Proteomes of Leaf ‐Growing Zones in Rice Genotypes with Contrasting Drought Tolerance
AbstractPlants require a distinctive cohort of enzymes to coordinate cell division and expansion. Proteomic analysis now enables interrogation of immature leaf bases where these processes occur. Hence, proteins in tissues sampled from leaves of a drought ‐tolerant rice (IAC1131) are investigated to provide insights into the effect of soil drying on gene expression relative to the drought‐sensitive genotype Nipponbare. Shoot growth zones are dissected to estimate the proportion of dividing cells and extract protein for subsequent tandem mass tags quantitative proteomic analysis. Gene ontology annotations of differential...
Source: Proteomics - April 18, 2019 Category: Biochemistry Authors: Yunqi Wu, Mehdi Mirzaei, Dana Pascovici, Paul A. Haynes, Brian J. Atwell Tags: Research Article Source Type: research

Quantitative, Label ‐Free Proteomics in the Symptomatic Niemann–Pick, Type C1 Mouse Model Using Standard Flow Liquid Chromatography and Thermal Focusing Electrospray Ionization
In this study, alterations are observed in proteins related to fatty acid homeostasis, calcium binding and regulation, lys osomal regulation, and inositol biosynthesis and metabolism, as well as signaling by Rho family GTPases. New observations from this study include altered expression of Pcp2 and Limp2 in Npc1 mutant mice relative to control, with Pcp2 exhibiting multiple isoforms and specific to the cerebella. This s tudy provides valuable insight into pathways altered in the late‐stage pathophysiology of NPC1. (Source: Proteomics)
Source: Proteomics - April 18, 2019 Category: Biochemistry Authors: Melissa R. Pergande, Thu T. A. Nguyen, Carol Haney ‐Ball, Cristin D. Davidson, Stephanie M. Cologna Tags: Research Article Source Type: research

Front Cover: Proteomic and Post ‐Translational Modification Profiling of Exosome‐Mimetic Nanovesicles Compared to Exosomes
DOI:10.1002/pmic.201800161Proteomic profiling of mimetic ‐nanovesicles (M‐NVs) generated from cells reveals a subset of proteins that are highly abundant in M‐NVs. M‐NVs are found to contain proteins associated with membrane and cytosolic components that largely represent the parental cell proteome, whereas the profile of exosomes highlights their endosomally derived origin. In article number1800161, Nasiri Kenari et al. demonstrate the potential advantage of M ‐NVs as an alternative nanocarrier when spontaneous endosomal sorting of therapeutics is limited. (Source: Proteomics)
Source: Proteomics - April 16, 2019 Category: Biochemistry Authors: Amirmohammad Nasiri Kenari, Kenneth Kastaniegaard, David W. Greening, Mitch Shambrook, Allan Stensballe, Lesley Cheng, Andrew F. Hill Tags: Front Cover Source Type: research

Contents: Proteomics 8'19
PROTEOMICS, Volume 19, Issue 8, April 2019. (Source: Proteomics)
Source: Proteomics - April 16, 2019 Category: Biochemistry Tags: Contents Source Type: research

Editorial Board: Proteomics 8'19
PROTEOMICS, Volume 19, Issue 8, April 2019. (Source: Proteomics)
Source: Proteomics - April 16, 2019 Category: Biochemistry Tags: Editorial Board Source Type: research

Standard abbreviations
PROTEOMICS, Volume 19, Issue 8, April 2019. (Source: Proteomics)
Source: Proteomics - April 16, 2019 Category: Biochemistry Tags: Standard abbreviations Source Type: research

Part II: Special Issue on Extracellular Vesicles and Exosomes
PROTEOMICS, Volume 19, Issue 8, April 2019. (Source: Proteomics)
Source: Proteomics - April 16, 2019 Category: Biochemistry Authors: Richard J. Simpson, David W. Greening Tags: Editorial Source Type: research

Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial cells
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - April 14, 2019 Category: Biochemistry Authors: Anil K. Madugundu, Chan Hyun Na, Raja Sekhar Nirujogi, Santosh Renuse, Kwang Pyo Kim, Kathleen H. Burns, Christopher Wilks, Ben Langmead, Shannon E. Ellis, Leonardo Collado ‐Torres, Marc K. Halushka, Min‐Sik Kim, Akhilesh Pandey Tags: Research Article Source Type: research

Improved Methodology for Sensitive and Rapid Quantitative Proteomic Analysis of Adult ‐Derived Mouse Microglia: Application to a Novel In Vitro Mouse Microglial Cell Model
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - April 12, 2019 Category: Biochemistry Authors: Jennifer Guergues, Ping Zhang, Bin Liu, Stanley M. Stevens Tags: Technical Brief Source Type: research

Identification, Quantification and Systems Analysis of Protein N ‐ε Lysine Methylation in Anucleate Blood Platelets
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - April 11, 2019 Category: Biochemistry Authors: Anne D. Rocheleau, Alexander R. Melrose, Jennifer M. Cunliffe, John Klimek, Özgün Babur, Samuel Tassi Yunga, Anh T.P. Ngo, Jiaqing Pang, Larry L. David, Owen J.T. McCarty, Joseph E. Aslan Tags: Dataset Brief Source Type: research

Proteomics Approaches to Define Senescence Heterogeneity and Chemotherapy Response
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - April 10, 2019 Category: Biochemistry Authors: Coralie Petit, Jordan Guillon, Bertrand Toutain, Alice Boissard, Anne Patsouris, Eric Leli èvre, Catherine Guette, Olivier Coqueret Tags: Viewpoint Source Type: research

Downregulation of CENPF Remodels Prostate Cancer Cells and Alters Cellular Metabolism
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - April 8, 2019 Category: Biochemistry Authors: Muhammad Shahid, Minhyung Kim, Min Young Lee, Austin Yeon, Sungyong You, Hyung L. Kim, Jayoung Kim Tags: Research Article Source Type: research

Challenges and Opportunities in Cancer Metabolomics
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - April 5, 2019 Category: Biochemistry Authors: Ashish Kumar, Biswapriya B. Misra Tags: Review Source Type: research

iTRAQ ‐Based Quantitative Proteomic Analysis of Duck Eggshell During Biomineralization
This study provides a new resource for avian eggshell proteomics, and augments the inventory of eggshell matrix proteins that will lead to a deeper understanding of calcitic biomineralization.This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - April 5, 2019 Category: Biochemistry Authors: Feng Zhu, Fan Zhang, Maxwell Hincke, Zhong ‐Tao Yin, Si‐Rui Chen, Ning Yang, Zhuo‐Cheng Hou Tags: Research Article Source Type: research

iTRAQ ‐based quantitative proteomic analysis strengthens transcriptomic subtyping of triple‐negative breast cancer tumors
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - April 5, 2019 Category: Biochemistry Authors: Pascal J ézéquel, Catherine Guette, Hamza Lasla, Wilfried Gouraud, Alice Boissard, Catherine Guérin‐Charbonnel, Mario Campone Tags: Research Article Source Type: research

Unique Protein Profiles of Extracellular Vesicles as Diagnostic Biomarkers for Early and Advanced Non ‐Small Cell Lung Cancer
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - April 5, 2019 Category: Biochemistry Authors: Taixue An, Sihua Qin, Dehua Sun, Yiyao Huang, Yanwei Hu, Shaopeng Li, Han Zhang, Bo Li, Bo Situ, Linmiao Lie, Yingsong Wu, Lei Zheng Tags: Research Article Source Type: research

Front Cover: Quantitative Proteomic Analysis of Low Linolenic Acid Transgenic Soybean Reveals Perturbations of Fatty Acid Metabolic Pathways
DOI:10.1002/pmic.201800379In article numberhttps://doi.org/10.1002/pmic.2018003791800379, Nazrul Islam et al. compare protein profile changes in normal and low linolenic acid transgenic soybeans using high ‐throughput tandem mass tag (TMT) based mass spectrometry. Proteomic analysis of the transgenic line unveils changes in several key enzymes involved in fatty acid metabolism. These results will be important for the understanding how plants adjust their biochemical processes when the genetic makeup changes. (Source: Proteomics)
Source: Proteomics - April 4, 2019 Category: Biochemistry Authors: Nazrul Islam, Philip D. Bates, K. M. Maria John, Hari B. Krishnan, Zhanyuan J. Zhang, Devanand L. Luthria, Savithiry S. Natarajan Tags: Front Cover Source Type: research

Contents: Proteomics 7'19
PROTEOMICS, Volume 19, Issue 7, April 2019. (Source: Proteomics)
Source: Proteomics - April 4, 2019 Category: Biochemistry Tags: Contents Source Type: research

Editorial Board: Proteomics 7'19
PROTEOMICS, Volume 19, Issue 7, April 2019. (Source: Proteomics)
Source: Proteomics - April 4, 2019 Category: Biochemistry Tags: Editorial Board Source Type: research

Standard abbreviations
PROTEOMICS, Volume 19, Issue 7, April 2019. (Source: Proteomics)
Source: Proteomics - April 4, 2019 Category: Biochemistry Tags: Standard abbreviations Source Type: research

Proteomic and Post ‐Translational Modification Profiling of Exosome‐Mimetic Nanovesicles Compared to Exosomes
This study also highlights differences in protein post‐translational modifications among M‐NVs, as distinct from exosomes. Overall this study provides key insights into defining the proteome com position of M‐NVs as a distinct from exosomes, and the potential advantage of M‐NVs as an alternative nanocarrier when spontaneous endosomal sorting of therapeutics are limited. (Source: Proteomics)
Source: Proteomics - April 3, 2019 Category: Biochemistry Authors: Amirmohammad Nasiri Kenari, Kenneth Kastaniegaard, David W. Greening, Mitch Shambrook, Allan Stensballe, Lesley Cheng, Andrew F. Hill Tags: Research Article Source Type: research

DeepFunc: A Deep Learning Framework for Accurate Prediction of Protein Functions from Protein Sequences and Interactions
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - April 2, 2019 Category: Biochemistry Authors: Fuhao Zhang, Hong Song, Min Zeng, Yaohang Li, Lukasz Kurgan, Min Li Tags: Research Article Source Type: research

Removal of serum lipids and lipid ‐derived metabolites to investigate breast cancer cell biology
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 27, 2019 Category: Biochemistry Authors: Viktor Brovkovych, Alyssa Aldrich, Nasi Li, G. Ekin Atilla ‐Gokcumen, Jonna Frasor Tags: Research Article Source Type: research

RAId: Knowledge Integrated Proteomics Web Service with Accurate Statistical Significance Assignment
Mass spectrometry based proteomics starts with identifications of peptides and proteins, which provide the bases for forming the next ‐level hypotheses whose “validations” are often employed for forming even higher level hypotheses and so forth. Scientifically meaningful conclusions are thus attainable only if the number of falsely identified peptides/proteins is accurately controlled. For this reason, we continue to develop RAId in the past decade. RAId employs rigorous statistics for peptides/proteins identification, hence assigning accurateP‐values/E‐values that can be used confidently to control the n...
Source: Proteomics - March 25, 2019 Category: Biochemistry Authors: Aleksey Y. Ogurtsov, Gelio Alves, Yi ‐Kuo Yu Tags: Technical Brief Source Type: research

Multi ‐Omics Profiling for NF1 Target Discovery in Neurofibromin (NF1) Deficient Cells
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 25, 2019 Category: Biochemistry Authors: Rachel Carnes, James A. Mobley, David K. Crossman, Hui Liu, Bruce R. Korf, Robert A. Kesterson, Deeann Wallis Tags: Research Article Source Type: research

Analysis of liver proteome and identification of critical proteins affecting milk fat, protein and lactose metabolism in dariy cattle with iTRAQ
In this study, we investigated the proteomes of liver tissues in three periods of the lactation cycle of Holstein cows by using isobaric tag for relative and absolute quantification (iTRAQ) technique to obtain liver proteome and identify functional proteins/genes involved with milk synthesis in dairy cattle. Based on iTRAQ analysis, we detected 3,252 proteins in the liver tissues (false discovery rate (FDR) ≤ 0.01). We identified 32 differently expressed proteins (DEPs) among the three periods byp‐value
Source: Proteomics - March 23, 2019 Category: Biochemistry Authors: Lingna Xu, Lijun Shi, Lin Liu, Ruobing Liang, Qian Li, Jianguo Li, Bo Han, Dongxiao Sun Tags: Research Article Source Type: research

The Protein Phosphorylation Landscape of Mouse Spermatids During Spermiogenesis
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 22, 2019 Category: Biochemistry Authors: Yan Li, Yiwei Cheng, Tianyu Zhu, Hao Zhang, Wen Li, Yueshuai Guo, Yaling Qi, Xu Chen, Jun Zhang, Jiahao Sha, Zuomin Zhou, Hui Zhu, Xuejiang Guo Tags: Dataset Brief Source Type: research

Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 22, 2019 Category: Biochemistry Authors: Martin Mehnert, Wenxue Li, Chongde Wu, Barbora Salovska, Yansheng Liu Tags: Research Article Source Type: research

Front Cover: On the Need to Develop Guidelines for Characterizing and Reporting Intrinsic Disorder in Proteins
DOI:10.1002/pmic.201800415In the last decades intrinsic disorder has emerged as a prevalent property amongst proteins expressed by organisms in all kingdoms of life. Improving the characterization of protein disorder will allow us to better understand its role in nature and illuminate the Dark Proteome. In article number1800415, Vincent et al. discuss the reasons to establish standard ‐based guidelines to evaluate protein disorder predictions with rigor and reproducibility. (Source: Proteomics)
Source: Proteomics - March 20, 2019 Category: Biochemistry Authors: Michael Vincent, Vladimir N. Uversky, Santiago Schnell Tags: Front Cover Source Type: research

Contents: Proteomics 6'19
PROTEOMICS, Volume 19, Issue 6, March 2019. (Source: Proteomics)
Source: Proteomics - March 20, 2019 Category: Biochemistry Tags: Contents Source Type: research

Editorial Board: Proteomics 6'19
PROTEOMICS, Volume 19, Issue 6, March 2019. (Source: Proteomics)
Source: Proteomics - March 20, 2019 Category: Biochemistry Tags: Editorial Board Source Type: research

Standard abbreviations
PROTEOMICS, Volume 19, Issue 6, March 2019. (Source: Proteomics)
Source: Proteomics - March 20, 2019 Category: Biochemistry Tags: Standard abbreviations Source Type: research

Torches, Candles, Lamps, Lanterns, Flashlights, Spotlights, Night Vision Goggles … You Need Them All to See in Darkness
AbstractArticles assembled in the second part of this Special Issue describe some experimental and computational approaches for the structural and functional characterization of intrinsically disordered proteins. Since these tools represent specialized gear for the focused analysis of various aspects of dark proteome, they can be viewed as torches, candles, lamps, lanterns, flashlights, spotlights, night vision goggles, and other means needed to see in darkness. (Source: Proteomics)
Source: Proteomics - March 20, 2019 Category: Biochemistry Authors: Vladimir N. Uversky Tags: Editorial Source Type: research

Oncogenic and Non ‐Malignant Pancreatic Exosome Cargo Reveal Distinct Expression of Oncogenic and Prognostic Factors Involved in Tumour Invasion and Metastasis
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 20, 2019 Category: Biochemistry Authors: Aikaterini Emmanouilidi, Dino Paladin, David W. Greening, Marco Falasca Tags: Research Article Source Type: research

GPX4 at the Crossroads of Lipid Homeostasis and Ferroptosis
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 19, 2019 Category: Biochemistry Authors: Giovanni C. Forcina, Scott J. Dixon Tags: Review Source Type: research

Quantitative, label ‐free proteomics in the symptomatic Niemann‐Pick, type C1 mouse model using standard flow liquid chromatography and thermal focusing electrospray ionization
This study provides valuable insight to pathways altered in the late‐stage pathophysiology of NPC1.This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 19, 2019 Category: Biochemistry Authors: Melissa R. Pergande, Thu T. A. Nguyen, Carol Haney ‐Ball, Cristin D. Davidson, Stephanie M. Cologna Tags: Research Article Source Type: research

Proteomes of leaf growing zones in rice genotypes with contrasting drought tolerance
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 19, 2019 Category: Biochemistry Authors: Yunqi Wu, Mehdi Mirzaei, Dana Pascovici, Paul A. Haynes, Brian J. Atwell Tags: Research Article Source Type: research

Refining a pathogen's genome to know the enemy better for the winning battles
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 18, 2019 Category: Biochemistry Authors: Hazara Begum Mohammad, Seung ‐Eun Lee, Min‐Sik Kim Tags: Commentary Source Type: research

Fungal Extracellular Vesicles with a Focus on Proteomic Analysis
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 18, 2019 Category: Biochemistry Authors: Mark R Bleackley, Charlotte S Dawson, Marilyn A Anderson Tags: Review Source Type: research

Hsp74/14 ‐3‐3σ Complex Mediates Centrosome Amplification by High Glucose, Insulin, and Palmitic Acid
In conclusion, the results suggest that the experimental treatment triggers centrosome ampl ification via upregulations of expression and binding of 14‐3‐3σ and Hsp74. (Source: Proteomics)
Source: Proteomics - March 14, 2019 Category: Biochemistry Authors: Yu Cheng Lu, Pu Wang, Qi Gui Wu, Rui Kai Zhang, Alice Kong, Yuan Fei Li, Shao Chin Lee Tags: Research Article Source Type: research

Proteogenomic Refinement of the Neomegalonema perideroedesT Genome Annotation
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 13, 2019 Category: Biochemistry Authors: Florian ‐Alexander Herbst, Sandra Cristina Lopes Gonçalves, Tobias Behr, Simon Jon McIlroy, Per Halkjær Nielsen Tags: Dataset Brief Source Type: research

The Nucleotide ‐dependent Interactome of Rice Heterotrimeric G‐Protein α ‐Subunit
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 13, 2019 Category: Biochemistry Authors: Akshaya Kumar Biswal, Evan Wesley Mcconnell, Emily Grace Werth, Shuen ‐Fang Lo, Su‐May Yu, Leslie Hicks, Alan M. Jones Tags: Dataset Brief Source Type: research

A Fast and Economical Sample Preparation Protocol for Interaction Proteomics Analysis
PROTEOMICS, Volume 0, Issue ja, -Not available-. (Source: Proteomics)
Source: Proteomics - March 13, 2019 Category: Biochemistry Authors: Miguel A. Gonzalez ‐Lozano, Frank Koopmans, Iryna Paliukhovich, August B. Smit, Ka Wan Li Tags: Technical Brief Source Type: research

Profiling of Histidine Phosphoproteome in Danio rerio by TiO2 Enrichment
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 13, 2019 Category: Biochemistry Authors: Gao Yan, Hyojin Lee, Oh Kwang Kwon, Zhongyi Cheng, Minjia Tan, Ki ‐Tae Kim, Sangkyu Lee Tags: Dataset Brief Source Type: research

Proteomic Analysis of Horseweed (Conyza canadensis) Subjected to Caprylic Acid Stress
Caprylic acid (CAP) is anticipated to be a potential biocontrol herbicide in the control of weeds, however the molecular mechanism of how CAP affects weeds is poorly understood. Here, we studied the physiological and biochemical (protein ‐level) changes in horseweed (Conyza canadensis L.) under CAP treatment, with infrared gas analyzer and label ‐free quantitative proteomics methods. In total, 112 differentially‐accumulated proteins (DAPs) (>1.5 fold change, P
Source: Proteomics - March 13, 2019 Category: Biochemistry Authors: Zuren Li, Wei Kuang, Yongbo Liu, Di Peng, Lianyang Bai Tags: Research Article Source Type: research

Surfaceome of exosomes secreted from the colorectal cancer cell line SW480: Peripheral and integral membrane proteins analyzed by proteolysis and TX114
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 13, 2019 Category: Biochemistry Authors: Rong Xu, David W. Greening, Maoshan Chen, Alin Rai, Hong Ji, Nobuhiro Takahashi, Richard J. Simpson Tags: Research Article Source Type: research

TMT ‐Based Proteomics Profiling of Bovine Liver Underscores Protein Markers of Anabolic Treatments
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 13, 2019 Category: Biochemistry Authors: Giancarlo Biancotto, Davide Bovo, Eleonora Mastrorilli, Elisabetta Manuali, Roberto Angeletti, Roberto Stella Tags: Research Article Source Type: research

Proteomic analysis of stromal and epithelial cell communications in human endometrial cancer using a unique 3D co ‐culture model
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 13, 2019 Category: Biochemistry Authors: Aminah Ali Abid Al ‐Juboori, Arnab Ghosh, M. Fairuz B. Jamaluddin, Manish Kumar, Subhransu S. Sahoo, Shafiq M. Syed, Pravin Nahar, Pradeep S. Tanwar Tags: Research Article Source Type: research

Front Cover: Redox Proteomic Analysis Reveals Oxidative Modifications of Proteins by Increased Levels of Intracellular Reactive Oxygen Species during Hypoxia Adaptation of Aspergillus fumigatus
DOI:10.1002/pmic.201800339The pathogenic mouldAspergillus fumigatus primarily causes invasive infections in immunocompromised patients. The infection microenvironment in the lungs is characterised by low oxygen availability. In article number1800339, Shekhova et al. show that elevated levels of ROS are produced during hypoxia. This leads to the activation of the antioxidative stress response regulator Yap1 and the oxidation of cysteine thiols in a subset of proteins including a mitochondrial complex IV assembly factor. (Source: Proteomics)
Source: Proteomics - March 4, 2019 Category: Biochemistry Authors: Elena Shekhova, Lia Ivanova, Thomas Kr üger, Maria C. Stroe, Juliane Macheleidt, Olaf Kniemeyer, Axel A. Brakhage Tags: Front Cover Source Type: research

Contents: Proteomics 5'19
PROTEOMICS, Volume 19, Issue 5, March 2019. (Source: Proteomics)
Source: Proteomics - March 4, 2019 Category: Biochemistry Tags: Contents Source Type: research