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1. Correction to: Structural analysis and proteomics studies on the Myoviridae vibriophage M4

Author:
Das, Sayani; Dutta, Moumita; Sen, Anindito; Ghosh, Amar N.
Source:
Archives of virology 2019 v.164 no.9 pp. 2431
ISSN:
0304-8608
Subject:
proteomics,   etc   ; Myoviridae; viral proteins;     Show all 3 Subjects
Abstract:
... Unfortunately, the original article was published with an incorrect figure. Figure 11 contains errors and needs to be withdrawn. ...
DOI:
10.1007/s00705-019-04315-9

2. False Discovery Rate Estimation for Hybrid Mass Spectral Library Search Identifications in Bottom-up Proteomics

Author:
Burke, Meghan C.; Zhang, Zheng; Mirokhin, Yuri A.; Tchekovskoi, Dmitrii V.; Liang, Yuxue; Stein, Stephen E.
Source:
Journal of proteome research 2019 v.18 no.9 pp. 3223-3234
ISSN:
1535-3907
Subject:
proteomics,   etc   ; peptides; proteome;     Show all 3 Subjects
Abstract:
... We present a method for FDR estimation of mass spectral library search identifications made by a recently developed method for peptide identification, the hybrid search, based on an extension of the target-decoy approach. In addition to estimating confidence for a given identification, this allows users to compare and integrate identifications from the hybrid mass spectral library search method wi ...
DOI:
10.1021/acs.jproteome.8b00863

3. Current affinity approaches for purification of recombinant proteins

Author:
Mahmoodi, Sahar; Pourhassan-Moghaddam, Mohammad; Wood, David W.; Majdi, Hasan; Zarghami, Nosratollah; Hatti Kaul, Rajni
Source:
Cogent biology 2019 v.5 no.1 pp. 1665406
ISSN:
2331-2025
Subject:
proteomics,   etc   ; hydrophobicity; oleosin; polymers;     Show all 4 Subjects
Abstract:
... Recombinant proteins have wide applications in the development of pharmaceutical compounds, industrial applications of enzymes, and basic proteomics research. In this way, efficient production of recombinant proteins with high purity needs efficient purification methods. Various strategies have been devised to improve these proteins purification such as affinity purification and physicochemical pu ...
DOI:
10.1080/23312025.2019.1665406

4. Quantitative Subcellular Proteomics of the Orbitofrontal Cortex of Schizophrenia Patients

Author:
Velásquez, Erika; Martins-de-Souza, Daniel; Velásquez, Ingrid; Carneiro, Gabriel Reis Alves; Schmitt, Andrea; Falkai, Peter; Domont, Gilberto B.; Nogueira, Fabio C. S.
Source:
Journal of proteome research 2019 v.18 no.12 pp. 4240-4253
ISSN:
1535-3907
Subject:
proteomics,   etc   ; patients; prefrontal cortex; schizophrenia;     Show all 4 Subjects
Abstract:
... Schizophrenia is a chronic disease characterized by the impairment of mental functions with a marked social dysfunction. A quantitative proteomic approach using iTRAQ labeling and SRM, applied to the characterization of mitochondria (MIT), crude nuclear fraction (NUC), and cytoplasm (CYT), can allow the observation of dynamic changes in cell compartments providing valuable insights concerning schi ...
DOI:
10.1021/acs.jproteome.9b00398

5. Correction: iTRAQ-based quantitative proteomic analysis for identification of biomarkers associated with emodin against severe acute pancreatitis in rats

Author:
Xiang, Hong; Zhang, Qingkai; Wang, Danqi; Xia, Shilin; Wang, Guijun; Zhang, Guixin; Chen, Hailong; Wu, Yingjie; Shang, Dong
Source:
RSC advances 2019 v.9 no.46 pp. 26548-26550
ISSN:
2046-2069
Subject:
proteomics,   etc   ; biomarkers; emodin; pancreatitis; rats;     Show all 5 Subjects
Abstract:
... Correction for ‘iTRAQ-based quantitative proteomic analysis for identification of biomarkers associated with emodin against severe acute pancreatitis in rats’ by Hong Xiang et al., RSC Adv., 2016, 6, 72447–72457. ...
DOI:
10.1039/c9ra90061f

6. Comprehensive multidimensional liquid chromatography for advancing environmental and natural products research

Author:
Brandão, Pedro F.; Duarte, Armando C.; Duarte, Regina M.B.O.
Source:
Trends in analytical chemistry 2019 v.116 pp. 186-197
ISSN:
0165-9936
Subject:
proteomics,   etc   ; detectors; liquid chromatography; polymers;     Show all 4 Subjects
Abstract:
... Chromatography is the separation method of choice in most laboratories worldwide. Nonetheless, the increasing need to decode complex samples has created a demand for better separation skills. The addition of extra separation dimensions to a conventional liquid chromatography system was one of the ways to answer to this demand. Although very common in proteomics and polymer research, the use of Mul ...
DOI:
10.1016/j.trac.2019.05.016

7. PANDA: A comprehensive and flexible tool for quantitative proteomics data analysis

Author:
Chang, Cheng; Li, Mansheng; Guo, Chaoping; Ding, Yuqing; Xu, Kaikun; Han, Mingfei; He, Fuchu; Zhu, Yunping; Stegle, Oliver
Source:
Bioinformatics 2019 v.35 no.5 pp. 898-900
ISSN:
1460-2059
Subject:
proteomics,   etc   ; bioinformatics; data collection; peptides;     Show all 4 Subjects
Abstract:
... As the experiment techniques and strategies in quantitative proteomics are improving rapidly, the corresponding algorithms and tools for protein quantification with high accuracy and precision are continuously required to be proposed. Here, we present a comprehensive and flexible tool named PANDA for proteomics data quantification. PANDA, which supports both label-free and labeled quantifications, ...
DOI:
10.1093/bioinformatics/bty727
PubMed:
30816924
PubMed Central:
PMC6394390

8. Differential Ion Mobility–Mass Spectrometry for Detailed Analysis of the Proteome

Author:
Winter, Daniel L.; Wilkins, Marc R.; Donald, William A.
Source:
Trends in biotechnology 2019 v.37 no.2 pp. 198-213
ISSN:
0167-7799
Subject:
proteomics,   etc   ; mass spectrometry; proteins; proteome;     Show all 4 Subjects
Abstract:
... The field of proteomics is increasingly concerned with the diversity and functional relevance of protein modifications. Differential ion mobility spectrometry (DMS) is emerging as a tool to detect and quantify additional peptide and protein species that are difficult to analyse with conventional instrumental methods. In this review, recent advances in DMS are discussed, with a focus on the differe ...
DOI:
10.1016/j.tibtech.2018.07.018

9. Improving Proteomics Data Reproducibility with a Dual-Search Strategy

Author:
Fernández-Costa, Carolina; Martínez-Bartolomé, Salvador; McClatchy, Daniel; Yates, John R.
Source:
Analytical chemistry 2019 v.92 no.2 pp. 1697-1701
ISSN:
1520-6882
Subject:
proteomics,   etc   ; data quality; databases; mass spectrometry; spectrometers;     Show all 5 Subjects
Abstract:
... Mass spectrometry-based proteomics is an invaluable tool for addressing important biological questions. Data-dependent acquisition methods effectuate stochastic acquisition of data in complex mixtures, which results in missing identifications across replicates. We developed a search approach that improves the reproducibility of data acquired from any mass spectrometer. In our approach, a spectral ...
DOI:
10.1021/acs.analchem.9b04955

10. ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion

Author:
Hulstaert, Niels; Shofstahl, Jim; Sachsenberg, Timo; Walzer, Mathias; Barsnes, Harald; Martens, Lennart; Perez-Riverol, Yasset
Source:
Journal of proteome research 2019 v.19 no.1 pp. 537-542
ISSN:
1535-3907
Subject:
proteomics,   etc   ; infrastructure; proteome; spectrometers; user interface;     Show all 5 Subjects
Abstract:
... The field of computational proteomics is approaching the big data age, driven both by a continuous growth in the number of samples analyzed per experiment as well as by the growing amount of data obtained in each analytical run. In order to process these large amounts of data, it is increasingly necessary to use elastic compute resources such as Linux-based cluster environments and cloud infrastru ...
DOI:
10.1021/acs.jproteome.9b00328

11. Proteomic and N-Terminomic TAILS Analyses of Human Alveolar Bone Proteins: Improved Protein Extraction Methodology and LysargiNase Digestion Strategies Increase Proteome Coverage and Missing Protein Identification

Author:
Bell, Peter A; Solis, Nestor; Kizhakkedathu, Jayachandran N; Matthew, Ian; Overall, Christopher M
Source:
Journal of proteome research 2019 v.18 no.12 pp. 4167-4179
ISSN:
1535-3907
Subject:
proteomics,   etc   ; enzymatic hydrolysis; humans; peptides; proteins; proteome;     Show all 6 Subjects
Abstract:
... With 2129 proteins still classified by the Human Proteome Organisation Human Proteome Project (HPP) as “missing” without compelling evidence of protein existence (PE) in humans, we hypothesized that in-depth proteomic characterization of tissues that are technically challenging to access and extract would yield evidence for tissue-specific missing proteins. Paradoxically, although the skeleton is ...
DOI:
10.1021/acs.jproteome.9b00445

12. shinyChromosome: An R/Shiny Application for Interactive Creation of Non-circular Plots of Whole Genomes

Author:
Yu, Yiming; Yao, Wen; Wang, Yuping; Huang, Fangfang
Source:
Genomics, proteomics & bioinformatics 2019 v.17 no.5 pp. 535-539
ISSN:
1672-0229
Subject:
proteomics,   etc   ; bioinformatics; genome; genomics; user interface;     Show all 5 Subjects
Abstract:
... Non-circular plots of whole genomes are natural representations of genomic data aligned along all chromosomes. Currently, there is no specialized graphical user interface (GUI) designed to produce non-circular whole genome diagrams, and the use of existing tools requires considerable coding effort from users. Moreover, such tools also require improvement, including the addition of new functionalit ...
DOI:
10.1016/j.gpb.2019.07.003
PubMed:
31931182
PubMed Central:
PMC7056921

13. Five simple yet essential steps to correctly estimate the rate of false differentially abundant proteins in mass spectrometry analyses

Author:
Wieczorek, Samuel; Giai Gianetto, Quentin; Burger, Thomas
Source:
Journal of proteomics 2019 v.207 pp. 103441
ISSN:
1874-3919
Subject:
proteomics,   etc   ; computer software; mass spectrometry; proteins;     Show all 4 Subjects
Abstract:
... Results from mass spectrometry based quantitative proteomics analysis correspond to a subset of proteins which are considered differentially abundant relative to a control. Their selection is delicate and often requires some statistical expertise in addition to a refined knowledge of the experimental data. To facilitate the selection process, we have considered differential analysis as a five-step ...
DOI:
10.1016/j.jprot.2019.103441

14. Maximizing Tandem Mass Spectrometry Acquisition Rates for Shotgun Proteomics

Author:
Trujillo, Edna A.; Hebert, Alexander S.; Brademan, Dain R.; Coon, Joshua J.
Source:
Analytical chemistry 2019 v.91 no.20 pp. 12625-12629
ISSN:
1520-6882
Subject:
proteomics,   etc   ; peptides; spectrometers; surveys; tandem mass spectrometry;     Show all 5 Subjects
Abstract:
... Advances in tandem mass spectrometry (MS/MS) acquisition rate have steadily led to increased performance in shotgun proteomics experiments. To that end, contemporary mass spectrometers are outfitted with multiple analyzers allowing for the simultaneous collection of survey (MS1) and MS/MS spectra. In the latest generation Orbitrap hybrid, MS/MS scans can be acquired at a high rate using the dual c ...
DOI:
10.1021/acs.analchem.9b02979
PubMed:
31509394
PubMed Central:
PMC6800818

15. Recent advances in nanomaterials for sample pre-treatment in phosphoproteomics research

Author:
Yan, Yinghua; Deng, Chunhui
Source:
Trends in analytical chemistry 2019
ISSN:
0165-9936
Subject:
proteomics,   etc   ; ionization; nanomaterials; phosphopeptides; phosphoproteins; protein phosphorylation;     Show all 6 Subjects
Abstract:
... Reversible protein phosphorylation plays a crucial role in many biological processes. Due to the low concentration, suppression of nonphosphopeptides as well as the insufficient ionization efficiencies, the direct identification and detection of phosphopeptides/phosphoproteins by MS are still faces many challenges. Enrichment of phosphopeptides/phosphoproteins from complicated coexisting matrixes ...
DOI:
10.1016/j.trac.2019.115655

16. Reductive methylation labeling, from quantitative to structural proteomics

Author:
Liu, Zheyi; Zhou, Ye; Liu, Jing; Chen, Jin; Heck, Albert J.R.; Wang, Fangjun
Source:
Trends in analytical chemistry 2019 v.118 pp. 771-778
ISSN:
0165-9936
Subject:
proteomics,   etc   ; isotopes; methylation; monitoring; structural genomics;     Show all 5 Subjects
Abstract:
... Reductive methylation is a highly reactive and selective chemical labeling method and plays an important role in proteomic analysis. Various applications of reductive methylation have been developed and have substantially promoted the scope of proteomic analysis to date. Aside from a well-known method for introducing isotopes, this reaction could also be conducted under biological conditions and h ...
DOI:
10.1016/j.trac.2019.07.009

17. A proteome-wide screen to identify transcription factors interacting with the Vibrio cholerae rpoS promoter

Author:
Ayala, Julio C.; Benitez, Jorge A.; Silva, Anisia J.
Source:
Journal of microbiological methods 2019
ISSN:
0167-7012
Subject:
proteomics,   etc   ; Vibrio cholerae; quorum sensing; transcription factors;     Show all 4 Subjects
Abstract:
... We describe a proteomic approach to identify transcription factors binding to a target promoter. The method's usefulness was tested by identifying proteins binding to the Vibrio cholerae rpoS promoter in response to cell density. Proteins identified in this screen included the nucleoid-associated protein Fis and the quorum sensing regulator HapR. ...
DOI:
10.1016/j.mimet.2019.105702

18. One Thousand and One Software for Proteomics: Tales of the Toolmakers of Science

Author:
Tsiamis, Vasileios; Ienasescu, Hans-Ioan; Gabrielaitis, Dovydas; Palmblad, Magnus; Schwämmle, Veit; Ison, Jon
Source:
Journal of proteome research 2019 v.18 no.10 pp. 3580-3585
ISSN:
1535-3907
Subject:
proteomics,   etc   ; computer software; half life; proteome;     Show all 4 Subjects
Abstract:
... Proteomics is a highly dynamic field driven by frequent introduction of new technological approaches, leading to high demand for new software tools and the concurrent development of many methods for data analysis, processing, and storage. The rapidly changing landscape of proteomics software makes finding a tool fit for a particular purpose a significant challenge. The comparison of software and t ...
DOI:
10.1021/acs.jproteome.9b00219

19. Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project

Author:
Omenn, Gilbert S.; Lane, Lydie; Overall, Christopher M.; Corrales, Fernando J.; Schwenk, Jochen M.; Paik, Young-Ki; Van Eyk, Jennifer E.; Liu, Siqi; Pennington, Stephen; Snyder, Michael P.; Baker, Mark S.; Deutsch, Eric W.
Source:
Journal of proteome research 2019 v.18 no.12 pp. 4098-4107
ISSN:
1535-3907
Subject:
proteomics,   etc   ; human diseases; humans; immunohistochemistry; proteins; proteome;     Show all 6 Subjects
Abstract:
... The Human Proteome Project (HPP) annually reports on progress made throughout the field in credibly identifying and characterizing the complete human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2019–01–11 contains 17 694 proteins with strong protein-level evidence (PE1), compliant with HPP Guidelines for Interp ...
DOI:
10.1021/acs.jproteome.9b00434
PubMed:
31430157
PubMed Central:
PMC6898754

20. Selection for Cheaper Amino Acids Drives Nucleotide Usage at the Start of Translation in Eukaryotic Genes

Author:
Gao, Na L.; He, Zilong; Zhu, Qianhui; Jiang, Puzi; Hu, Songnian; Chen, Wei-Hua
Source:
Genomics, proteomics & bioinformatics 2019
ISSN:
1672-0229
Subject:
proteomics,   etc   ; bioinformatics; energy efficiency; genomics; start codon;     Show all 5 Subjects
Abstract:
... Coding regions have complex interaction among multiple selective forces, which are manifested as biases in nucleotide composition. Previous studies have revealed a decreasing GC gradient from the 5′- to 3′- ends of coding regions in various organisms. We confirmed that this gradient is universal in eukaryotic genes but the decrease only starts from the ∼25th codon. This trend is mostly found in no ...
DOI:
10.1016/j.gpb.2021.03.002