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Proteomes, Volume 6, Issue 1

2018 March - 13 articles

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Articles (13)

  • Feature Paper
  • Review
  • Open Access
12 Citations
5,880 Views
15 Pages

27 February 2018

Soybean, which is rich in protein and oil, is cultivated in several climatic zones; however, its growth is markedly decreased by flooding. Proteomics is a useful tool for understanding the flooding-response mechanism in soybean. Subcellular proteomic...

  • Article
  • Open Access
2 Citations
4,453 Views
12 Pages

The Gene-Centric Content Management System and Its Application for Cognitive Proteomics

  • Ekaterina V. Poverennaya,
  • Alexander V. Shargunov,
  • Elena A. Ponomarenko and
  • Andrey V. Lisitsa

23 February 2018

The Human Proteome Project is moving into the next phase of creating and/or reconsidering the functional annotations of proteins using the chromosome-centric paradigm. This challenge cannot be solved exclusively using automated means, but rather requ...

  • Feature Paper
  • Article
  • Open Access
13 Citations
6,928 Views
12 Pages

Pilot Study on Mass Spectrometry–Based Analysis of the Proteome of CD34+CD123+ Progenitor Cells for the Identification of Potential Targets for Immunotherapy in Acute Myeloid Leukemia

  • Johannes R. Schmidt,
  • Elke Rücker-Braun,
  • Katharina Heidrich,
  • Malte Von Bonin,
  • Friedrich Stölzel,
  • Christian Thiede,
  • Jan M. Middeke,
  • Gerhard Ehninger,
  • Martin Bornhäuser and
  • Falk Heidenreich
  • + 3 authors

12 February 2018

Targeting of leukemic stem cells with specific immunotherapy would be an ideal approach for the treatment of myeloid malignancies, but suitable epitopes are unknown. The comparative proteome-level characterization of hematopoietic stem and progenitor...

  • Article
  • Open Access
5 Citations
4,464 Views
18 Pages

8 February 2018

A protein family has similar and diverse functions locally conserved as aligned sequence segments. Further discovering their association patterns could reveal subtle family subgroup characteristics. Since aligned residues associations (ARAs) in Align...

  • Feature Paper
  • Article
  • Open Access
12 Citations
5,786 Views
8 Pages

Proteome Profiling of Diabetic Mellitus Patient Urine for Discovery of Biomarkers by Comprehensive MS-Based Proteomics

  • Yoshitoshi Hirao,
  • Suguru Saito,
  • Hidehiko Fujinaka,
  • Shigeru Miyazaki,
  • Bo Xu,
  • Ali F. Quadery,
  • Amr Elguoshy,
  • Keiko Yamamoto and
  • Tadashi Yamamoto

Diabetic mellitus (DM) is a disease that affects glucose homeostasis and causes complications, such as diabetic nephropathy (DN). For early diagnosis of DN, microalbuminuria is currently one of the most frequently used biomarkers. However, more early...

(This article belongs to the Special Issue Proteomic Biomarkers in Human Diseases)
  • Article
  • Open Access
14 Citations
6,491 Views
13 Pages

In-Depth Proteomic Characterization of Classical and Non-Classical Monocyte Subsets

  • Víctor Segura,
  • M. Luz Valero,
  • Laura Cantero,
  • Javier Muñoz,
  • Eduardo Zarzuela,
  • Fernando García,
  • Kerman Aloria,
  • Javier Beaskoetxea,
  • Jesús M. Arizmendi and
  • Manuel M. Sánchez del Pino
  • + 9 authors

Monocytes are bone marrow-derived leukocytes that are part of the innate immune system. Monocytes are divided into three subsets: classical, intermediate and non-classical, which can be differentiated by their expression of some surface antigens, mai...

  • Article
  • Open Access
41 Citations
10,299 Views
15 Pages

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework

  • Clemens Blank,
  • Caleb Easterly,
  • Bjoern Gruening,
  • James Johnson,
  • Carolin A. Kolmeder,
  • Praveen Kumar,
  • Damon May,
  • Subina Mehta,
  • Bart Mesuere and
  • Pratik D. Jagtap
  • + 9 authors

The impact of microbial communities, also known as the microbiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes r...

(This article belongs to the Special Issue Metaproteomics)
  • Feature Paper
  • Article
  • Open Access
23 Citations
5,914 Views
14 Pages

The so-called tube-gel method is a sample preparation protocol allowing for management of SDS for protein solubilization through in-gel protein trapping. Because of its simplicity, we assumed that once miniaturized, this method could become a standar...

(This article belongs to the Special Issue Plant Proteomics 2017)
  • Feature Paper
  • Review
  • Open Access
26 Citations
7,297 Views
8 Pages

Psoriatic arthritis (PsA) is an inflammatory arthritis which develops in up to one-third of patients suffering from the cutaneous disorder, psoriasis. The complex and heterogeneous nature of PsA renders it difficult to diagnose, leading to poor outco...

(This article belongs to the Special Issue Proteomic Biomarkers in Human Diseases)
  • Article
  • Open Access
19 Citations
7,888 Views
21 Pages

Background: Zinc accumulates in the embryo, aleurone, and subaleurone layers at different amounts in cereal grains. Our hypothesis is that zinc could be stored bound, not only to low MW metabolites/proteins, but also to high MW proteins as well. Meth...

  • Article
  • Open Access
47 Citations
8,499 Views
25 Pages

Comparative Proteomics Analysis of Urine Reveals Down-Regulation of Acute Phase Response Signaling and LXR/RXR Activation Pathways in Prostate Cancer

  • Katarina Davalieva,
  • Sanja Kiprijanovska,
  • Ivana Maleva Kostovska,
  • Sotir Stavridis,
  • Oliver Stankov,
  • Selim Komina,
  • Gordana Petrusevska and
  • Momir Polenakovic

29 December 2017

Detecting prostate cancer (PCa) using non-invasive diagnostic markers still remains a challenge. The aim of this study was the identification of urine proteins that are sufficiently sensitive and specific to detect PCa in the early stages. Comparativ...

  • Article
  • Open Access
53 Citations
9,770 Views
17 Pages

MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data

  • Michael Riffle,
  • Damon H. May,
  • Emma Timmins-Schiffman,
  • Molly P. Mikan,
  • Daniel Jaschob,
  • William Stafford Noble and
  • Brook L. Nunn

27 December 2017

Metaproteomics is the characterization of all proteins being expressed by a community of organisms in a complex biological sample at a single point in time. Applications of metaproteomics range from the comparative analysis of environmental samples (...

(This article belongs to the Special Issue Metaproteomics)
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Proteomes - ISSN 2227-7382