular Proteomics : MCP - December 30, 2019 Category: Molecular Biology Authors: Roberts JT, Patel KR, Barb AW Tags: Mol Cell Proteomics Source Type: research

Combining Precursor and Fragment Information for Improved Detection of Differential Abundance in Data Independent Acquisition.
Abstract In bottom-up, label-free discovery proteomics, biological samples are acquired in a data dependent (DDA) or data independent (DIA) manner, with peptide signals recorded in an intact (MS1) and fragmented (MS2) form. While DDA has only the MS1 space for quantification, DIA contains both MS1 and MS2 at high quantitative quality. DIA profiles of complex biological matrices such as tissues or cells can contain quantitative interferences, and the interferences at the MS1 and the MS2 signals are often independent. When comparing biological conditions, the interferences can compromise the detection of differentia...
Source: Molecular and Cellular Proteomics : MCP - December 30, 2019 Category: Molecular Biology Authors: Huang T, Bruderer R, Muntel J, Xuan Y, Vitek O, Reiter L Tags: Mol Cell Proteomics Source Type: research

Thorough performance evaluation of 213 nm ultraviolet photodissociation for top-down proteomics.
Abstract Top-down proteomics studies intact proteoform mixtures and offers important advantages over more common bottom-up proteomics technologies, as it avoids the protein inference problem. However, achieving complete molecular characterization of investigated proteoforms using existing technologies remains a fundamental challenge for top-down proteomics. Here, we benchmark the performance of ultraviolet photodissociation (UVPD) using 213 nm photons generated by a solid-state laser applied to the study of intact proteoforms from three organisms. Notably, the described UVPD setup applies multiple laser pulses to ...
Source: Molecular and Cellular Proteomics : MCP - December 30, 2019 Category: Molecular Biology Authors: Fornelli L, Srzentić K, Toby TK, Doubleday PF, Huguet R, Mullen C, Melani RD, Dos Santos Seckler H, DeHart CJ, Weisbrod CR, Durbin KR, Greer JB, Early BP, Fellers RT, Zabrouskov V, Thomas P, Compton PD, Kelleher NL Tags: Mol Cell Proteomics Source Type: research

Peptidomic analysis of urine from youths with early type 1 diabetes reveals novel bioactivity of uromodulin peptides in vitro.
Abstract Chronic hyperglycemia is known to disrupt the proteolytic milieu, initiating compensatory and maladaptive pathways in the diabetic kidney. Such changes in intrarenal proteolysis are captured by the urinary peptidome. To elucidate the early kidney response to chronic hyperglycemia, we conducted a peptidomic investigation into urines from otherwise healthy youths with type 1 diabetes and their non-diabetic peers using unbiased and targeted mass spectrometry-based techniques. This cross-sectional study included two separate cohorts for the discovery (N = 30) and internal validation (N = 30) of differential p...
Source: Molecular and Cellular Proteomics : MCP - December 26, 2019 Category: Molecular Biology Authors: Van JAD, Clotet-Freixas S, Zhou J, Batruch I, Sun C, Glogauer M, Rampoldi L, Elia Y, Mahmud F, Sochett E, Diamandis EP, Scholey J, Konvalinka A Tags: Mol Cell Proteomics Source Type: research

Upregulation of CD73 Confers Acquired Radioresistance and is Required for Maintaining Irradiation-Selected Pancreatic Cancer Cells in a Mesenchymal State.
Abstract The molecular mechanisms underlying exceptional radioresistance in pancreatic cancer remain elusive. In the present study, we established a stable radioresistant pancreatic cancer cell line MIA PaCa-2-R by exposing the parental MIA PaCa-2 cells to fractionated ionizing radiation (IR). Systematic proteomics and bioinformatics analysis of protein expression in MIA PaCa-2 and MIA PaCa-2-R cells revealed that several growth factor-/cytokine-mediated pathways, including the OSM/STAT3, PI3K/AKT and MAPK/ERK pathways, were activated in the radioresistant cells, leading to inhibition of apoptosis and increased ep...
Source: Molecular and Cellular Proteomics : MCP - December 26, 2019 Category: Molecular Biology Authors: Nguyen AM, Zhou J, Sicairos B, Sonney S, Du Y Tags: Mol Cell Proteomics Source Type: research

Blistering1 modulates Penicillium expansum virulence via vesicle-mediated protein secretion.
Abstract The blue mold fungus, Penicillium expansum, is a postharvest apple pathogen that contributes to food waste by rotting fruit and by producing harmful mycotoxins (e.g. patulin). To identify genes controlling pathogen virulence, a random T-DNA insertional library was created from wild-type P. expansum strain R19. One transformant, T625, had reduced virulence in apples, blistered mycelial hyphae, and a T-DNA insertion that abolished transcription of the single copy locus in which it was inserted.  The gene, Blistering1, encodes a protein with a DnaJ domain, but otherwise has little homology outside the A...
Source: Molecular and Cellular Proteomics : MCP - December 23, 2019 Category: Molecular Biology Authors: Jurick WM, Peng H, Beard HS, Garrett WM, Lichtner FJ, Luciano-Rosario D, Macarisin O, Liu Y, Peter KA, Gaskins VL, Yang T, Mowery J, Bauchan G, Keller N, Cooper B Tags: Mol Cell Proteomics Source Type: research

Molecular Basis of the Mechanisms controlling MASTL.
Abstract The human MASTL (Microtubule-associated serine/threonine kinase-like) gene encodes an essential protein in the cell cycle. MASTL is a key factor preventing early dephosphorylation of M-phase targets of Cdk1/CycB. Little is known about the mechanism of MASTL activation and regulation. MASTL contains a non-conserved insertion of 550 residues within its activation loop, splitting the kinase domain, and making it unique. Here, we show that this non-conserved middle region (NCMR) of the protein is crucial for target specificity and activity. We performed a phosphoproteomic assay with different MASTL constructs...
Source: Molecular and Cellular Proteomics : MCP - December 18, 2019 Category: Molecular Biology Authors: Hermida D, Mortuza GB, Pedersen AK, Pozdnyakova I, Nguyen TTTN, Maroto M, Williamson M, Ebersole T, Cazzamali G, Rand KD, Olsen JV, Malumbres M, Montoya G Tags: Mol Cell Proteomics Source Type: research

Proteomic analysis reveals Topoisomerase 2A is associated with defective sperm head morphology.
Abstract Male infertility is widespread and estimated to affect 1 in 20 men. Whilst in some cases the aetiology of the condition is well understood, for at least 50% of men, the underlying cause is yet to be classified. Male infertility, or sub-fertility, is often diagnosed by looking at total sperm produced, motility of the cells and overall morphology. Whilst counting spermatozoa and their associated motility is routine, morphology assessment is highly subjective, mainly due to the procedure being based on microscopic examination. A failure to diagnose male-infertility or sub-fertility has led to a situation whe...
Source: Molecular and Cellular Proteomics : MCP - December 17, 2019 Category: Molecular Biology Authors: Netherton JK, Ogle RA, Hetherington L, Silva Balbin Villaverde AI, Hondermarck H, Baker MA Tags: Mol Cell Proteomics Source Type: research

Advances in Tools to Determine the Glycan-Binding Specificities of Lectins and Antibodies.
Abstract Proteins that bind carbohydrate structures can serve as tools to quantify or localize specific glycans in biological specimens. Such proteins, including lectins and glycan-binding antibodies, are particularly valuable if accurate information is available about the glycans that a protein binds. Glycan arrays have been transformational for uncovering rich information about the nuances and complexities of glycan-binding specificity. A challenge, however, has been the analysis of the data. Because protein-glycan interactions are so complex, simplistic modes of analyzing the data and describing glycan-binding ...
Source: Molecular and Cellular Proteomics : MCP - December 17, 2019 Category: Molecular Biology Authors: Haab B, Klamer Z Tags: Mol Cell Proteomics Source Type: research

Mass spectrometry based immunopeptidomics leads to robust predictions of phosphorylated HLA class I ligands.
r D Abstract The presentation of peptides on class I human leukocyte antigen (HLA-I) molecules plays a central role in immune recognition of infected or malignant cells. In cancer, non-self HLA-I ligands can arise from many different alterations, including non-synonymous mutations, gene fusion, cancer-specific alternative mRNA splicing or aberrant post-translational modifications. Identifying HLA-I ligands remains a challenging task that requires either heavy experimental work for in-vivo identification or optimized bioinformatics tools for accurate predictions. To date, no HLA-I ligand predictor includes post-tra...
Source: Molecular and Cellular Proteomics : MCP - December 17, 2019 Category: Molecular Biology Authors: Solleder M, Guillaume P, Racle J, Michaux J, Pak HS, Müller M, Coukos G, Bassani-Sternberg M, Gfeller D Tags: Mol Cell Proteomics Source Type: research

Phosphoproteomic Approaches to Discover Novel Substrates of Mycobacterial Ser/Thr Protein Kinases.
Abstract Mycobacterial Ser/Thr protein kinases (STPKs) play a critical role in signal transduction pathways that ultimately determine mycobacterial growth and metabolic adaptation. Identification of key physiological substrates of these protein kinases is, therefore, crucial to better understand how Ser/Thr phosphorylation contributes to mycobacterial environmental adaptation, including response to stress, cell division and host-pathogen interactions. Various substrate detection methods have been employed with limited success, with direct targets of STPKs remaining elusive. Recently developed mass spectrometry (MS...
Source: Molecular and Cellular Proteomics : MCP - December 15, 2019 Category: Molecular Biology Authors: Baros SS, Blackburn JM, Da Cruz Soares NA Tags: Mol Cell Proteomics Source Type: research

MaXLinker: proteome-wide cross-link identifications with high specificity and sensitivity.
Abstract Protein-protein interactions play a vital role in nearly all cellular functions. Hence, understanding their interaction patterns and three-dimensional structural conformations can provide crucial insights about various biological processes and underlying molecular mechanisms for many disease phenotypes. Cross-linking mass spectrometry (XL-MS) has the unique capability to detect protein-protein interactions at a large scale along with spatial constraints between interaction partners. The inception of MS-cleavable cross-linkers enabled the MS2-MS3 XL-MS acquisition strategy that provides cross-link informat...
Source: Molecular and Cellular Proteomics : MCP - December 15, 2019 Category: Molecular Biology Authors: Yugandhar K, Wang TY, Leung AK, Lanz MC, Motorykin I, Liang J, Shayhidin EE, Smolka MB, Zhang S, Yu H Tags: Mol Cell Proteomics Source Type: research

Multi-omic characterisation of the mode of action of a potent new antimalarial compound, JPC-3210, against Plasmodium falciparum.
Abstract The increasing incidence of antimalarial drug resistance to the first-line artemisinin combination therapies underpins an urgent need for new antimalarial drugs, ideally with a novel mode of action. The recently developed 2-aminomethylphenol, JPC-3210, (MMV 892646) is an erythrocytic schizonticide with potent in vitro antimalarial activity against multidrug-resistant Plasmodium falciparum lines, low cytotoxicity, potent in vivo efficacy against murine malaria, and favourable preclinical pharmacokinetics including a lengthy plasma elimination half-life. To investigate the impact of JPC-3210 on biochemical ...
Source: Molecular and Cellular Proteomics : MCP - December 13, 2019 Category: Molecular Biology Authors: Birrell GW, Challis MP, De Paoli A, Anderson D, Devine SM, Heffernan GD, Jacobus DP, Edstein MD, Siddiqui G, Creek DJ Tags: Mol Cell Proteomics Source Type: research

Next-generation interactomics: considerations for the use of co-elution to measure protein interaction networks.
Abstract Understanding how proteins interact is crucial to understanding cellular processes. Among the available interactome mapping methods, co-elution stands out as a method that is simultaneous in nature and capable of identifying interactions between all the proteins detected in a sample. The general workflow in co-elution methods involves the mild extraction of protein complexes and their separation into a number of fractions, across which proteins bound together in the same complex will show similar co-elution profiles when analyzed appropriately. In this review we discuss the different separation, quantific...
Source: Molecular and Cellular Proteomics : MCP - December 2, 2019 Category: Molecular Biology Authors: Salas D, Stacey RG, Akinlaja M, Foster LJ Tags: Mol Cell Proteomics Source Type: research

Profiling the surfaceome identifies therapeutic targets for cells with hyperactive mTORC1 signaling.
Abstract Aberrantly high mTORC1 signaling is a known driver of many cancers and human disorders, yet pharmacological inhibition of mTORC1 rarely confers durable clinical responses. To explore alternative therapeutic strategies, herein we conducted a proteomics survey to identify cell surface proteins upregulated by mTORC1. A comparison of the surfaceome from Tsc1-/- versus Tsc1+/+ mouse embryonic fibroblasts revealed 59 proteins predicted to be significantly overexpressed in Tsc1-/- cells. Further validation of the data in multiple mouse and human cell lines showed that mTORC1 signaling most dramatically induced t...
Source: Molecular and Cellular Proteomics : MCP - December 2, 2019 Category: Molecular Biology Authors: Wei J, Leung K, Truillet C, Ruggero D, Wells J, Evans MJ Tags: Mol Cell Proteomics Source Type: research

Interaction proteomics identifies estrogen receptor beta association with multiple chromatin repressive complexes to inhibit cholesterol biosynthesis and exert an oncosuppressive role in triple-negative breast cancer.
Abstract Triple-negative breast cancer (TNBC) is characterized by poor response to therapy and low overall patient survival. Recently, Estrogen Receptor beta (ERβ) has been found to be expressed in a fraction of TNBCs where, due to its oncosuppressive actions on the genome, it represents a potential therapeutic target, provided a better understanding of its actions in these tumors becomes available. To this end, the cell lines Hs 578T, MDA-MB-468 and HCC1806, representing the claudin-low, basal-like 1 and 2 TNBC molecular subtypes respectively, were engineered to express ERβ under the control of a Tetrac...
Source: Molecular and Cellular Proteomics : MCP - December 2, 2019 Category: Molecular Biology Authors: Alexandrova E, Giurato G, Saggese P, Pecoraro G, Lamberti J, Ravo M, Rizzo F, Rocco D, Tarallo R, Nyman TA, Collina F, Cantile M, Di Bonito M, Botti G, Nassa G, Weisz A Tags: Mol Cell Proteomics Source Type: research

Combined EGFR and ROCK inhibition in TNBC leads to cell death via impaired autophagic flux.
Abstract Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with very limited therapeutic options. We have recently shown that the combined inhibition of EGFR and ROCK in TNBC cells results in cell death, however, the underlying mechanisms remain unclear. To investigate this, here we applied a mass spectrometry-based proteomic approach to identify proteins altered upon single and combination treatments. Our proteomic data revealed autophagy as the major molecular mechanism implicated in the cells' response to combinatorial treatment. In particular, we here show that EGFR inhibition by g...
Source: Molecular and Cellular Proteomics : MCP - November 26, 2019 Category: Molecular Biology Authors: Rontogianni S, Iskit S, van Doorn S, Peeper DS, Altelaar M Tags: Mol Cell Proteomics Source Type: research

Deep Characterization of the Human Antibody Response to Natural Infection Using Longitudinal Immune Repertoire Sequencing.
Abstract Human antibody response studies are largely restricted to periods of high immune activity (e.g., vaccination). To comprehensively understand the healthy B cell immune repertoire and how this changes over time and through natural infection, we conducted immune repertoire RNA sequencing on flow cytometry-sorted B cell subsets to profile a single individual's antibodies over 11 months through two periods of natural viral infection. We found that 1) a baseline of healthy variable (V) gene usage in antibodies exists and is stable over time, but antibodies in memory cells consistently have a different usage pro...
Source: Molecular and Cellular Proteomics : MCP - November 25, 2019 Category: Molecular Biology Authors: Mitsunaga EM, Snyder MP Tags: Mol Cell Proteomics Source Type: research

Citrullinome of Porphyromonas gingivalis Outer Membrane Vesicles: Confident Identification of Citrullinated Peptides.
rup P Abstract Porphyromonas gingivalis is a key pathogen in chronic periodontitis and has recently been mechanistically linked to the development of rheumatoid arthritis via the activity of peptidyl arginine deiminase generating citrullinated epitopes in the periodontium. In this project the outer membrane vesicles (OMV) from P. gingivalis W83 wild-type (WT), a W83 knock-out mutant of peptidyl arginine deiminase (ΔPPAD), and a mutant strain expressing PPAD with the active site cysteine mutated to alanine (C351A), have been analyzed using a two-dimensional HFBA-based separation system combined with LC-MS. Fo...
Source: Molecular and Cellular Proteomics : MCP - November 21, 2019 Category: Molecular Biology Authors: Larsen DN, Mikkelsen CE, Kierkegaard M, Bereta GP, Nowakowska ZM, Kaczmarek JZ, Potempa J, Højrup P Tags: Mol Cell Proteomics Source Type: research

Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics based on Acid Extraction.
We report a detergent-free method, named Sample Preparation by Easy Extraction and Digestion (SPEED), which consists of three mandatory steps, acidification, neutralization and digestion. SPEED is a universal method for peptide generation from various sources and is easily applicable even for lysis-resistant sample types as pure trifluoroacetic acid (TFA) is used for highly efficient protein extraction by complete sample dissolution. The protocol is highly reproducible, virtually loss-less, enables very rapid sample processing and is superior to the detergent/chaotropic agent-based methods FASP, ISD-Urea and SP3 for quanti...
Source: Molecular and Cellular Proteomics : MCP - November 21, 2019 Category: Molecular Biology Authors: Doellinger J, Schneider A, Hoeller M, Lasch P Tags: Mol Cell Proteomics Source Type: research

The Human Immunopeptidome Project: a roadmap to predict and treat immune diseases.
ron E Abstract The science that investigates the ensembles of all peptides associated to human leukocyte antigen (HLA) molecules is termed "immunopeptidomics" and is typically driven by mass spectrometry (MS) technologies. Recent advances in MS technologies, neoantigen discovery and cancer immunotherapy have catalyzed the launch of the Human Immunopeptidome Project (HIPP) with the goal of providing a complete map of the human immunopeptidome and making the technology so robust that it will be available in every clinic. Here, we provide a long-term perspective of the field and we use this framework to exp...
Source: Molecular and Cellular Proteomics : MCP - November 19, 2019 Category: Molecular Biology Authors: Vizcaíno JA, Kubiniok P, Kovalchik K, Ma Q, Duquette JD, Mongrain I, Deutsch EW, Peters B, Sette A, Sirois I, Caron E Tags: Mol Cell Proteomics Source Type: research

Assessing protein sequence database suitability using de novo sequencing.
We describe the use of automated de novo sequencing for evaluating both the quality of a collection of tandem mass spectra and the suitability of a given protein sequence database for searching that data. Applications of this method include the proteome analysis of closely related species, metaproteomics, and proteomics of extinct organisms. PMID: 31732549 [PubMed - as supplied by publisher] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - November 15, 2019 Category: Molecular Biology Authors: Johnson R, Searle BC, Nunn BL, Gilmore JM, Phillips M, Amemiya CT, Heck M, MacCoss MJ Tags: Mol Cell Proteomics Source Type: research

Mitochondrial oxidative phosphorylation complex regulates NLRP3 inflammasome activation and predicts patient survival in nasopharyngeal carcinoma.
In this study, we used proteomic iTRAQ analysis to analyze the proteomes of NPC cells that differ in their ASC speck formation upon cisplatin treatment. We identified proteins that were differentially over-expressed in cells with specks, and found that they fell into two Gene ontology (GO) pathways: mitochondrial oxidative phosphorylation (OxPhos) and ubiquinone metabolism. We observed up-regulation of various components of the OxPhos machinery (including NDUFB3, NDUFB8 and ATP5B), and subsequently found that these changes lead to mitochondrial ROS (mtROS) production, which promotes the formation and activation of NLRP3 in...
Source: Molecular and Cellular Proteomics : MCP - November 13, 2019 Category: Molecular Biology Authors: Chung IC, Chen LC, Tsang NM, Chuang WY, Liao TC, Yuan SN, OuYang CN, Ojcius DM, Wu CC, Chang YS Tags: Mol Cell Proteomics Source Type: research

Reproducibility, specificity and accuracy of relative quantification using spectral library-based data-independent acquisition.
Abstract Currently data-dependent acquisition (DDA) is the method of choice for mass spectrometry-based proteomics discovery experiments, but data-independent acquisition (DIA) is steadily becoming more important. One of the most important requirements to perform a DIA analysis is the availability of suitable spectral libraries for peptide identification and quantification. Several studies were performed addressing the evaluation of spectral library performance for protein identification in DIA measurements. But so far only few experiments estimate the effect of these libraries on the quantitative level.In this wo...
Source: Molecular and Cellular Proteomics : MCP - November 7, 2019 Category: Molecular Biology Authors: Barkovits K, Pacharra S, Pfeiffer K, Steinbach S, Eisenacher M, Marcus K, Uszkoreit J Tags: Mol Cell Proteomics Source Type: research

The proteome of the dentate terminal zone of the perforant path indicates presynaptic impairment in Alzheimer disease.
Abstract Synaptic dysfunction is an early pathogenic event in Alzheimer disease (AD) that contributes to network disturbances and cognitive decline. Some synapses are more vulnerable than others, including the synapses of the perforant path, which provides the main excitatory input to the hippocampus. To elucidate the molecular mechanisms underlying the dysfunction of these synapses, we performed an explorative proteomic study of the dentate terminal zone of the perforant path. The outer two-thirds of the molecular layer of the dentate gyrus, where the perforant path synapses are located, was microdissected from f...
Source: Molecular and Cellular Proteomics : MCP - November 7, 2019 Category: Molecular Biology Authors: Haytural H, Mermelekas G, Emre C, Nigam SM, Carroll SL, Winblad B, Bogdanovic N, Barthet G, Granholm AC, Orre LM, Tjernberg LO, Frykman S Tags: Mol Cell Proteomics Source Type: research

Proteomic analysis reveals a role for RSK in p120-catenin phosphorylation and melanoma cell-cell adhesion.
In this study, we used a proximity-based labeling approach to identify RSK proximity partners in cells. We identified many potential RSK interacting proteins, including p120ctn (p120-catenin), which is an essential component of adherens junction (AJ). We found that RSK phosphorylates p120ctn on Ser320, which appears to be constitutively phosphorylated in melanoma cells. We also found that RSK inhibition increases melanoma cell-cell adhesion, suggesting that constitutive RAS/MAPK signaling negatively regulates AJ integrity. Together, our results indicate that RSK plays an important role in the regulation of melanoma cell-ce...
Source: Molecular and Cellular Proteomics : MCP - November 2, 2019 Category: Molecular Biology Authors: Meant A, Gao B, Lavoie G, Nourreddine S, Jung F, Aubert L, Tcherkezian J, Gingras AC, Roux PP Tags: Mol Cell Proteomics Source Type: research

Proteomics profiling of autologous blood and semen exosomes from HIV-infected and uninfected individuals reveals compositional and functional variabilities.
Abstract Blood and semen are important body-fluids that carry exosomes for bioinformation transmission. Therefore, characterization of their proteomes is necessary for understanding body-fluid-specific physiologic and pathophysiologic functions. Using systematic multifactorial proteomic profiling, we characterized the proteomes of exosomes and exosome-free fractions from autologous blood and semen from three HIV-uninfected and three HIV-infected participants (total of 24 samples). We identified exosome-based protein signatures specific to blood and semen along with HIV-induced tissue-dependent proteomic perturbati...
Source: Molecular and Cellular Proteomics : MCP - November 1, 2019 Category: Molecular Biology Authors: Kaddour H, Lyu Y, Welch JL, Paromov V, Mandape SN, Sakhare SS, Pandhare J, Stapleton JT, Pratap S, Dash C, Okeoma CM Tags: Mol Cell Proteomics Source Type: research

The mitochondrial acyl-carrier protein interaction network highlights important roles for LYRM family members in complex I and mitoribosome assembly.
Abstract NDUFAB1 is the mitochondrial acyl carrier protein (ACP) essential for cell viability. Through its pantetheine-4'-phosphate post-translational modification, NDUFAB1 interacts with members of the leucine-tyrosine-arginine motif (LYRM) protein family. Although a number of LYRM proteins have been described to participate in a variety of defined processes, the functions of others remain either partially or entirely unknown. We profiled the interaction network of NDUFAB1 to reveal associations with 9 known LYRM proteins as well as more than 20 other proteins involved in mitochondrial respiratory chain complex a...
Source: Molecular and Cellular Proteomics : MCP - October 30, 2019 Category: Molecular Biology Authors: Dibley MG, Formosa LE, Lyu B, Reljic B, McGann D, Muellner-Wong L, Kraus F, Sharpe AJ, Stroud DA, Ryan MT Tags: Mol Cell Proteomics Source Type: research

Immune signature against Plasmodium falciparum antigens predicts clinical immunity in distinct malaria endemic communities.
In this study, using samples collected from young children in Ghana at multiple time points during a longitudinal study, we adapted a predictive modelling framework which combines feature selection and machine learning techniques to identify an antigen signature of clinical immunity to malaria. Our results show that an individual's immune status can be accurately predicted by measuring antibody responses to a small defined set of 15 target antigens. We further demonstrate that the identified immune signature is highly versatile and capable of providing precise and accurate estimates of clinical protection from malaria in a...
Source: Molecular and Cellular Proteomics : MCP - October 28, 2019 Category: Molecular Biology Authors: Proietti C, Krause L, Trieu A, Dodoo D, Gyan B, Koram KA, Rogers WO, Richie TL, Crompton P, Felgner P, Doolan D Tags: Mol Cell Proteomics Source Type: research

PACAP and other neuropeptides link chronic migraine and opioid-induced hyperalgesia in mouse models.
Abstract Chronic use of opioids can produce opioid-induced hyperalgesia (OIH), and when used to treat migraine, these drugs can result in increased pain and headache chronicity. We hypothesized that overlapping mechanisms between OIH and chronic migraine occur through neuropeptide dysregulation. Using label-free, non-biased liquid chromatography-mass spectrometry to identify and measure changes in more than 1500 neuropeptides under these two conditions, we observed only 16 neuropeptides that were altered between the two conditions. The known pro-migraine molecule, calcitonin-gene related peptide, was among seven p...
Source: Molecular and Cellular Proteomics : MCP - October 24, 2019 Category: Molecular Biology Authors: Anapindi KDB, Yang N, Romanova EV, Rubakhin SS, Tipton A, Dripps I, Sheets Z, Sweedler JV, Pradhan AA Tags: Mol Cell Proteomics Source Type: research

Sample preparation scale-up for deep N-glycomic analysis of human serum by capillary electrophoresis and CE-ESI-MS.
Abstract We introduce an efficient sample preparation workflow to facilitate deep N-glycomics analysis of the human serum by capillary electrophoresis with laser induced fluorescence (CE-LIF) detection and to accommodate the higher sample concentration requirement of electrospray ionization mass spectrometry connected to capillary electrophoresis (CE-ESI-MS). A novel, temperature gradient denaturing protocol was applied on amine functionalized magnetic bead partitioned glycoproteins to circumvent the otherwise prevalent precipitation issue. During this process, the free sugar content of the serum was significantly...
Source: Molecular and Cellular Proteomics : MCP - October 18, 2019 Category: Molecular Biology Authors: Szigeti M, Guttman A Tags: Mol Cell Proteomics Source Type: research

Why glycosylation matters in building a better flu vaccine.
Abstract Low vaccine efficacy against seasonal influenza A virus (IAV) stems from the ability of the virus to evade existing immunity while maintaining fitness. While most potent neutralizing antibodies bind antigenic sites on the globular head domain of the IAV envelope glycoprotein hemagglutinin (HA), the error-prone IAV polymerase enables rapid evolution of key antigenic sites, resulting in immune escape.  Significantly, the appearance of new N-glycosylation consensus sequences (sequons, NXT/NXS, rarely NXC) on the HA globular domain occurs among the more prevalent mutations as an IAV strain undergoes anti...
Source: Molecular and Cellular Proteomics : MCP - October 11, 2019 Category: Molecular Biology Authors: Chang D, Zaia J Tags: Mol Cell Proteomics Source Type: research

DECA, a comprehensive, automatic post-processing program for HDX-MS data.
Abstract Amide hydrogen-deuterium exchange mass spectrometry (HDX-MS) has become widely popular for mapping protein-ligand interfaces, for understanding protein-protein interactions, and for discovering dynamic allostery. Several platforms are now available which provide large datasets of amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) data. Although many of these platforms provide some down-stream processing, a comprehensive software that provides  the most commonly used down-stream processing tools such as automatic back-exchange correction options, analysis of overlapping peptides, calculation...
Source: Molecular and Cellular Proteomics : MCP - October 8, 2019 Category: Molecular Biology Authors: Lumpkin R, Komives EA Tags: Mol Cell Proteomics Source Type: research