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1. Towards detecting regulatory protein–metabolite interactions

Author:
Diether, Maren; Sauer, Uwe
Source:
Current opinion in microbiology 2017 v.39 pp. 16-23
ISSN:
1369-5274
Subject:
proteomics,   etc   ; metabolites; proteins;     Show all 3 Subjects
Abstract:
... New mapping approaches have greatly expanded our view on the cellular landscape of protein–metabolite interactions. These methods either identify proteins interacting with a selected metabolite or vice versa. By reviewing recent developments, we found that comprehensive mapping of the protein–metabolite interaction space can be achieved eventually using existing methods, amongst which proteomics t ...
DOI:
10.1016/j.mib.2017.07.006

2. Shaping and Reshaping Transcriptome Plasticity during Evolution

Author:
Hussain, Shobbir
Source:
Trends in biochemical sciences 2017 v.42 no.9 pp. 682-684
ISSN:
0968-0004
Subject:
proteomics,   etc   ; RNA; evolution; transcriptome;     Show all 4 Subjects
Abstract:
... Transcriptome plasticity, usually associated with alternative isoform generation, is recognised as a key mechanism driving proteomic diversity and biological complexity. Recent findings of Liscovitch-Brauer et al. and Ma et al. suggest that RNA base modifications are an additional central mode of transcriptome malleability that have the potential to determine evolutionary outcomes. ...
DOI:
10.1016/j.tibs.2017.06.009

3. Do the complementarities of electrokinetic and chromatographic procedures represent the “Swiss knife” in proteomic investigation? An overview of the literature in the past decade

Author:
Di Venere, Monica; Viglio, Simona; Sassera, Davide; Fumagalli, Marco; Bardoni, Anna; Salvini, Roberta; Cagnone, Maddalena; Iadarola, Paolo
Source:
Electrophoresis 2017 v.38 no.12 pp. 1538-1550
ISSN:
0173-0835
Subject:
proteomics,   etc   ; chromatography; electrophoresis; proteome;     Show all 4 Subjects
Abstract:
... This report reviews the literature of the past decade dealing with the combination of electrokinetic and chromatographic strategies in the proteomic field. Aim of this article is to highlight how the application of complementary techniques may contribute to substantially improve protein identification. Several studies here considered demonstrate that exploring the combination of these approaches c ...
DOI:
10.1002/elps.201600504

4. Liquid‐phase based separation systems for depletion, prefractionation, and enrichment of proteins in biological fluids and matrices for in‐depth proteomics analysis—An update covering the period 2014–2016

Author:
El Rassi, Ziad; Puangpila, Chanida
Source:
Electrophoresis 2017 v.38 no.1 pp. 150-161
ISSN:
0173-0835
Subject:
proteomics,   etc   ; chromatography; electrophoresis; proteins;     Show all 4 Subjects
Abstract:
... This review article is an update of our previous one by C. Puangpila, E. Mayadunne, and Z. El Rassi, Electrophoresis 2015, 36, 238–252. Similarly to the previous article, this review has two main topics, including (i) proteomic sample preparation (e.g., depletion of high‐abundance proteins, reduction of the protein dynamic concentration range, and enrichment of a particular subproteome), and (ii) ...
DOI:
10.1002/elps.201600413

5. Going beyond genetics to discover cancer targets

Author:
Sandoval, Gabriel J.; Hahn, William C.
Source:
Genome biology 2017 v.18 no.1 pp. 95
ISSN:
1474-760X
Subject:
proteomics,   etc   ; breast neoplasms; epigenetics; genotype;     Show all 4 Subjects
Abstract:
... Two recent studies demonstrate the power of integrating tumor genotype information with epigenetic and proteomic studies to discover potential therapeutic targets in breast cancer. ...
DOI:
10.1186/s13059-017-1238-7
PubMed:
28532420
PubMed Central:
PMC5439228

6. NetProt: Complex-based Feature Selection

Author:
Goh, Wilson Wen Bin; Wong, Limsoon
Source:
Journal of Proteome Research 2017 v.16 no.8 pp. 3102-3112
ISSN:
1535-3907
Subject:
proteomics,   etc   ; computer software; phenotype; proteome;     Show all 4 Subjects
Abstract:
... Protein complex-based feature selection (PCBFS) provides unparalleled reproducibility with high phenotypic relevance on proteomics data. Currently, there are five PCBFS paradigms, but not all representative methods have been implemented or made readily available. To allow general users to take advantage of these methods, we developed the R-package NetProt, which provides implementations of represe ...
DOI:
10.1021/acs.jproteome.7b00363

7. Novel proteins from proteomic analysis of the trunk disease fungus Lasiodiplodia theobromae (Botryosphaeriaceae)

Author:
Uranga, Carla C.; Ghassemian, Majid; Hernández-Martínez, Rufina
Source:
Biochimie open 2017 v.4 pp. 88-98
ISSN:
2214-0085
Subject:
proteomics,   etc   ; Lasiodiplodia theobromae; fungi; proteins;     Show all 4 Subjects
Abstract:
... Many basic science questions remain regarding protein functions in the pathogen: host interaction, especially in the trunk disease fungi family, the Botryosphaeriaceae, which are a global problem for economically important plants, especially fruiting trees. Proteomics is a highly useful technology for studying protein expression and for discovering novel proteins in unsequenced and poorly annotate ...
DOI:
10.1016/j.biopen.2017.03.001
PubMed:
29450146
PubMed Central:
PMC5802045

8. Proceedings of the EuBIC Winter School 2017

Author:
Willems, Sander; Bouyssié, David; David, Matthieu; Locard-Paulet, Marie; Mechtler, Karl; Schwämmle, Veit; Uszkoreit, Julian; Vaudel, Marc; Dorfer, Viktoria
Source:
Journal of proteomics 2017 v.161 pp. 78-80
ISSN:
1874-3919
Subject:
proteomics,   etc   ; bioinformatics; researchers; winter; Austria;     Show all 5 Subjects
Abstract:
... The 2017 EuBIC Winter School was held from January 10th to January 13th 2017 in Semmering, Austria. This meeting gathered international researchers in the fields of bioinformatics and proteomics to discuss current challenges in data analysis and biological interpretation. This article outlines the scientific program and exchanges that took place on this occasion and presents the current challenges ...
DOI:
10.1016/j.jprot.2017.04.001

9. A structural appraisal of sterol carrier protein 2 Proteins and proteomics

Author:
Burgardt, Noelia I.; Gianotti, Alejo R.; Ferreyra, Raúl G.; Ermácora, Mario R.
Source:
Biochimica et biophysica acta 2017 v.1865 no.5 pp. 565-577
ISSN:
1570-9639
Subject:
proteomics,   etc   ; acetyltransferases; binding proteins; sterols;     Show all 4 Subjects
Abstract:
... Sterol Carrier Protein 2 (SCP2) has been associated with lipid binding and transfer activities. However, genomic, proteomic, and structural studies revealed that it is an ubiquitous domain of complex proteins with a variety functions in all forms of life. High-resolution structures of representative SCP2 domains are available, encouraging a comprehensive review of the structural basis for its succ ...
DOI:
10.1016/j.bbapap.2017.03.002

10. Param-Medic: A Tool for Improving MS/MS Database Search Yield by Optimizing Parameter Settings

Author:
May, Damon H.; Tamura, Kaipo; Noble, William S.
Source:
Journal of Proteome Research 2017 v.16 no.4 pp. 1817-1824
ISSN:
1535-3907
Subject:
proteomics,   etc   ; databases; peptides; proteome; spectrometers;     Show all 5 Subjects
Abstract:
... In shotgun proteomics analysis, user-specified parameters are critical to database search performance and therefore to the yield of confident peptide-spectrum matches (PSMs). Two of the most important parameters are related to the accuracy of the mass spectrometer. Precursor mass tolerance defines the peptide candidates considered for each spectrum. Fragment mass tolerance or bin size determines h ...
DOI:
10.1021/acs.jproteome.7b00028
PubMed:
28263070
PubMed Central:
PMC5738039

11. Row versus column correlations: avoiding the ecological fallacy in RNA/protein expression studies

Author:
O’Brien, Jonathon J; Gunawardena, Harsha P; Qaqish, Bahjat F
Source:
Briefings in bioinformatics 2017 v.19 no.5 pp. 946-953
ISSN:
1477-4054
Subject:
proteomics,   etc   ; RNA; guidelines; protein synthesis;     Show all 4 Subjects
Abstract:
... Biomedical researchers are often interested in computing the correlation between RNA and protein abundance. However, correlations can be computed between rows of a data matrix or between columns, and the results are not the same. The belief that these two types of correlation are estimating the same phenomenon is a special case of a well-known logical error called the ecological fallacy. In this a ...
DOI:
10.1093/bib/bbx021
PubMed:
28369202
PubMed Central:
PMC6171494

12. Peptide Selection for Targeted Protein Quantitation

Author:
Chiva, Cristina; Sabidó, Eduard
Source:
Journal of Proteome Research 2017 v.16 no.3 pp. 1376-1380
ISSN:
1535-3907
Subject:
proteomics,   etc   ; compliance; flavor; peptides; proteome;     Show all 5 Subjects
Abstract:
... Targeted proteomics methods in their different flavors rely on the use of a few peptides as proxies for protein quantitation, which need to be specified either prior to or after data acquisition. However, in contrast with discovery methods that use all identified peptides for a given protein to estimate its abundance, targeted proteomics methods are limited in the number of peptides that are used ...
DOI:
10.1021/acs.jproteome.6b00115

13. An Interaction Landscape of Ubiquitin Signaling

Author:
Zhang, Xiaofei; Smits, Arne H.; van Tilburg, Gabrielle B.A.; Jansen, Pascal W.T.C.; Makowski, Matthew M.; Ovaa, Huib; Vermeulen, Michiel
Source:
Molecular cell 2017 v.65 no.5 pp. 941-955.e8
ISSN:
1097-2765
Subject:
proteomics,   etc   ; DNA damage; spectroscopy; ubiquitin;     Show all 4 Subjects
Abstract:
... Intracellular signaling via the covalent attachment of different ubiquitin linkages to protein substrates is fundamental to many cellular processes. Although linkage-selective ubiquitin interactors have been studied on a case-by-case basis, proteome-wide analyses have not been conducted yet. Here, we present ubiquitin interactor affinity enrichment-mass spectrometry (UbIA-MS), a quantitative inter ...
DOI:
10.1016/j.molcel.2017.01.004

14. Serine ADP-Ribosylation Depends on HPF1

Author:
Bonfiglio, Juan José; Fontana, Pietro; Zhang, Qi; Colby, Thomas; Gibbs-Seymour, Ian; Atanassov, Ilian; Bartlett, Edward; Zaja, Roko; Ahel, Ivan; Matic, Ivan
Source:
Molecular cell 2017 v.65 no.5 pp. 932-940.e6
ISSN:
1097-2765
Subject:
proteomics,   etc   ; DNA damage; genome; histones;     Show all 4 Subjects
Abstract:
... ADP-ribosylation (ADPr) regulates important patho-physiological processes through its attachment to different amino acids in proteins. Recently, by precision mapping on all possible amino acid residues, we identified histone serine ADPr marks in the DNA damage response. However, the biochemical basis underlying this serine modification remained unknown. Here we report that serine ADPr is strictly ...
DOI:
10.1016/j.molcel.2017.01.003
PubMed:
28190768
PubMed Central:
PMC5344681

15. A peptide-retrieval strategy enables significant improvement of quantitative performance without compromising confidence of identification

Author:
Tu, Chengjian; Shen, Shichen; Sheng, Quanhu; Shyr, Yu; Qu, Jun
Source:
Journal of proteomics 2017 v.152 pp. 276-282
ISSN:
1874-3919
Subject:
proteomics,   etc   ; data collection; peptides; proteins;     Show all 4 Subjects
Abstract:
... Reliable quantification of low-abundance proteins in complex proteomes is challenging largely owing to the limited number of spectra/peptides identified. In this study we developed a straightforward method to improve the quantitative accuracy and precision of proteins by strategically retrieving the less confident peptides that were previously filtered out using the standard target-decoy search st ...
DOI:
10.1016/j.jprot.2016.11.020

16. Definitive screening design enables optimization of LC–ESI–MS/MS parameters in proteomics

Author:
Aburaya, Shunsuke; Aoki, Wataru; Minakuchi, Hiroyoshi; Ueda, Mitsuyoshi
Source:
Bioscience, biotechnology, and biochemistry 2017 v.81 no.12 pp. 2237-2243
ISSN:
1347-6947
Subject:
proteomics,   etc   ; biotechnology; digestion; humans; peptides; proteome;     Show all 6 Subjects
Abstract:
... In proteomics, more than 100,000 peptides are generated from the digestion of human cell lysates. Proteome samples have a broad dynamic range in protein abundance; therefore, it is critical to optimize various parameters of LC–ESI–MS/MS to comprehensively identify these peptides. However, there are many parameters for LC–ESI–MS/MS analysis. In this study, we applied definitive screening design to ...
DOI:
10.1080/09168451.2017.1391685

17. Improved Method for Determining Absolute Phosphorylation Stoichiometry Using Bayesian Statistics and Isobaric Labeling

Author:
Lim, Matthew Y.; O’Brien, Jonathon; Paulo, Joao A.; Gygi, Steven P.
Source:
Journal of Proteome Research 2017 v.16 no.11 pp. 4217-4226
ISSN:
1535-3907
Subject:
proteomics,   etc   ; Bayesian theory; phosphopeptides; phosphorylation; proteome; stoichiometry;     Show all 6 Subjects
Abstract:
... Phosphorylation stoichiometry, or occupancy, is one element of phosphoproteomics that can add useful biological context (Gerber et al. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 6940–5). We previously developed a method to assess phosphorylation stoichiometry on a proteome-wide scale (Wu et al. Nat. Methods 2011, 8, 677–83). The stoichiometry calculation relies on identifying and measuring the lev ...
DOI:
10.1021/acs.jproteome.7b00571
PubMed:
28985074
PubMed Central:
PMC6301010

18. MS/MS-Free Protein Identification in Complex Mixtures Using Multiple Enzymes with Complementary Specificity

Author:
Ivanov, Mark V.; Tarasova, Irina A.; Levitsky, Lev I.; Solovyeva, Elizaveta M.; Pridatchenko, Marina L.; Lobas, Anna A.; Bubis, Julia A.; Gorshkov, Mikhail V.
Source:
Journal of Proteome Research 2017 v.16 no.11 pp. 3989-3999
ISSN:
1535-3907
Subject:
proteomics,   etc   ; chromatography; databases; digestion; enzymes; proteins; proteome;     Show all 7 Subjects
Abstract:
... In this work, we present the results of evaluation of a workflow that employs a multienzyme digestion strategy for MS1-based protein identification in “shotgun” proteomic applications. In the proposed strategy, several cleavage reagents of different specificity were used for parallel digestion of the protein sample followed by MS1 and retention time (RT) based search. Proof of principle for the pr ...
DOI:
10.1021/acs.jproteome.7b00365

19. A Method for Microalgae Proteomics Analysis Based on Modified Filter-Aided Sample Preparation

Author:
Li, Song; Cao, Xupeng; Wang, Yan; Zhu, Zhen; Zhang, Haowei; Xue, Song; Tian, Jing
Source:
Applied biochemistry and biotechnology 2017 v.183 no.3 pp. 923-930
ISSN:
0273-2289
Subject:
proteomics,   etc   ; Chlamydomonas reinhardtii; biofuels; microalgae; models;     Show all 5 Subjects
Abstract:
... With the fast development of microalgal biofuel researches, the proteomics studies of microalgae increased quickly. A filter-aided sample preparation (FASP) method is widely used proteomics sample preparation method since 2009. Here, a method of microalgae proteomics analysis based on modified filter-aided sample preparation (mFASP) was described to meet the characteristics of microalgae cells and ...
DOI:
10.1007/s12010-017-2473-9

20. On the importance of protein diffusion in biological systems: The example of the Bicoid morphogen gradient Proteins and proteomics

Author:
Fradin, Cécile
Source:
Biochimica et biophysica acta 2017 v.1865 no.11 pp. 1676-1686
ISSN:
1570-9639
Subject:
proteomics,   etc   ; Drosophila melanogaster; biophysics; proteins; tissues; Canada;     Show all 6 Subjects
Abstract:
... Morphogens are proteins that form concentration gradients in embryos and developing tissues, where they act as postal codes, providing cells with positional information and allowing them to behave accordingly. Bicoid was the first discovered morphogen, and remains one of the most studied. It regulates segmentation in flies, forming a striking exponential gradient along the anterior-posterior axis ...
DOI:
10.1016/j.bbapap.2017.09.002