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1. Antibody validation: a view from the mountains

Author:
Taussig, Michael J.; Fonseca, Cláudia; Trimmer, James S.
Source:
New biotechnology 2018 v.45 pp. 1-8
ISSN:
1871-6784
Subject:
proteomics,   etc   ; antibodies; mountains;     Show all 3 Subjects
Abstract:
... Validation of antibodies and other protein binders is a subject of pressing concern for the research community and one which is uppermost in the minds of all who use antibodies as research and diagnostic reagents. Assessing an antibody’s fitness for purpose includes accurate ascertainment of its target specificity and suitability for the envisaged task. Moreover, standardised procedures are essent ...
DOI:
10.1016/j.nbt.2018.08.002
PubMed:
30086383
PubMed Central:
PMC6128662

2. DIA+: A Data-Independent Acquisition Method Combining Multiple Precursor Charges to Improve Peptide Signal

Author:
Borràs, Eva; Sabidó, Eduard
Source:
Analytical chemistry 2018 v.90 no.21 pp. 12339-12341
ISSN:
1520-6882
Subject:
proteomics,   etc   ; ions; peptides; proteome;     Show all 4 Subjects
Abstract:
... Data-independent acquisition methods that acquire fragment ions from virtually any peptide in a sample have expanded the benefits of low-throughput targeted proteomics to proteome-wide analyses. While these methods have increased the reproducibility of peptide quantification across multiple samples, their sensitivity is still limited, and the quantification of complete proteomes remains a challeng ...
DOI:
10.1021/acs.analchem.8b03418

3. Limits for Resolving Isobaric Tandem Mass Tag Reporter Ions Using Phase-Constrained Spectrum Deconvolution

Author:
Kelstrup, Christian D.; Aizikov, Konstantin; Batth, Tanveer S.; Kreutzman, Arne; Grinfeld, Dmitry; Lange, Oliver; Mourad, Daniel; Makarov, Alexander A.; Olsen, Jesper V.
Source:
Journal of proteome research 2018 v.17 no.11 pp. 4008-4016
ISSN:
1535-3907
Subject:
proteomics,   etc   ; ions; proteome; spectrometers;     Show all 4 Subjects
Abstract:
... A popular method for peptide quantification relies on isobaric labeling such as tandem mass tags (TMT), which enables multiplexed proteome analyses. Quantification is achieved by reporter ions generated by fragmentation in a tandem mass spectrometer. However, with higher degrees of multiplexing, the smaller mass differences between the reporter ions increase the mass resolving power requirements. ...
DOI:
10.1021/acs.jproteome.8b00381

4. Ultra-High Pressure (>30,000 psi) Packing of Capillary Columns Enhancing Depth of Shotgun Proteomic Analyses

Author:
Shishkova, Evgenia; Hebert, Alexander S.; Westphall, Michael S.; Coon, Joshua J.
Source:
Analytical chemistry 2018 v.90 no.19 pp. 11503-11508
ISSN:
1520-6882
Subject:
proteomics,   etc   ; chromatography; proteome;     Show all 3 Subjects
Abstract:
... Extreme sample complexity is an inherent challenge in shotgun proteomics that positions quality of chromatographic separations as one of the key determinants of attainable proteome coverage. In search of better separations, macroscopic physical characteristics of capillary columns, i.e., length and properties of stationary phase particles, are typically considered and optimized, while significance ...
DOI:
10.1021/acs.analchem.8b02766
PubMed:
30179449
PubMed Central:
PMC6478162

5. Lys-C/Arg-C, a More Specific and Efficient Digestion Approach for Proteomics Studies

Author:
Wu, Zhen; Huang, Jichang; Huang, Jingnan; Li, Qingqing; Zhang, Xumin
Source:
Analytical chemistry 2018 v.90 no.16 pp. 9700-9707
ISSN:
1520-6882
Subject:
proteomics,   etc   ; proteolysis; trypsin;     Show all 3 Subjects
Abstract:
... Nowadays, bottom-up approaches are predominantly adopted in proteomics studies, which necessitate a proteolysis step prior to MS analysis. Trypsin is often the best protease in choice due to its high specificity and MS-favored proteolytic products. A lot of efforts have been made to develop a superior digestion approach but hardly succeed, especially in large-scale proteomics studies. Herein, we r ...
DOI:
10.1021/acs.analchem.8b02448

6. SearchGUI: A Highly Adaptable Common Interface for Proteomics Search and de Novo Engines

Author:
Barsnes, Harald; Vaudel, Marc
Source:
Journal of proteome research 2018 v.17 no.7 pp. 2552-2555
ISSN:
1535-3907
Subject:
proteomics,   etc   ; bioinformatics; proteins; proteome;     Show all 4 Subjects
Abstract:
... Mass-spectrometry-based proteomics has become the standard approach for identifying and quantifying proteins. A vital step consists of analyzing experimentally generated mass spectra to identify the underlying peptide sequences for later mapping to the originating proteins. We here present the latest developments in SearchGUI, a common open-source interface for the most frequently used freely avai ...
DOI:
10.1021/acs.jproteome.8b00175

7. Correction to: The role of proteomics in the age of immunotherapies

Author:
Hayes, Sarah A.; Clarke, Stephen; Pavlakis, Nick; Howell, Viive M.
Source:
Mammalian genome 2018 v.29 no.11-12 pp. 770
ISSN:
0938-8990
Subject:
proteomics,   etc   ; human diseases; immunotherapy; proteome;     Show all 4 Subjects
Abstract:
... Some parts of the Abstract, Introduction and Discussion included uncited text from the following previously published chapter. ...
DOI:
10.1007/s00335-018-9785-0

8. Proteomics of cyanobacteria: current horizons

Author:
Battchikova, Natalia; Muth-Pawlak, Dorota; Aro, Eva-Mari
Source:
Current opinion in biotechnology 2018 v.54 pp. 65-71
ISSN:
0958-1669
Subject:
proteomics,   etc   ; Cyanobacteria; protein synthesis; proteins;     Show all 4 Subjects
Abstract:
... Application of proteomics has made a profound impact on the cyanobacterial research. It has not only provided a global identification of expressed proteins in cyanobacterial cells, but has also brought valuable insights into dynamics of cell responses to environmental challenges, regulation mechanisms, structure of protein complexes, compartmentalization, and other important biological questions. ...
DOI:
10.1016/j.copbio.2018.02.012

9. apQuant: Accurate Label-Free Quantification by Quality Filtering

Author:
Doblmann, Johannes; Dusberger, Frederico; Imre, Richard; Hudecz, Otto; Stanek, Florian; Mechtler, Karl; Dürnberger, Gerhard
Source:
Journal of proteome research 2018 v.18 no.1 pp. 535-541
ISSN:
1535-3907
Subject:
proteomics,   etc   ; algorithms; bioinformatics; peptides; proteome;     Show all 5 Subjects
Abstract:
... Label-free quantification of shotgun proteomics data is a frequently used strategy, offering high dynamic range, sensitivity, and the ability to compare a high number of samples without additional labeling effort. Here, we present a bioinformatics approach that significantly improves label-free quantification results. We employ Percolator to assess the quality of quantified peptides. This allows t ...
DOI:
10.1021/acs.jproteome.8b00113

10. Deep learning in omics: a survey and guideline

Author:
Zhang, Zhiqiang; Zhao, Yi; Liao, Xiangke; Shi, Wenqiang; Li, Kenli; Zou, Quan; Peng, Shaoliang
Source:
Briefings in functional genomics 2018 v.18 no.1 pp. 41-57
ISSN:
2041-2657
Subject:
proteomics,   etc   ; genomics; guidelines; surveys; transcriptome;     Show all 5 Subjects
Abstract:
... Omics, such as genomics, transcriptome and proteomics, has been affected by the era of big data. A huge amount of high dimensional and complex structured data has made it no longer applicable for conventional machine learning algorithms. Fortunately, deep learning technology can contribute toward resolving these challenges. There is evidence that deep learning can handle omics data well and resolv ...
DOI:
10.1093/bfgp/ely030

11. Proceedings of the EuBIC developer's meeting 2018

Author:
Willems, Sander; Bouyssié, David; Deforce, Dieter; Dorfer, Viktoria; Gorshkov, Vladimir; Kopczynski, Dominik; Laukens, Kris; Locard-Paulet, Marie; Schwämmle, Veit; Uszkoreit, Julian; Valkenborg, Dirk; Vaudel, Marc; Bittremieux, Wout
Source:
Journal of proteomics 2018 v.187 pp. 25-27
ISSN:
1874-3919
Subject:
proteomics,   etc   ; bioinformatics; experts; protocols; Belgium;     Show all 5 Subjects
Abstract:
... The inaugural European Bioinformatics Community (EuBIC) developer's meeting was held from January 9th to January 12th 2018 in Ghent, Belgium. While the meeting kicked off with an interactive keynote session featuring four internationally renowned experts in the field of computational proteomics, its primary focus were the hands-on hackathon sessions which featured six community-proposed projects r ...
DOI:
10.1016/j.jprot.2018.05.015

12. Minimally Invasive and Portable Method for the Identification of Proteins in Ancient Paintings

Author:
Cicatiello, Paola; Ntasi, Georgia; Rossi, Manuela; Marino, Gennaro; Giardina, Paola; Birolo, Leila
Source:
Analytical chemistry 2018 v.90 no.17 pp. 10128-10133
ISSN:
1520-6882
Subject:
proteomics,   etc   ; fungal proteins; peptides; trypsin;     Show all 4 Subjects
Abstract:
... A novel method for the analysis of proteinaceous materials present on painted surfaces was developed by taking advantage of the adhesive ability of some fungal proteins which can form a stable and homogeneous layer on flexible transparency sheets able to capture trypsin in a fully active form. We demonstrated that the bioactive sheets were able to efficiently digest proteins, present as such, on s ...
DOI:
10.1021/acs.analchem.8b01718

13. Automated Chemical Oligosaccharide Synthesis: Novel Approach to Traditional Challenges

Author:
Panza, Matteo; Pistorio, Salvatore G.; Stine, Keith J.; Demchenko, Alexei V.
Source:
Chemical reviews 2018 v.118 no.17 pp. 8105-8150
ISSN:
1520-6890
Subject:
proteomics,   etc   ; automation; chemistry; genomics; oligosaccharides;     Show all 5 Subjects
Abstract:
... Advances in carbohydrate chemistry have certainly made common oligosaccharides much more accessible. However, many current methods still rely heavily upon specialized knowledge of carbohydrate chemistry. The application of automated technologies to chemical and life science applications such as genomics and proteomics represents a vibrant field. These automated technologies also present opportunit ...
DOI:
10.1021/acs.chemrev.8b00051
PubMed:
29953217
PubMed Central:
PMC6522228

14. Pyteomics 4.0: Five Years of Development of a Python Proteomics Framework

Author:
Levitsky, Lev I.; Klein, Joshua A.; Ivanov, Mark V.; Gorshkov, Mikhail V.
Source:
Journal of proteome research 2018 v.18 no.2 pp. 709-714
ISSN:
1535-3907
Subject:
proteomics,   etc   ; bioinformatics; computer software; information processing; proteome;     Show all 5 Subjects
Abstract:
... Many of the novel ideas that drive today’s proteomic technologies are focused essentially on experimental or data-processing workflows. The latter are implemented and published in a number of ways, from custom scripts and programs, to projects built using general-purpose or specialized workflow engines; a large part of routine data processing is performed manually or with custom scripts that remai ...
DOI:
10.1021/acs.jproteome.8b00717

15. Response to “Determining Allele-Specific Protein Expression (ASPE) Using a Novel Quantitative Concatamer Based Proteomics Method”

Author:
Achour, Brahim; Rostami-Hodjegan, Amin; Barber, Jill
Source:
Journal of proteome research 2018 v.18 no.1 pp. 574
ISSN:
1535-3907
Subject:
proteomics,   etc   ; Whites; alleles; protein synthesis; proteome;     Show all 5 Subjects
Abstract:
... A recent publication in this journal reported the application of a targeted proteomic strategy using a quantitative concatemer (QconCAT) standard to the assessment of allele-specific expression of UGT2B15 claiming this methodology to be a “novel” approach (J. Proteome Res. 2018, 17 (10), 3606–3612, DOI: 10.1021/acs.jproteome.8b00620). While the application is not common, the method was previously ...
DOI:
10.1021/acs.jproteome.8b00871

16. Protein Dynamics in Solution by Quantitative Crosslinking/Mass Spectrometry

Author:
Chen, Zhuo A.; Rappsilber, Juri
Source:
Trends in biochemical sciences 2018 v.43 no.11 pp. 908-920
ISSN:
0968-0004
Subject:
proteomics,   etc   ; crosslinking; mass spectrometry; protein structure; proteins;     Show all 5 Subjects
Abstract:
... The dynamics of protein structures and their interactions are responsible for many cellular processes. The rearrangements and interactions of proteins, which are often transient, occur in solution and may require a biological environment that is difficult to maintain in traditional structural biological approaches. Quantitative crosslinking/mass spectrometry (QCLMS) has emerged as an excellent met ...
DOI:
10.1016/j.tibs.2018.09.003
PubMed:
30318267
PubMed Central:
PMC6240160

17. Reagents for Isobaric Labeling Peptides in Quantitative Proteomics

Author:
Ren, Yan; He, Yanbin; Lin, Zhilong; Zi, Jin; Yang, Huanming; Zhang, Shenyan; Lou, Xiaomin; Wang, Quanhui; Li, Shuwei; Liu, Siqi
Source:
Analytical chemistry 2018 v.90 no.21 pp. 12366-12371
ISSN:
1520-6882
Subject:
proteomics,   etc   ; human cell lines; monitoring; phosphopeptides; phosphoproteome;     Show all 5 Subjects
Abstract:
... Currently, the commercial reagents for isobaric peptides labeling (TMT and iTRAQ) have some drawbacks, such as high cost in experiments, especially in quantitation for the modified peptides, and inconvenient handling for variable sizes of samples. Herein, we developed a set of 10-plex isobaric tags (IBT) with high stability and low cost. The labeled peptides were sensitively detected on Orbitrap Q ...
DOI:
10.1021/acs.analchem.8b00321

18. Analyzing the Structure of Pathways and Its Influence on the Interpretation of Biomedical Proteomics Data Sets

Author:
Burger, Bram; Hernández Sánchez, Luis Francisco; Lereim, Ragnhild Reehorst; Barsnes, Harald; Vaudel, Marc
Source:
Journal of proteome research 2018 v.17 no.11 pp. 3801-3809
ISSN:
1535-3907
Subject:
proteomics,   etc   ; biochemical pathways; data collection; proteome;     Show all 4 Subjects
Abstract:
... Biochemical pathways are commonly used as a reference to conduct functional analysis on biomedical omics data sets, where experimental results are mapped to knowledgebases comprising known molecular interactions collected from the literature. Due to their central role, the content of the functional knowledgebases directly influences the outcome of pathway analyses. In this study, we investigate th ...
DOI:
10.1021/acs.jproteome.8b00464

19. Mass spectrometry-based proteomics for system-level characterization of biological responses to engineered nanomaterials

Author:
Zhang, Tong; Gaffrey, Matthew J.; Thrall, Brian D.; Qian, Wei-Jun
Source:
Analytical and bioanalytical chemistry 2018 v.410 no.24 pp. 6067-6077
ISSN:
1618-2642
Subject:
proteomics,   etc   ; mass spectrometry; nanomaterials; oxidative stress;     Show all 4 Subjects
Abstract:
... The widespread use of engineered nanomaterials or nanotechnology makes the characterization of biological responses to nanomaterials an important area of research. The application of omics approaches, such as mass spectrometry-based proteomics, has revealed new insights into the cellular responses of exposure to nanomaterials, including how nanomaterials interact and alter cellular pathways. In ad ...
DOI:
10.1007/s00216-018-1168-6
PubMed:
29947897
PubMed Central:
PMC6119095

20. ‘Omic’ technologies as a helpful tool in radioecological research

Author:
Volkova, Polina Yu.; Geras'kin, Stanislav A.
Source:
Journal of environmental radioactivity 2018 v.189 pp. 156-167
ISSN:
0265-931X
Subject:
proteomics,   etc   ; epigenetics; genomics; metabolomics; radioactivity; transcriptomics;     Show all 6 Subjects
Abstract:
... This article presents a brief review of the modern ‘omic’ technologies, namely genomics, epigenomics, transcriptomics, proteomics, and metabolomics, as well as the examples of their possible use in radioecology. For each technology, a short description of advances, limitations, and instrumental applications is given. In addition, the review contains examples of successful use of ‘omic’ technologie ...
DOI:
10.1016/j.jenvrad.2018.04.011