In depth characterization of the Staphylococcus aureus phosphoproteome reveals new targets of Stk1.
Abstract Staphylococcus aureus is a major cause of infections worldwide and infection results in a variety of diseases. As of no surprise, protein phosphorylation is an important game player in signaling cascades and has been shown to be involved in S. aureus virulence. Albeit long neglected, eukaryotic-type serine/threonine kinases in S. aureus have been implicated in this complex signaling cascades. Due to the sub-stoichiometric nature of protein phosphorylation and a lack of suitable analysis tools, the knowledge of these cascades is however, to date, still limited. Here, were apply an optimized protocol for ef...
Source: Molecular and Cellular Proteomics : MCP - January 11, 2021 Category: Molecular Biology Authors: Prust N, van der Laarse S, van den Toorn H, van Sorge NM, Lemeer S Tags: Mol Cell Proteomics Source Type: research

Plasma proteomes can be re-identifiable and potentially contain personally sensitive and incidental findings.
Abstract The goal of clinical proteomics is to identify, quantify, and characterize proteins in body fluids or tissue to assist diagnosis, prognosis, and treatment of patients. In this way, it is similar to more mature omics technologies, such as genomics, that are increasingly applied in biomedicine. We argue that, similar to those fields, proteomics also faces ethical issues related to the kinds of information that is inherently obtained through sample measurement, although their acquisition was not the primary purpose. Specifically, we demonstrate the potential to identify individuals both by their characterist...
Source: Molecular and Cellular Proteomics : MCP - January 11, 2021 Category: Molecular Biology Authors: Geyer PE, Mann SP, Treit PV, Mann M Tags: Mol Cell Proteomics Source Type: research

Ethical principles, opportunities and constraints in clinical proteomics.
Abstract Recent advances in MS-based proteomics have vastly increased the quality and scope of biological information that can be derived from human samples. These advances have rendered current workflows increasingly applicable in biomedical and clinical contexts. As proteomics is poised to take an important role in the clinic, associated ethical responsibilities increase in tandem with the impact on the health, privacy, and well-being of individuals. Here we conducted and report a systematic literature review of ethical issues in clinical proteomics. We add our perspectives from a background of bioethics, the re...
Source: Molecular and Cellular Proteomics : MCP - January 4, 2021 Category: Molecular Biology Authors: Porsdam Mann S, Treit PV, Geyer PE, Omenn GS, Mann M Tags: Mol Cell Proteomics Source Type: research

Separation and identification of permethylated glycan isomers by reversed phase nanoLC-NSI-MSn.
We report baseline separation and MSn fragmentation of isomeric N- and O-glycan structures, aided by supplementing mobile phases with Li+, which simplifies adduct heterogeneity and facilitates cross-ring fragmentation to obtain valuable monosaccharide linkage information. Our workflow has been adapted from standard proteomics-based workflows and, therefore, provides opportunities for laboratories with expertise in proteomics to acquire glycomic data with minimal deviation from existing buffer systems, chromatography media, and instrument configurations. Furthermore, our workflow does not require a mass spectrometer with hi...
Source: Molecular and Cellular Proteomics : MCP - December 29, 2020 Category: Molecular Biology Authors: Kurz S, Sheikh MO, Lu S, Wells L, Tiemeyer M Tags: Mol Cell Proteomics Source Type: research

High-throughput and site-specific N-glycosylation analysis of human alpha-1-acid glycoprotein offers a great potential for new biomarker discovery.
Abstract Alpha-1-acid glycoprotein (AGP) is an acute phase glycoprotein in blood, which is primarily synthetized in the liver and whose biological role is not completely understood. It consists of 45% carbohydrates that are present in the form of five N-linked complex glycans. AGP N-glycosylation was shown to be changed in many different diseases and some changes appear to be disease-specific, thus it has a great diagnostic and prognostic potential. However, AGP glycosylation was mainly analyzed in small cohorts and without detailed site-specific glycan information. Here, we developed a cost-effective method for a...
Source: Molecular and Cellular Proteomics : MCP - December 29, 2020 Category: Molecular Biology Authors: Keser T, Tijardović M, Gornik I, Lukic E, Lauc G, Gornik O, Novokmet M Tags: Mol Cell Proteomics Source Type: research

Global lysine acetylation and 2-hydroxyisobutyrylation reveal the metabolism conversion mechanism in Giardia lamblia.
This study aimed to reveal the dynamic metabolism-conversion mechanism in G. lamblia under sugar starvation by detecting global lysine acetylation and 2-hydroxyisobutyrylation sites combined with quantitative proteome analyses. A total of 2999 acetylation sites on 956 proteins and 8877 2-hydroxyisobutyryl sites on 1546 proteins were quantified under sugar starvation. Integrated Kac and Khib data revealed that modified proteins were associated with arginine biosynthesis, glycolysis/gluconeogenesis, and alanine, aspartate, and glutamate metabolism. These findings suggested that lysine acetylation and 2-hydroxyisobutyrylation...
Source: Molecular and Cellular Proteomics : MCP - December 29, 2020 Category: Molecular Biology Authors: Zhu W, Jiang X, Sun H, Li Y, Shi W, Zheng M, Liu D, Ma A, Feng X Tags: Mol Cell Proteomics Source Type: research

The role of Data-Independent Acquisition for Glycoproteomics.
Abstract Data independent acquisition (DIA) is now an emerging method in bottom-up proteomics and capable of achieving deep proteome coverage and accurate label-free quantification. However, for post-translational modifications (PTM), such as glycosylation, DIA methodology is still in the early stage of development. The full characterization of glycoproteins requires site specific glycan identification as well as subsequent quantification of glycan structures at each site. The tremendous complexity of glycosylation represents a significant analytical challenge in glycoproteomics. This review focuses on the develop...
Source: Molecular and Cellular Proteomics : MCP - December 28, 2020 Category: Molecular Biology Authors: Ye Z, Vakhrushev SY Tags: Mol Cell Proteomics Source Type: research

Interspecies differences in proteome turnover kinetics are correlated with lifespans and energetic demands.
Abstract Cells continually degrade and replace damaged proteins. However, the high energetic demand of protein turnover generates reactive oxygen species (ROS) that compromise the long-term health of the proteome. Thus, the relationship between aging, protein turnover and energetic demand remains unclear. Here, we used a proteomic approach to measure rates of protein turnover within primary fibroblasts isolated from a number of species with diverse lifespans including the longest-lived mammal, the bowhead whale. We show that organismal lifespan is negatively correlated with turnover rates of highly abundant protei...
Source: Molecular and Cellular Proteomics : MCP - December 28, 2020 Category: Molecular Biology Authors: Swovick K, Firsanov D, Welle KA, Hryhorenko J, Wise JP, George C, Sformo TL, Seluanov A, Gorbunova V, Ghaemmaghami S Tags: Mol Cell Proteomics Source Type: research

Unraveling the MAX2 Protein Network in Arabidopsis thaliana: Identification of the Protein Phosphatase PAPP5 as a Novel MAX2 Interactor.
Abstract The F-box protein MORE AXILLARY GROWTH 2 (MAX2) is a central component in the signaling cascade of strigolactones (SLs) as well as of the smoke derived karrikins (KARs) and the so far unknown endogenous KAI2 ligand (KL). The two groups of molecules are involved in overlapping and unique developmental processes, and signal-specific outcomes are attributed to perception by the paralogous α/β-hydrolases DWARF14 (D14) for SL and KARRIKIN INSENSITIVE 2/ HYPOSENSITIVE TO LIGHT (KAI2/HTL) for KAR/KL. Additionally, depending on which receptor is activated, specific members of the SUPPRESSOR OF MAX2 1 (...
Source: Molecular and Cellular Proteomics : MCP - December 28, 2020 Category: Molecular Biology Authors: Struk S, De Cuyper C, Jacobs A, Braem L, Walton A, De Keyser A, Depuydt S, Vu LD, De Smet I, Boyer FD, Eeckhout D, Persiau G, Gevaert K, De Jaeger G, Goormachtig S Tags: Mol Cell Proteomics Source Type: research

Identification of novel serological autoantibodies in Takayasu arteritis patients using HuProt arrays.
Abstract To identify novel autoantibodies of Takayasu arteritis (TAK) using HuProt array-based approach. A two-phase approach was adopted. In Phase I, serum samples collected from 40 TAK patients, 15 autoimmune disease patients, and 20 healthy subjects were screened to identify TAK-specific autoantibodies using human protein (HuProt) arrays. In Phase II, the identified candidate autoantibodies were validated with TAK-focused arrays using an additional cohort comprised of 109 TAK patients, 110 autoimmune disease patients, and 96 healthy subjects. Subsequently, the TAK-specific autoantibodies validated in Phase II w...
Source: Molecular and Cellular Proteomics : MCP - December 17, 2020 Category: Molecular Biology Authors: Wen XT, Song G, Hu CJ, Pan J, Wu ZY, Li L, Liu C, Tian X, Zhang FC, Qian J, Zhu H, Li YZ Tags: Mol Cell Proteomics Source Type: research

In depth characterization of the Staphylococcus aureus phosphoproteome reveals new targets of Stk1.
Abstract Staphylococcus aureus is a major cause of infections worldwide and infection results in a variety of diseases. As of no surprise, protein phosphorylation is an important game player in signaling cascades and has been shown to be involved in S. aureus virulence. Albeit long neglected, eukaryotic-type serine/threonine kinases in S. aureus have been implicated in this complex signaling cascades. Due to the sub-stoichiometric nature of protein phosphorylation and a lack of suitable analysis tools, the knowledge of these cascades is however, to date, still limited.Here, were apply an optimized protoc...
Source: Molecular and Cellular Proteomics : MCP - December 17, 2020 Category: Molecular Biology Authors: Prust N, van der Laarse SAM, van den Toorn H, van Sorge NM, Lemeer S Tags: Mol Cell Proteomics Source Type: research

Plasma proteomic data can contain personally identifiable, sensitive information and incidental findings.
Abstract The goal of clinical proteomics is to identify, quantify, and characterize proteins in body fluids or tissue to assist diagnosis, prognosis, and treatment of patients. In this way, it is similar to more mature omics technologies, such as genomics, that are increasingly applied in biomedicine. We argue that, similar to those fields, proteomics also faces ethical issues related to the kinds of information that is inherently obtained through sample measurement, although their acquisition was not the primary purpose. Specifically, we demonstrate the potential to identify individuals both by their characterist...
Source: Molecular and Cellular Proteomics : MCP - December 17, 2020 Category: Molecular Biology Authors: Geyer PE, Porsdam Mann S, Treit PV, Mann M Tags: Mol Cell Proteomics Source Type: research

A potential role  for the Gsdf-eEF1α complex in inhibiting germ cell proliferation: A protein-interaction analysis in medaka (Oryzias latipes) from a proteomics perspective.
A potential role for the Gsdf-eEF1α complex in inhibiting germ cell proliferation: A protein-interaction analysis in medaka (Oryzias latipes) from a proteomics perspective. Mol Cell Proteomics. 2020 Dec 08;: Authors: Zhang X, Chang Y, Zhai W, Qian F, Zhang Y, Xu S, Guo H, Wang S, Hu R, Zhong X, Zhao X, Chen L, Guan G Abstract Gonadal soma-derived factor (gsdf) has been demonstrated to be essential for testicular differentiation in medaka (Oryzias latipes). To understand the protein dynamics of Gsdf in spermatogenesis regulation, we used a His-tag "pull-down" assay coupled with sho...
Source: Molecular and Cellular Proteomics : MCP - December 8, 2020 Category: Molecular Biology Authors: Zhang X, Chang Y, Zhai W, Qian F, Zhang Y, Xu S, Guo H, Wang S, Hu R, Zhong X, Zhao X, Chen L, Guan G Tags: Mol Cell Proteomics Source Type: research

A proteomics-based assessment of inflammation signatures in endotoxemia.
In conclusion, the rise in multimeric PTX3 upon LPS injection correlates with neutrophil-related protein changes in plasma and in aortas. MPO and myeloid Nox2 are not required for the multimerisation of PTX3; instead, neutrophil extravasation is responsible for the LPS-induced deposition of multimeric PTX3 in the aorta. PMID: 33288685 [PubMed - as supplied by publisher] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - December 7, 2020 Category: Molecular Biology Authors: Burnap SA, Mayr U, Shankar-Hari M, Cuello F, Thomas MR, Shah AM, Sabroe I, Storey RF, Mayr M Tags: Mol Cell Proteomics Source Type: research

The peptide vaccine of the future.
Abstract The approach of peptide-based anti-cancer vaccination has proven the ability to induce cancer-specific immune responses in multiple studies for various cancer entities. However, clinical responses remain so far limited to single patients and broad clinical applicability was not achieved. Therefore, further efforts are required to improve peptide vaccination in order to integrate this low side effect therapy into the clinical routine of cancer therapy. To design clinically effective peptide vaccines in the future, different issues have to be addressed and optimized comprising antigen target selection as we...
Source: Molecular and Cellular Proteomics : MCP - December 7, 2020 Category: Molecular Biology Authors: Nelde A, Rammensee HG, Walz JS Tags: Mol Cell Proteomics Source Type: research

The Mechanism of NEDD8 Activation of CUL5 Ubiquitin E3 Ligases.
Abstract Cullin RING E3 Ligases (CRLs) ubiquitylate hundreds of important cellular substrates. Here we have assembled and purified the Ankyrin repeat and SOCS Box protein 9 CUL5 RBX2 Ligase (ASB9-CRL) in vitro and show how it ubiquitylates one of its substrates, CKB. CRLs occasionally collaborate with RING between RING E3 ligases (RBRLs) and indeed, mass spectrometry analysis showed that CKB is specifically ubiquitylated by the ASB9-CRL-ARIH2-UBE2L3 complex. Addition of other E2s such as UBE2R1 or UBE2D2 contribute to polyubiquitylation but do not alter the sites of CKB ubiquitylation. Hydrogen-deuterium exchange ...
Source: Molecular and Cellular Proteomics : MCP - December 2, 2020 Category: Molecular Biology Authors: Lumpkin RJ, Ahmad AS, Blake R, Condon CJ, Komives EA Tags: Mol Cell Proteomics Source Type: research

PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results.
Abstract Open searching has proven to be an effective strategy for identifying both known and unknown modifications in shotgun proteomics experiments. Rather than being limited to a small set of user-specified modifications, open searches identify peptides with any mass shift that may correspond to a single modification or a combination of several modifications. Here we present PTM-Shepherd, a bioinformatics tool that automates characterization of PTM profiles detected in open searches based on attributes such as amino acid localization, fragmentation spectra similarity, retention time shifts, and relative modific...
Source: Molecular and Cellular Proteomics : MCP - December 1, 2020 Category: Molecular Biology Authors: Geiszler DJ, Kong AT, Avtonomov DM, Yu F, da Veiga Leprevost F, Nesvizhskii AI Tags: Mol Cell Proteomics Source Type: research

Proteomic analyses identify differentially expressed proteins and pathways between low-risk and high-risk subtypes of early-stage lung adenocarcinoma and their prognostic impacts.
In conclusion, we discovered key differentially expressed proteins and pathways between low-risk and high-risk subtypes of early-stage LUAD. Some of these proteins could serve as potential biomarkers in prognostic evaluation. PMID: 33257500 [PubMed - as supplied by publisher] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - November 30, 2020 Category: Molecular Biology Authors: Zhou J, Liu B, Li Z, Li Y, Chen X, Ma Y, Yan S, Yang X, Zhong L, Wu N Tags: Mol Cell Proteomics Source Type: research

Proteome Turnover in the Spotlight: Approaches, Applications & Perspectives.
Proteome Turnover in the Spotlight: Approaches, Applications & Perspectives. Mol Cell Proteomics. 2020 Nov 30;: Authors: Ross AB, Langer JD, Jovanovic M Abstract In all cells, proteins are continuously synthesized and degraded in order to maintain protein homeostasis and modify gene expression levels in response to stimuli. Collectively, the processes of protein synthesis and degradation are referred to as protein turnover. At steady state, protein turnover is constant to maintain protein homeostasis, but in dynamic responses, proteins change their rates of synthesis and degradation in order to ad...
Source: Molecular and Cellular Proteomics : MCP - November 30, 2020 Category: Molecular Biology Authors: Ross AB, Langer JD, Jovanovic M Tags: Mol Cell Proteomics Source Type: research

A proteomic approach to understand the clinical significance of acute myeloid leukemia-derived extracellular vesicles reflecting essential characteristics of leukemia.
Abstract Extracellular vesicle (EV) proteins from acute myeloid leukemia (AML) cell lines were analyzed using mass spectrometry. The analyses identified 2450 proteins, including 461 differentially expressed proteins (290 upregulated and 171 downregulated). CD53 and CD47 were upregulated and were selected as candidate biomarkers. The association between survival of patients with AML and the expression levels of CD53 and CD47 at diagnosis was analyzed using mRNA expression data from The Cancer Genome Atlas database. Patients with higher expression levels showed significantly inferior survival than those with lower e...
Source: Molecular and Cellular Proteomics : MCP - November 30, 2020 Category: Molecular Biology Authors: Kang KW, Kim H, Hur W, Jung JH, Jeong SJ, Shin H, Seo D, Jeong H, Choi B, Hong S, Kim HK, Choi Y, Park JH, Lee KY, Kim KP, Park Y Tags: Mol Cell Proteomics Source Type: research

Prediction and validation of mouse meiosis-essential genes based on spermatogenesis proteome dynamics.
Abstract The molecular mechanism associated with mammalian meiosis has yet to be fully explored, and one of the main reasons for this lack of exploration is that some meiosis-essential genes are still unknown. The profiling of gene expression during spermatogenesis has been performed in previous studies, yet few studies have aimed to find new functional genes. Since there is a huge gap between the number of genes that are able to be quantified and the number of genes that can be characterized by phenotype screening in one assay, an efficient method to rank quantified genes according to phenotypic relevance is of g...
Source: Molecular and Cellular Proteomics : MCP - November 30, 2020 Category: Molecular Biology Authors: Fang K, Li Q, Wei Y, Zhou C, Guo W, Shen J, Wu R, Ying W, Yu L, Zi J, Zhang Y, Yang H, Liu S, Chen CD Tags: Mol Cell Proteomics Source Type: research

Imaging Mass Spectrometry and Lectin Analysis of N-linked Glycans in Carbohydrate Antigen Defined Pancreatic Cancer Tissues.
Abstract The early detection of pancreatic ductal adenocarcinoma is a complex clinical obstacle yet is key to improving the overall likelihood of patient survival. Current and prospective carbohydrate biomarkers CA19-9 and sTRA are sufficient for surveilling disease progression yet are not approved for delineating PDAC from other abdominal cancers and non-cancerous pancreatic pathologies. To further understand these glycan epitopes, an imaging mass spectrometry approach was utilized to assess the N-glycome of the human pancreas and pancreatic cancer in a cohort of PDAC patients represented by tissue microarrays an...
Source: Molecular and Cellular Proteomics : MCP - November 24, 2020 Category: Molecular Biology Authors: McDowell CT, Klamer Z, Hall J, West CA, Wisniewski L, Powers TW, Angel P, Mehta AS, Lewin DN, Haab B, Drake R Tags: Mol Cell Proteomics Source Type: research

Proteogenomic characterization of the pathogenic fungus Aspergillus flavus reveals novel genes involved in aflatoxin production.
Abstract Aspergillus flavus (A. flavus), a pathogenic fungus, can produce carcinogenic and toxic aflatoxins that are a serious agricultural and medical threat worldwide. Attempts to decipher the aflatoxin biosynthetic pathway have been hampered by the lack of a high-quality genome annotation for A. flavus. To address this gap, we performed a comprehensive proteogenomic analysis using high-accuracy mass spectrometry data for this pathogen. The resulting high-quality dataset confirmed the translation of 8,724 previously-predicted genes, and identified 732 novel proteins, 269 splice variants, 447 single amino acid va...
Source: Molecular and Cellular Proteomics : MCP - November 24, 2020 Category: Molecular Biology Authors: Yang M, Zhu Z, Zhuang Z, Bai Y, Wang S, Ge F Tags: Mol Cell Proteomics Source Type: research

Proteome analysis reveals a significant host-specific response in Rhizobium leguminosarum bv viciae endosymbiotic cells.
o T, Palacios J Abstract The Rhizobium-legume symbiosis is a beneficial interaction in which the bacterium converts atmospheric nitrogen into ammonia and delivers it to the plant in exchange for carbon compounds. This symbiosis implies the adaptation of bacteria to live inside host plant cells. In this work we apply RP-LC-MS/MS and  iTRAQ techniques to study the proteomic profile of endosymbiotic cells (bacteroids) induced by Rhizobium leguminosarum bv viciae strain UPM791 in legume nodules. Nitrogenase subunits, tricarboxylic acid cycle enzymes, and stress response proteins are amongst the most abundant...
Source: Molecular and Cellular Proteomics : MCP - November 19, 2020 Category: Molecular Biology Authors: Durán D, Albareda M, Marina A, García C, Ruiz-Argüeso T, Palacios J Tags: Mol Cell Proteomics Source Type: research

Thyroglobulin interactome profiling defines altered proteostasis topology associated with thyroid dyshormonogenesis.
Abstract Thyroglobulin (Tg) is a secreted iodoglycoprotein serving as the precursor for T3 and T4 hormones. Many characterized Tg gene mutations produce secretion-defective variants resulting in congenital hypothyroidism (CH). Tg processing and secretion is controlled by extensive interactions with chaperone, trafficking, and degradation factors comprising the secretory proteostasis network. While dependencies on individual proteostasis network components are known, the integration of proteostasis pathways mediating Tg protein quality control and the molecular basis of mutant Tg misprocessing remain poorly underst...
Source: Molecular and Cellular Proteomics : MCP - November 18, 2020 Category: Molecular Biology Authors: Wright MT, Kouba L, Plate L Tags: Mol Cell Proteomics Source Type: research

Quantitative proteomics reveal neuron projection development genes ARF4, KIF5B and RAB8A associated with Hirschsprung disease.
Abstract Hirschsprung disease (HSCR) is a heterogeneous group of neurocristopathy characterized by the absence of the enteric ganglia along a variable length of the intestine. Genetic defects play a major role in the pathogenesis of HSCR while family studies of pathogenic variants in all the known genes (loci) only demonstrate incomplete penetrance and variable expressivity for unknown reasons. Here, we applied large-scale, quantitative proteomics of human colon tissues from 21 patients using iTRAQ method followed by bioinformatics analysis. Selected findings were confirmed by parallel reaction monitoring (PRM) ve...
Source: Molecular and Cellular Proteomics : MCP - November 17, 2020 Category: Molecular Biology Authors: Zhang Q, Wu L, Bai B, Li D, Xiao P, Li Q, Zhang Z, Wang H, Li L, Jiang Q Tags: Mol Cell Proteomics Source Type: research

Accelerating the field of epigenetic histone modification through mass spectrometry-based approaches.
Abstract Histone post-translational modifications (PTMs) are one of the main mechanisms of epigenetic regulation. Dysregulation of histone PTMs leads to many human diseases, such as cancer. Due to its high-throughput, accuracy, and flexibility, mass spectrometry (MS) has emerged as a powerful tool in the epigenetic histone modification field, allowing the comprehensive and unbiased analysis of histone PTMs and chromatin-associated factors. Coupled with various techniques from molecular biology, biochemistry, chemical biology and biophysics, MS has been employed to characterize distinct aspects of histone PTMs in t...
Source: Molecular and Cellular Proteomics : MCP - November 17, 2020 Category: Molecular Biology Authors: Lu C, Coradin M, Porter EG, Garcia BA Tags: Mol Cell Proteomics Source Type: research

Proteomic identification of Coxiella burnetii effector proteins targeted to the host cell mitochondria during infection.
Abstract Modulation of the host cell is integral to the survival and replication of microbial pathogens. Several intracellular bacterial pathogens deliver bacterial proteins, termed 'effector proteins' into the host cell during infection by sophisticated protein translocation systems, which manipulate cellular processes and functions. The functional contribution of individual effectors is poorly characterised, particularly in intracellular bacterial pathogens with large effector protein repertoires. Technical caveats have limited the capacity to study these proteins during a native infection, with many effector pr...
Source: Molecular and Cellular Proteomics : MCP - November 11, 2020 Category: Molecular Biology Authors: Fielden LF, Scott NE, Palmer CS, Khoo CA, Newton HJ, Stojanovski D Tags: Mol Cell Proteomics Source Type: research

Peptidomics-driven strategy reveals peptides and predicted proteases associated with oral cancer prognosis.
e AFP Abstract Protease activity has been associated with pathological processes that can lead to cancer development and progression. However, understanding the pathological unbalance in proteolysis is challenging since changes can occur simultaneously at protease, their inhibitor and substrate levels. Here, we present a pipeline that combines peptidomics, proteomics and peptidase predictions for studying proteolytic events in the saliva of seventy-nine patients and their association with oral squamous cell carcinoma (OSCC) prognosis. Our findings revealed differences in the saliva peptidome of patients with (pN+)...
Source: Molecular and Cellular Proteomics : MCP - November 11, 2020 Category: Molecular Biology Authors: Neves LX, Granato DC, Busso-Lopes AF, Carnielli CM, Patroni FMS, De Rossi T, Oliveira AK, Ribeiro ACP, Brandão TB, Rodrigues AN, Lacerda PA, Uno M, Cervigne NK, Santos-Silva AR, Kowalski LP, Lopes MA, Leme AFP Tags: Mol Cell Proteomics Source Type: research

On the robustness of graph-based clustering to random network alterations.
Abstract Biological functions emerge from complex and dynamic networks of protein-protein interactions. Because these protein-protein interaction networks, or interactomes, represent pairwise connections within a hierarchically organized system, it is often useful to identify higher-order associations embedded within them, such as multi-member protein complexes. Graph-based clustering techniques are widely used to accomplish this goal, and dozens of field-specific and general clustering algorithms exist. However, interactomes can be prone to errors, especially when inferred from high-throughput biochemical assays....
Source: Molecular and Cellular Proteomics : MCP - November 4, 2020 Category: Molecular Biology Authors: Stacey RG, Skinnider MA, Foster LJ Tags: Mol Cell Proteomics Source Type: research

Protein modification characteristics of the malaria parasite Plasmodium falciparum and the infected erythrocytes.
Abstract Malaria elimination is still pending on the development of novel tools that rely on a deep understanding of parasite biology. Proteins of all living cells undergo a myriad number of posttranslational modifications (PTMs) that are critical to multifarious life processes. An extensive proteome-wide dissection revealed a fine PTM map of most proteins in both Plasmodium falciparum, the causative agent of severe malaria, and the infected red blood cells. More than two-thirds of proteins of the parasite and its host cell underwent extensive and dynamic modification throughout the erythrocytic developmental stag...
Source: Molecular and Cellular Proteomics : MCP - November 4, 2020 Category: Molecular Biology Authors: Wang J, Jiang N, Sang X, Yang N, Feng Y, Chen R, Wang X, Chen Q Tags: Mol Cell Proteomics Source Type: research

Isolation of acetylated and unmodified protein N-terminal peptides by strong cation exchange chromatographic separation of TrypN-digested peptides.
Abstract We developed a simple and rapid method to enrich protein N-terminal peptides, in which the protease TrypN is first employed to generate protein N-terminal peptides without Lys or Arg and internal peptides with two positive charges at their N-termini, and then the N-terminal peptides with or without N-acetylation are separated from the internal peptides by strong cation exchange chromatography according to a retention model based on the charge/orientation of peptides. This approach was applied to 20 μg of human HEK293T cell lysate proteins to profile the N-terminal proteome. On average, 1,550 acetylated...
Source: Molecular and Cellular Proteomics : MCP - November 2, 2020 Category: Molecular Biology Authors: Chang CH, Chang HY, Rappsilber J, Ishihama Y Tags: Mol Cell Proteomics Source Type: research

The complexity and dynamics of the tissue glycoproteome associated with prostate cancer progression.
In conclusion, integrated glycomics and glycoproteomics have enabled new insight into the complexity and dynamics of the tissue glycoproteome associated with PCa progression generating an important resource to explore the underpinning disease mechanisms. PMID: 33127837 [PubMed - as supplied by publisher] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - October 30, 2020 Category: Molecular Biology Authors: Kawahara R, Recuero S, Srougi M, Leite KRM, Thaysen-Andersen M, Palmisano G Tags: Mol Cell Proteomics Source Type: research

Blockade of High-Fat Diet Proteomic Phenotypes using Exercise as Prevention or Treatment.
Abstract The increasing consumption of high-fat foods combined with a lack of exercise is a major contributor to the burden of obesity in humans. Aerobic exercise such as running is known to provide metabolic benefits, but how the over-consumption of a high fat diet (HFD) and exercise interact is not well characterized at the molecular level. Here, we examined the plasma proteome in mice for the effects of aerobic exercise as both a treatment and as a preventative regime for animals on either HFD or a healthy control diet. This analysis detected large changes in the plasma proteome induced by the HFD, such as incr...
Source: Molecular and Cellular Proteomics : MCP - October 29, 2020 Category: Molecular Biology Authors: Martinez-Huenchullan SF, Shipsey I, Hatchwell L, Min D, Twigg SM, Larance M Tags: Mol Cell Proteomics Source Type: research

Thermal proteome profiling in zebrafish reveals effects of napabucasin on retinoic acid metabolism.
Abstract Thermal proteome profiling (TPP) allows for the unbiased detection of drug - target protein engagements in vivo. Traditionally, one cell type is used for TPP studies, with the risk of missing important differentially expressed target proteins. The use of whole organisms would circumvent this problem. Zebrafish embryos are amenable to such an approach. Here, we used TPP on whole zebrafish embryo lysate to identify protein targets of napabucasin, a compound that may affect Signal transducer and activator of transcription 3 (Stat3) signaling through an ill-understood mechanism. In zebrafish embryos, napabuca...
Source: Molecular and Cellular Proteomics : MCP - October 28, 2020 Category: Molecular Biology Authors: Leijten NM, Bakker P, Spaink HP, den Hertog J, Lemeer S Tags: Mol Cell Proteomics Source Type: research

Antibody binding epitope Mapping (AbMap) of hundred antibodies in a single run.
Abstract Antibodies play essential roles in both diagnostics and therapeutics. Epitope mapping is essential to understand how an antibody works and to protect intellectual property. Given the millions of antibodies for which epitope information is lacking, there is a need for high-throughput epitope mapping. To address this, we developed a strategy, Antibody binding epitope Mapping (AbMap), by combining a phage displayed peptide library with next generation sequencing. Using AbMap, profiles of the peptides bound by 202 antibodies were determined in a single test, and linear epitopes were identified for>50% of t...
Source: Molecular and Cellular Proteomics : MCP - October 27, 2020 Category: Molecular Biology Authors: Qi H, Ma M, Hu C, Xu ZW, Wu FL, Wang N, Lai DY, Li Y, Zhang H, Jiang HW, Meng QF, Guo S, Kang Y, Zhao X, Li H, Tao SC Tags: Mol Cell Proteomics Source Type: research

N-glycomic signature of stage II colorectal cancer and its association with the tumor microenvironment.
We report here the N-glycosylation signatures of the different cell populations in a group of stage II CRC tissue samples. The cancer cells, compared to normal epithelial cells, have increased levels of sialylation and high-mannose glycans, as well as decreased levels of fucosylation and highly branched N-glycans. When looking at the interface between cancer and its microenvironment, it seems that the cancer N-glycosylation signature spreads into the surrounding stroma at the invasive front of the tumor. This finding was more outspoken in patients with a worse outcome within this sample group. PMID: 33082215 [PubMed -...
Source: Molecular and Cellular Proteomics : MCP - October 20, 2020 Category: Molecular Biology Authors: Boyaval F, Van Zeijl R, Dalebout H, Holst S, van Pelt GW, Fariña-Sarasqueta A, Mesker WE, Tollenaar R, Morreau H, Wuhrer M, Heijs B Tags: Mol Cell Proteomics Source Type: research

Transcriptome and secretome analysis of intra-mammalian life-stages of the emerging helminth pathogen, Calicophoron daubneyi reveals adaptation to a unique host environment.
Abstract Paramphistomosis, caused by the rumen fluke, Calicophoron daubneyi, is a parasitic infection of ruminant livestock which has seen a rapid rise in prevalence throughout Western Europe in recent years. Following ingestion of metacercariae (parasite cysts) by the mammalian host, newly-excysted juveniles (NEJs) emerge and invade the duodenal submucosa which causes significant pathology in heavy infections. The immature larvae then migrate upwards, along the gastrointestinal tract, and enter the rumen where they mature and begin to produce eggs. Despite their emergence, and sporadic outbreaks of acute disease,...
Source: Molecular and Cellular Proteomics : MCP - October 20, 2020 Category: Molecular Biology Authors: Huson KM, Atcheson E, Oliver NAM, Best P, Barley JP, Hanna REB, McNeilly TN, Fang Y, Haldenby S, Paterson S, Robinson MW Tags: Mol Cell Proteomics Source Type: research

Site-specific N-glycosylation Characterization of Recombinant SARS-CoV-2 Spike Proteins.
Abstract The glycoprotein spike (S) on the surface of SARS-CoV-2 is a determinant for viral invasion and host immune response. Herein, we characterized the site-specific N-glycosylation of S protein at the level of intact glycopeptides. All 22 potential N-glycosites were identified in the S-protein protomer and were found to be preserved among the 753 SARS-CoV-2 genome sequences. The glycosites exhibited glycoform heterogeneity as expected for a human cell-expressed protein subunit. We identified masses that correspond to 157 N-glycans, primarily of the complex type. In contrast, the insect cell-expressed S protei...
Source: Molecular and Cellular Proteomics : MCP - October 19, 2020 Category: Molecular Biology Authors: Zhang Y, Zhao W, Mao Y, Chen Y, Wang S, Zhong Y, Su T, Gong M, Du D, Lu X, Cheng J, Yang H Tags: Mol Cell Proteomics Source Type: research

Systematic Proteome and Lysine Succinylome Analysis Reveals the Enhanced Cell Migration by Hyposuccinylation in Esophageal Squamous Cell Cancer.
Abstract Esophageal squamous cell cancer (ESCC) is an aggressive malignancy with poor therapeutic outcomes. However, the alterations in proteins and post-translational modifications (PTMs) leading to the pathogenesis of ESCC remains unclear. Here, we provide the comprehensive characterization of the proteome, phosphorylome, lysine acetylome and succinylome for ESCC and matched control cells using quantitative proteomic approach. We identify abnormal protein and post-translational modification (PTM) pathways, including significantly downregulated lysine succinylation sites in cancer cells. Focusing on hyposuccinyla...
Source: Molecular and Cellular Proteomics : MCP - October 19, 2020 Category: Molecular Biology Authors: Guo Z, Pan F, Peng L, Tian S, Jiao J, Liao L, Lu C, Zhai G, Wu Z, Dong H, Xu X, Wu J, Chen P, Bai X, Lin D, Xu LY, Li EM, Zhang K Tags: Mol Cell Proteomics Source Type: research

OpenPepXL: An open-source tool for sensitive identification of cross-linked peptides in XL-MS.
Abstract Cross-linking mass spectrometry (XL-MS) has been recognized as an effective source of information about protein structures and interactions. In contrast to regular peptide identification, XL-MS has to deal with a quadratic search space, where peptides from every protein could potentially be cross-linked to any other protein. To cope with this search space, most tools apply different heuristics for search space reduction. We introduce a new open-source XL-MS database search algorithm, OpenPepXL, which offers increased sensitivity compared to other tools. OpenPepXL searches the full search space of an XL-MS...
Source: Molecular and Cellular Proteomics : MCP - October 16, 2020 Category: Molecular Biology Authors: Netz E, Dijkstra TMH, Sachsenberg T, Zimmermann L, Walzer M, Monecke T, Ficner R, Dybkov O, Urlaub H, Kohlbacher O Tags: Mol Cell Proteomics Source Type: research

Chromatin proteomics to study epigenetics - challenges and opportunities.
Abstract Regulation of gene expression is essential for the functioning of all eukaryotic organisms. Understanding gene expression regulation requires determining which proteins interact with regulatory elements in chromatin. Mass spectrometry-based analysis of chromatin has emerged as a powerful tool to identify proteins associated with gene regulation, as it allows studying protein function and protein complex formation in their in vivo chromatin-bound context. Total chromatin isolated from cells can be directly analysed using mass spectrometry or further fractionated into transcriptionally active and inactive c...
Source: Molecular and Cellular Proteomics : MCP - October 15, 2020 Category: Molecular Biology Authors: Mierlo GV, Vermeulen M Tags: Mol Cell Proteomics Source Type: research

Spatially resolved activity-based proteomic profiles of the murine small intestinal lipases.
Abstract Despite the crucial function of the small intestine in nutrient uptake our understanding of the molecular events underlying the digestive function is still rudimentary. Recent studies demonstrated that enterocytes do not direct the entire dietary triacylglycerol toward immediate chylomicron synthesis. Especially after high-fat challenges, parts of the resynthesized triacylglycerol are packaged into cytosolic lipid droplets for transient storage in the endothelial layer of the small intestine. The reason for this temporary storage of triacylglycerol is not completely understood. To utilize lipids from cyto...
Source: Molecular and Cellular Proteomics : MCP - October 6, 2020 Category: Molecular Biology Authors: Schittmayer M, Vujic N, Darnhofer B, Korbelius M, Honeder S, Kratky D, Birner-Gruenberger R Tags: Mol Cell Proteomics Source Type: research

ProAlanase is an effective alternative to trypsin for proteomics applications and disulfide bond mapping.
In this study we characterize ProAlanase, a protease from the fungus Aspergillus niger that cleaves primarily on the C-terminal side of proline and alanine residues. ProAlanase achieves high proteolytic activity and specificity when digestion is carried out at acidic pH (1.5) for relatively short (2 h) time periods. To elucidate the potential of ProAlanase in proteomics applications, we conducted a series of investigations comprising comparative multi-enzymatic profiling of a human cell line proteome, histone PTM analysis, ancient bone protein identification, phosphosite mapping and de novo sequencing of a proline-rich pro...
Source: Molecular and Cellular Proteomics : MCP - October 4, 2020 Category: Molecular Biology Authors: Samodova D, Hosfield CM, Cramer CN, Giuli MV, Cappellini E, Franciosa G, Rosenblatt M, Kelstrup CD, Olsen JV Tags: Mol Cell Proteomics Source Type: research

Novel proteomic profiling of epididymal extracellular vesicles in the domestic cat reveals proteins related to sequential sperm maturation with differences observed between normospermic and teratospermic individuals.
Abstract Extracellular vesicles (EVs) secreted by the epididymal epithelium transfer to spermatozoa key proteins that are essential in promoting motility and subsequent fertilization success. Using the domestic cat model, the objectives were to (1) characterize and compare protein content of EVs between segments of the epididymis, and (2) compare EV protein compositions between normo- and teratospermic individuals (producing>60% of abnormal spermatozoa). Epididymal EVs from adult cats were isolated and assessed via liquid chromatography tandem mass spectrometry. Both male types shared 3,008 proteins in total, w...
Source: Molecular and Cellular Proteomics : MCP - October 1, 2020 Category: Molecular Biology Authors: Rowlison T, Cleland TP, Ottinger MA, Comizzoli P Tags: Mol Cell Proteomics Source Type: research

Correction: Concentration Determination of > 200 Proteins in Dried Blood Spots for Biomarker Discovery and Validation.
Correction: Concentration Determination of>200 Proteins in Dried Blood Spots for Biomarker Discovery and Validation. Mol Cell Proteomics. 2020 Oct;19(10):1738 Authors: Eshghi A, Pistawka AJ, Liu J, Chen M, Sinclair NJT, Hardie DB, Elliott M, Chen L, Newman R, Mohammed Y, Borchers CH PMID: 33004661 [PubMed] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - September 30, 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

Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in silico Peptide Mass Libraries.
Abstract Over the past decade, modern methods of mass spectrometry (MS) have emerged that allow reliable, fast and cost-effective identification of pathogenic microorganisms. While MALDI-TOF MS has already revolutionized the way microorganisms are identified, recent years have witnessed also substantial progress in the development of liquid chromatography (LC)-MS based proteomics for microbiological applications. For example, LC-tandem mass spectrometry (LC-MS2) has been proposed for microbial characterization by means of multiple discriminative peptides that enable identification at the species, or sometimes at t...
Source: Molecular and Cellular Proteomics : MCP - September 29, 2020 Category: Molecular Biology Authors: Lasch P, Schneider A, Blumenscheit C, Doellinger J Tags: Mol Cell Proteomics Source Type: research

Glycomics, Glycoproteomics and Glycogenomics: an Inter-Taxa Evolutionary Perspective.
Abstract Glycosylation is a highly diverse set of co- and post-translational modification of proteins. For mammalian glycoproteins, glycosylation is often site-, tissue- and species-specific, and diversified by microheterogeneity. Multitudinous biochemical, cellular, physiological and organismic effects of their glycans have been revealed, either intrinsic to the carrier proteins or mediated by endogenous reader proteins with carbohydrate recognition domains. Furthermore, glycans frequently form the first line of access by or defense from foreign invaders, and new roles for nucleocytoplasmic glycosylation are blos...
Source: Molecular and Cellular Proteomics : MCP - September 28, 2020 Category: Molecular Biology Authors: West CM, Malzl D, Hykollari A, Wilson IBH Tags: Mol Cell Proteomics Source Type: research

Kinome Profiling of Primary Endometrial Tumors Using Multiplexed Inhibitor Beads and Mass Spectrometry Identifies SRPK1 As Candidate Therapeutic Target.
an JS Abstract Endometrial carcinoma (EC) is the most common gynecologic malignancy in the United States, with limited effective targeted therapies. Endometrial tumors exhibit frequent alterations in protein kinases, yet only a small fraction of the kinome has been therapeutically explored. To identify kinase therapeutic avenues for EC, we profiled the kinome of endometrial tumors and normal endometrial tissues using Multiplexed Inhibitor Beads and Mass Spectrometry (MIB-MS). Our proteomics analysis identified a network of kinases overexpressed in tumors, including Serine/Arginine-Rich Splicing Factor Kinase 1 (SR...
Source: Molecular and Cellular Proteomics : MCP - September 28, 2020 Category: Molecular Biology Authors: Kurimchak AM, Kumar V, Herrera-Montávez C, Johnson KJ, Srivastava N, Devarajan K, Peri S, Cai KQ, Mantia-Smaldone GM, Duncan JS Tags: Mol Cell Proteomics Source Type: research

Mutation-independent proteomic signatures of pathological progression in murine models of Duchenne muscular dystrophy.
This study provides novel insights into mutation-independent proteomic signatures characteristic of the dystrophic phenotype and its progression with aging. PMID: 32994316 [PubMed - as supplied by publisher] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - September 28, 2020 Category: Molecular Biology Authors: van Westering TLE, Johansson HJ, Hanson B, Coenen-Stass AML, Lomonosova Y, Tanihata J, Motohashi N, Yokota T, Takeda S, Lehtiö J, Wood MJA, El Andaloussi S, Aoki Y, Roberts TC Tags: Mol Cell Proteomics Source Type: research