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Molecular & Cellular Proteomics: MCP

Christina Schiza, Dimitrios Korbakis, Keith Jarvi, Eleftherios P Diamandis, Andrei P Drabovich
TEX101 is a germ cell-specific protein and a validated biomarker of male infertility. Mouse TEX101 was found essential for male fertility, and was suggested to function as a cell surface chaperone involved in maturation of proteins required for sperm migration and sperm-oocyte interaction. However, the precise functional role of human TEX101 is not known and cannot be studied in vitro due to the lack of human germ cell lines. Here, we genotyped 386 men for a common missense variant rs35033974 of TEX101, and identified 52 heterozygous and 4 homozygous men...
November 14, 2018: Molecular & Cellular Proteomics: MCP
Zhi-Wu An, Linhui Zhai, Wantao Ying, Xiaohong Qian, Fuzhong Gong, Minjia Tan, Yan Fu
The open (mass tolerant) search of tandem mass spectra of peptides shows great potential in the comprehensive detection of post-translational modifications (PTMs) in shotgun proteomics. However, this search strategy has not been widely used by the community, and one bottleneck of it is the lack of appropriate algorithms for automated and reliable post-processing of the coarse and error-prone search results. Here we present PTMiner, a software tool for confident filtering and localization of modifications (mass shifts) detected in an open search...
November 12, 2018: Molecular & Cellular Proteomics: MCP
Shivantika Bisen, David Kakhniashvili, Daniel L Johnson, Anna N Bukiya
Alcohol is one of the most widely misused substances in the world. Alcohol consumption by pregnant women often results in an array of fetal developmental abnormalities, but the damage to the fetus by alcohol remains poorly understood. The limited knowledge regarding the molecular targets of alcohol in the developing fetus constitutes one of the major obstacles in developing effective pharmacological interventions that could prevent fetal damage after alcohol consumption by pregnant women. The fetal cerebral artery is emerging as an important mediator of fetal cerebral damage by maternal alcohol drinking...
November 9, 2018: Molecular & Cellular Proteomics: MCP
Lu-Guang Jiang, Bo Li, Sheng-Xue Liu, Hong-Wei Wang, Cui-Ping Li, Shu-Hui Song, Mary Beatty, Gina Zastrow-Hayes, Xiao-Hong Yang, Feng Qin, Yan He
The success of modern maize breeding has been demonstrated by remarkable increases in productivity with tremendous modification of agricultural phenotypes over the last century. Although the underlying genetic changes of the maize adaptation from tropical to temperate regions have been extensively studied, our knowledge is limited regarding the accordance of protein and mRNA expression levels accompanying such adaptation. Here we conducted an integrative analysis of proteomic and transcriptomic changes in a maize association panel...
November 8, 2018: Molecular & Cellular Proteomics: MCP
Satu-Marja Myllymäki, Ulla-Reetta Kämäräinen, Xiaonan Liu, Sara Pereira Cruz, Sini Miettinen, Mikko Vuorela, Markku Varjosalo, Aki Manninen
Integrin-mediated laminin adhesions mediate epithelial cell anchorage to basement membranes and are critical regulators of epithelial cell polarity. Integrins assemble large multiprotein complexes that link to the cytoskeleton and convey signals into the cells. Comprehensive proteomic analyses of actin network-linked focal adhesions (FA) have been performed, but the molecular composition of intermediate filament-linked hemidesmosomes (HD) remains incompletely characterized. Here we have utilized proximity-dependent biotin identification (BioID) technology to label and characterize the interactome of epithelia-specific β4-integrin that, as α6β4-heterodimer, forms the core of HDs...
November 7, 2018: Molecular & Cellular Proteomics: MCP
Jeremy D Volkening, Kelly E Stecker, Michael R Sussman
Modern tandem MS-based sequencing technologies allow for the parallel measurement of concentration and covalent modifications for proteins within a complex sample. Recently, this capability has been extended to probe a proteome's three-dimensional structure and conformational state by determining the thermal denaturation profile of thousands of proteins simultaneously. While many animals and their resident microbes exist under a relatively narrow, regulated physiological temperature range, plants take on the often widely ranging temperature of their surroundings, possibly influencing the evolution of protein thermal stability...
November 6, 2018: Molecular & Cellular Proteomics: MCP
Florian Meier, Andreas-David Brunner, Scarlet Koch, Heiner Koch, Markus Lubeck, Michael Krause, Niels Goedecke, Jens Decker, Thomas Kosinski, Melvin A Park, Nicolai Bache, Ole Hoerning, Jürgen Cox, Oliver Räther, Matthias Mann
In bottom-up proteomics, peptides are separated by liquid chromatography with elution peak widths in the range of seconds, while mass spectra are acquired in about 100 microseconds with time-of-flight (TOF) instruments. This allows adding ion mobility as a third dimension of separation. Among several formats, trapped ion mobility spectrometry (TIMS) is attractive due to its small size, low voltage requirements and high efficiency of ion utilization. We have recently demonstrated a scan mode termed parallel accumulation - serial fragmentation (PASEF), which multiplies the sequencing speed without any loss in sensitivity (Meier et al...
November 1, 2018: Molecular & Cellular Proteomics: MCP
Daiki Kobayashi, Takaho Tokuda, Kyosuke Sato, Hiroki Okanishi, Megumi Nagayama, Mio Hirayama, Sumio Ohtsuki, Norie Araki
Neurofibromatosis type 1 (NF1) is an autosomal dominant disease that predisposes individuals to developing benign neurofibromas and malignant peripheral nerve sheath tumors (MPNST). The mechanism of NF1-tumorigenesis or the curatives have not been established. Using unique trascriptome and proteome integration method, iPEACH (1), we previously identified translationally controlled tumor protein (TCTP) as a novel biological target for NF1-associated tumors (2). Here, we identified specific TCTP-interacting proteins by sequential affinity purification and data-independent mass spectrometry acquisition (AP-DIA/SWATH), to investigate the role of TCTP in NF1-associated malignant tumors...
October 31, 2018: Molecular & Cellular Proteomics: MCP
Sergey I Kovalchuk, Ole N Jensen, Adelina Rogowska-Wrzesinska
Capillary ultra-high-pressure liquid chromatography (cUHPLC) is essential for in-depth characterization of complex biomolecule mixtures by LC-MS. We developed a simple and fast method called FlashPack for custom packing of capillary columns of 50-100 cm length with sub-2-mm sorbent particles. FlashPack uses high sorbent concentrations of 500-1000 mg/ml for packing at relatively low pressure of 100 bar. Column blocking by sorbent aggregation is avoided during the packing by gentle mechanical tapping of the capillary proximal end by a slowly rotating magnet bar...
October 29, 2018: Molecular & Cellular Proteomics: MCP
Etna Abad, Yoelsis García-Mayea, Cristina Mir, David Sebastian, Antonio Zorzano, David Potesil, Zbynek Zdrahal, Alex Lyakhovich, Matilde Lleonart
Cancer cells are known to reprogram their metabolism to adapt to adverse conditions dictated by tumour growth and microenvironment. A subtype of cancer cells with stem-like properties, known as cancer stem cells (CSC), is thought to be responsible for tumour recurrence. In this study, we demonstrated that CSC and chemoresistant cells derived from triple negative breast cancer cells display an enrichment of up- and down-regulated proteins from metabolic pathways that suggests their dependence on mitochondria for survival...
October 29, 2018: Molecular & Cellular Proteomics: MCP
Yinghui Wei, Qian Gao, Pengxia Niu, Kui Xu, Yiqing Qiu, Yanqing Hu, Shasha Liu, Xue Zhang, Miaoying Yu, Zhiguo Liu, Bingyuan Wang, Yulian Mu, Kui Li
Mice lacking wild-type p53-induced phosphatase 1 (Wip1) display male reproductive defects including smaller testes, subfertility and spermatogenesis defects at the round- and elongating-spermatid stages. However the molecular mechanisms underlying these abnormalities remain unclear. Here we examined the proteome and phosphoproteome of testes from Wip1-knockout mice using a quantitative proteomic approach. From a total of 6872 proteins and 4280 phosphorylation sites identified, 58 proteins and 159 phosphorylation sites were found to be differentially regulated compared to wild type mice...
October 25, 2018: Molecular & Cellular Proteomics: MCP
Zujie Yao, Zhuang Guo, Yuqian Wang, Wanxin Li, Yuying Fu, Yuexu Lin, Wenxiong Lin, Xiangmin Lin
Protein modification by lysine succinylation is a newly identified post-translational modification (PTM) of lysine residues and plays an important role in diverse physiological functions, although their associated biological characteristics are still largely unknown. Here, we investigated the effects of lysine succinylation on the physiological regulation within a well-known fish pathogen, Aeromonas hydrophila. A high affinity purification method was used to enrich peptides with lysine succinylation in A. hydrophilaATCC 7966, and a total of 2,174 lysine succinylation sites were identified on 666 proteins using LC-MS/MS...
October 23, 2018: Molecular & Cellular Proteomics: MCP
Fadi E El-Rami, Ryszard A Zielke, Teodora Wi, Aleksandra E Sikora, Magnus Unemo
The sexually transmitted disease gonorrhea (causative agent: Neisseria gonorrhoeae ) remains an urgent public health threat globally due to its reproductive health repercussions, high incidence, widespread antimicrobial resistance (AMR), and absence of a vaccine. To mine gonorrhea antigens and enhance our understanding of gonococcal AMR at the proteome level, we performed the first large-scale proteomic profiling of a diverse panel (n=15) of gonococcal strains, including the 2016 World Health Organization (WHO) reference strains...
October 23, 2018: Molecular & Cellular Proteomics: MCP
Andrea Goya Grocin, Remigiusz A Serwa, Julia Morales Sanfrutos, Markus Ritzefeld, Edward W Tate
N -myristoylation is the covalent addition of a 14-carbon saturated fatty acid (myristate) to the N-terminal glycine of specific protein substrates by N -myristoyltransferase (NMT) and plays an important role in protein regulation by controlling localization, stability, and interactions. We developed a novel method for whole-proteome profiling of free N-terminal glycines through labeling with S. Aureus sortase A (SrtA) and used it for assessment of target engagement by an NMT inhibitor. Analysis of the SrtA-labeling pattern with an engineered biotinylated depsipeptide SrtA substrate (Biotin-ALPET-Haa, Haa = 2-hydroxyacetamide) enabled whole proteome identification and quantification of de novo generated N-terminal Gly proteins in response to NMT inhibition by nanoLC-MS/MS proteomics, and was confirmed for specific substrates across multiple cell lines by gel-based analyses and ELISA...
October 19, 2018: Molecular & Cellular Proteomics: MCP
Katrin Erich, Kevin Reinle, Torsten Müller, Bogdan Munteanu, Denis A Sammour, Isabel Hinsenkamp, Tobias Gutting, Elke Burgermeister, Peter Findeisen, Matthias P Ebert, Jeroen Krijgsveld, Carsten Hopf
Aberrant protease activity has been implicated in the etiology of various prevalent diseases including neurodegeneration and cancer, in particular metastasis. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) has recently been established as a key technology for bioanalysis of multiple biomolecular classes such as proteins, lipids, and glycans. However, it has not yet been systematically explored for investigation of a tissue's endogenous protease activity. In this study, we demonstrate that different tissues, spray-coated with substance P as a tracer, digest this peptide with different time-course profiles...
October 7, 2018: Molecular & Cellular Proteomics: MCP
Zhe Ren, Da Qi, Pugh Nina, Kai Li, Bo Wen, Ruo Zhou, Shaohang Xu, Siqi Liu, Andrew R Jones
Rice (Oryza sativa) is one of the most important worldwide crops. The genome has been available for over 10 years and has undergone several rounds of annotation. We created a comprehensive database of transcripts from 29 public RNA sequencing datasets, officially predicted genes from Ensembl plants, and common contaminants in which to search for protein-level evidence. We re-analysed nine publicly accessible rice proteomics datasets. In total, we identified 420K peptide spectrum matches from 47K peptides and 8,187 protein groups...
October 6, 2018: Molecular & Cellular Proteomics: MCP
Ryan Arvidson, Maayan Kaiser, Sang Soo Lee, Jean Paul Urenda, Christopher J Dail, Haroun Mohammed, Cebrina Nolan, Song-Qing Pan, Jason E Stajich, Frederic Libersat, Michael E Adams
The parasitoid emerald jewel wasp Ampulex compressa induces a compliant state of hypokinesia in its host, the American cockroach Periplaneta americana through direct envenomation of the central nervous system (CNS). To elucidate the biochemical strategy underlying venom-induced hypokinesia, we subjected the venom apparatus and milked venom to RNAseq and proteomics analyses to construct a comprehensive "venome", consisting of 264 proteins. Abundant in the venome are enzymes endogenous to the host brain, including M13 family metalloproteases, phospholipases, adenosine deaminase, hyaluronidase, and neuropeptide precursors...
October 6, 2018: Molecular & Cellular Proteomics: MCP
Irem Sepil, Ben R Hopkins, Rebecca Dean, Marie-Laëtitia Thézénas, Philip D Charles, Rebecca Konietzny, Roman Fischer, Benedikt Kessler, Stuart Wigby
Seminal fluid contains some of the fastest evolving proteins currently known. These seminal fluid proteins (Sfps) play crucial roles in reproduction, such as supporting sperm function, and particularly in insects, modifying female physiology and behaviour. Identification of Sfps in small animals is challenging, and often relies on samples taken from the female reproductive tract after mating. A key pitfall of this method is that it might miss Sfps that are of low abundance due to dilution in the female-derived sample or rapid processing in females...
October 4, 2018: Molecular & Cellular Proteomics: MCP
Dmitry Malioutov, Tianchi Chen, Edoardo Airoldi, Jacob D Jaffe, Bogdan Budnik, Nikolai Slavov
Many proteoforms - arising from alternative splicing, post-translational modifications (PTM), or paralogous genes - have distinct biological functions, such as histone PTM proteoforms. However, their quantification by existing bottom-up mass-spectrometry (MS) methods is undermined by peptide-specific biases. To avoid these biases, we developed and implemented a first-principles model (HIquant ) for quantifying proteoform stoichiometries. We characterized when MS data allow inferring proteoform stoichiometries by HIquant and derived an algorithm for optimal inference...
October 3, 2018: Molecular & Cellular Proteomics: MCP
Shinya Ohta, Takako Taniguchi, Nobuko Sato, Mayako Hamada, Hisaaki Taniguchi, Juri Rappsilber
In mitosis, chromosomes achieve their characteristic shape through condensation, an essential process for proper segregation of the genome during cell division. A classical model for mitotic chromosome condensation proposes that non-histone proteins act as a structural framework called the chromosome scaffold. The components of the chromosome scaffold, such as DNA topoisomerase IIα(TOP2A) and structural maintenance of chromosomes protein 2 (SMC2), are necessary to generate stable mitotic chromosomes; however, the existence of this scaffold remains controversial...
September 28, 2018: Molecular & Cellular Proteomics: MCP
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