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1. HSP70 interacts with Rheb, inhibiting mTORC1 signaling

Author:
Ryu, Hyang Hwa; Ha, Sang Hoon
Source:
Biochemical and biophysical research communications 2020 v.533 no.4 pp. 1198-1203
ISSN:
0006-291X
Subject:
proteomics,   etc   ; guanosinetriphosphatase; research;     Show all 3 Subjects
Abstract:
... The small GTPase Rheb binds and activates mTORC1, which plays a pivotal role in diverse cellular physiologies. To increase our understanding of how Rheb regulates mTORC1 signaling, we set out to identify Rheb binding proteins using shotgun proteomics approaches. In this study, we characterized HSP70, one of the identified proteins, as a new Rheb binding protein. The present study showed that Rheb ...
DOI:
10.1016/j.bbrc.2020.07.053

2. Profiling of post-translational modifications by chemical and computational proteomics

Author:
Yang, Fan; Wang, Chu
Source:
Chemical communications 2020 v.56 no.88 pp. 13506-13519
ISSN:
1364-548X
Subject:
proteomics,   etc   ; humans; proteome; therapeutics;     Show all 4 Subjects
Abstract:
... Post-translational modifications (PTMs) diversify the molecular structures of proteins and play essential roles in regulating their functions. Abnormal PTM status has been linked to a variety of developmental disorders and human diseases, highlighting the importance of studying PTMs in understanding physiological processes and discovering novel nodes and links with therapeutic intervention potenti ...
DOI:
10.1039/d0cc05447j

3. Numerical Representations of Metabolic Systems

Author:
Smilde, Age K.; Hankemeier, Thomas
Source:
Analytical chemistry 2020 v.92 no.20 pp. 13614-13621
ISSN:
1520-6882
Subject:
proteomics,   etc   ; analytical chemistry; metabolomics;     Show all 3 Subjects
Abstract:
... Metabolomics is becoming a mature part of analytical chemistry as evidenced by the growing number of publications and attendees of international conferences dedicated to this topic. Yet, a systematic treatment of the fundamental structure and properties of metabolomics data is lagging behind. We want to fill this gap by introducing two fundamental theories concerning metabolomics data: data theory ...
DOI:
10.1021/acs.analchem.9b05613

4. Proteomic analysis of Trypanosoma cruzi spliceosome complex

Author:
Barbosa, Rosicler L.; da Cunha, Julia Pinheiro Chagas; Menezes, Arthur T.; Melo, Raíssa de F.P.; Elias, Maria Carolina; Silber, Ariel M.; Coltri, Patricia P.
Source:
Journal of proteomics 2020 v.223 pp. 103822
ISSN:
1874-3919
Subject:
proteomics,   etc   ; Trypanosoma cruzi; spliceosomes;     Show all 3 Subjects
Abstract:
... The unicellular protists of the group Kinetoplastida include the genera Leishmania and Trypanosoma, which are pathogens of invertebrate and vertebrate animals. Despite their medical and economical importance, critical aspects of their biology such as specific molecular characteristics of gene expression regulation are just beginning to be deciphered. Gene expression regulation also depends on post ...
DOI:
10.1016/j.jprot.2020.103822

5. Impact of the Identification Strategy on the Reproducibility of the DDA and DIA Results

Author:
Fernández-Costa, Carolina; Martínez-Bartolomé, Salvador; McClatchy, Daniel B.; Saviola, Anthony J.; Yu, Nam-Kyung; Yates, John R.
Source:
Journal of proteome research 2020 v.19 no.8 pp. 3153-3161
ISSN:
1535-3907
Subject:
proteomics,   etc   ; databases; proteome;     Show all 3 Subjects
Abstract:
... Data-independent acquisition (DIA) is a promising technique for the proteomic analysis of complex protein samples. A number of studies have claimed that DIA experiments are more reproducible than data-dependent acquisition (DDA), but these claims are unsubstantiated since different data analysis methods are used in the two methods. Data analysis in most DIA workflows depends on spectral library se ...
DOI:
10.1021/acs.jproteome.0c00153

6. Quantitative Proteomics Reveals the Development of HBV-Associated Glomerulonephritis Triggered by the Downregulation of SLC7A7

Author:
Zuo, Tao; Chen, Peiru; Jing, Sha; Zhang, Tao; Chang, Lei; Xu, Feng; Zhao, Chao; Xu, Ping
Source:
Journal of proteome research 2020 v.19 no.4 pp. 1556-1564
ISSN:
1535-3907
Subject:
proteomics,   etc   ; data collection; glomerulonephritis;     Show all 3 Subjects
Abstract:
... As a hepadnavirus, hepatitis B virus (HBV) can cause damage to extrahepatic organs. The kidney is one of the organs that is more susceptible to damage. Research studies on HBV-associated glomerulonephritis (HBV-GN) have been going on for decades. However, the underlying molecular mechanism remains obscure. Here, we applied a tandem mass tag (TMT) isobaric labeling-based method to quantitatively pr ...
DOI:
10.1021/acs.jproteome.9b00799

7. Fast Deisotoping Algorithm and Its Implementation in the MSFragger Search Engine

Author:
Teo, Guo Ci; Polasky, Daniel A.; Yu, Fengchao; Nesvizhskii, Alexey I.
Source:
Journal of proteome research 2020 v.20 no.1 pp. 498-505
ISSN:
1535-3907
Subject:
proteomics,   etc   ; algorithms; databases; proteome; research;     Show all 5 Subjects
Abstract:
... Deisotoping, or the process of removing peaks in a mass spectrum resulting from the incorporation of naturally occurring heavy isotopes, has long been used to reduce complexity and improve the effectiveness of spectral annotation methods in proteomics. We have previously described MSFragger, an ultrafast search engine for proteomics, that did not utilize deisotoping in processing input spectra. He ...
DOI:
10.1021/acs.jproteome.0c00544

8. MACMIC Reveals A Dual Role of CTCF in Epigenetic Regulation of Cell Identity Genes

Author:
Wang, Guangyu; Xia, Bo; Zhou, Man; Lv, Jie; Zhao, Dongyu; Li, Yanqiang; Bu, Yiwen; Wang, Xin; Cooke, John P.; Cao, Qi; Gyu Lee, Min; Zhang, Lili; Chen, Kaifu
Source:
Genomics, proteomics & bioinformatics 2020
ISSN:
1672-0229
Subject:
proteomics,   etc   ; bioinformatics; epigenetics; epigenome; genomics;     Show all 5 Subjects
Abstract:
... Numerous studies of relationship between epigenomic features have focused on their strong correlation across the genome, likely because such relationship can be easily identified by many established methods for correlation analysis. However, two features with little correlation may still colocalize at many genomic sites to implement important functions. There is no bioinformatic tool for researche ...
DOI:
10.1016/j.gpb.2020.10.008

9. Improved Monoisotopic Mass Estimation for Deeper Proteome Coverage

Author:
Rad, Ramin; Li, Jiaming; Mintseris, Julian; O’Connell, Jeremy; Gygi, Steven P.; Schweppe, Devin K.
Source:
Journal of proteome research 2020 v.20 no.1 pp. 591-598
ISSN:
1535-3907
Subject:
proteomics,   etc   ; algorithms; peptides; proteome; research;     Show all 5 Subjects
Abstract:
... Accurate assignment of monoisotopic peaks is essential for the identification of peptides in bottom-up proteomics. Misassignment or inaccurate attribution of peptidic ions leads to lower sensitivity and fewer total peptide identifications. In the present work, we present a performant, open-source, cross-platform algorithm, Monocle, for the rapid reassignment of instrument-assigned precursor peaks ...
DOI:
10.1021/acs.jproteome.0c00563

10. Importance of Block Randomization When Designing Proteomics Experiments

Author:
Burger, Bram; Vaudel, Marc; Barsnes, Harald
Source:
Journal of proteome research 2020 v.20 no.1 pp. 122-128
ISSN:
1535-3907
Subject:
proteomics,   etc   ; experimental design; proteome; research;     Show all 4 Subjects
Abstract:
... Randomization is used in experimental design to reduce the prevalence of unanticipated confounders. Complete randomization can however create imbalanced designs, for example, grouping all samples of the same condition in the same batch. Block randomization is an approach that can prevent severe imbalances in sample allocation with respect to both known and unknown confounders. This feature provide ...
DOI:
10.1021/acs.jproteome.0c00536

11. Quick microbial molecular phenotyping by differential shotgun proteomics

Author:
Gouveia, Duarte; Grenga, Lucia; Pible, Olivier; Armengaud, Jean
Source:
Environmental microbiology 2020 v.22 no.8 pp. 2996-3004
ISSN:
1462-2912
Subject:
proteomics,   etc   ; phenotype; tandem mass spectrometry;     Show all 3 Subjects
Abstract:
... Differential shotgun proteomics identifies proteins that discriminate between sets of samples based on differences in abundance. This methodology can be easily applied to study (i) specific microorganisms subjected to a variety of growth or stress conditions or (ii) different microorganisms sampled in the same condition. In microbiology, this comparison is particularly successful because differing ...
DOI:
10.1111/1462-2920.14975

12. Adaptation strategies of Pseudomonas protegens SN15‐2 to hyperosmotic growth environment

Author:
Wang, X.; Tang, D.; Wang, W.
Source:
Journal of applied microbiology 2020 v.128 no.6 pp. 1720-1734
ISSN:
1364-5072
Subject:
proteomics,   etc   ; Pseudomonas protegens; microbiology; transcriptomics;     Show all 4 Subjects
Abstract:
... AIMS: This study investigated the adaptation strategies of Pseudomonas protegens to hyperosmotic growth environments (HGE). METHODS AND RESULTS: The current study combined transcriptomics and proteomics to provide an overview of the molecular mechanism of P. protegens adaptation to HGE. The results revealed that HGE exerted prominent impact on the synthesis of proteins involved in multiple cellula ...
DOI:
10.1111/jam.14582

13. Label-free Proteomics for Discovering Biomarker Candidates for Controlling Krypton Misuse in Castrated Horses (Geldings)

Author:
Wong, Kin-Sing; Cheung, Hiu Wing; Choi, Timmy L. S.; Kwok, Wai Him; Curl, Peter; Mechie, Stewart C.; Prabhu, Anil; Wan, Terence S. M.; Ho, Emmie N. M.
Source:
Journal of proteome research 2020 v.19 no.3 pp. 1196-1208
ISSN:
1535-3907
Subject:
proteomics,   etc   ; biomarkers; castration; geldings; krypton;     Show all 5 Subjects
Abstract:
... Recent advances in label-free quantitative proteomics may support its application in identifying and monitoring biomarkers for the purpose of doping control in equine sports. In this study, we developed a workflow of label-free quantitative proteomics to propose plasma protein biomarkers in horses after administration with krypton (Kr), a potential erythropoiesis-stimulating agent. Plasma proteome ...
DOI:
10.1021/acs.jproteome.9b00724

14. Quantitative Proteomic Analysis of the Central Amygdala in Neuropathic Pain Model Rats

Author:
Karu, Kersti; Swanwick, Richard S.; Novejarque-Gadea, Amparo; Antunes-Martins, Ana; Thomas, Benjamin; Yoshimi, Eiji; Foster, William; Fang, Min; McMahon, Stephen B.; Bennett, David L. H.; Rice, Andrew S. C.; Okuse, Kenji
Source:
Journal of proteome research 2020 v.19 no.4 pp. 1592-1619
ISSN:
1535-3907
Subject:
proteomics,   etc   ; amygdala; models; pain; rats;     Show all 5 Subjects
Abstract:
... Pain and emotional distress have a reciprocal relation. The amygdala has been implicated in emotional processing. The central nucleus of the amygdala (CeA) receives nociceptive information from the dorsal horn of spinal cord and is responsible for the central plasticity in chronic pain. Neuropathic pain is a type of severe chronic pain and can be strongly influenced by emotional components. Plasti ...
DOI:
10.1021/acs.jproteome.9b00805

15. BatchServer: A Web Server for Batch Effect Evaluation, Visualization, and Correction

Author:
Zhu, Tiansheng; Sun, Rui; Zhang, Fangfei; Chen, Guo-Bo; Yi, Xiao; Ruan, Guan; Yuan, Chunhui; Zhou, Shuigeng; Guo, Tiannan
Source:
Journal of proteome research 2020 v.20 no.1 pp. 1079-1086
ISSN:
1535-3907
Subject:
proteomics,   etc   ; Internet; proteome; research; transcriptomics; variance;     Show all 6 Subjects
Abstract:
... Batch effects are unwanted data variations that may obscure biological signals, leading to bias or errors in subsequent data analyses. Effective evaluation and elimination of batch effects are necessary for omics data analysis. In order to facilitate the evaluation and correction of batch effects, here we present BatchSever, an open-source R/Shiny based user-friendly interactive graphical web plat ...
DOI:
10.1021/acs.jproteome.0c00488

16. Systems biology approaches integrated with artificial intelligence for optimized metabolic engineering

Author:
Helmy, Mohamed; Smith, Derek; Selvarajoo, Kumar
Source:
Metabolic Engineering Communications 2020 v.11 pp. e00149
ISSN:
2214-0301
Subject:
proteomics,   etc   ; artificial intelligence; biotechnology; metabolomics; multiomics; transcriptomics;     Show all 6 Subjects
Abstract:
... Metabolic engineering aims to maximize the production of bio-economically important substances (compounds, enzymes, or other proteins) through the optimization of the genetics, cellular processes and growth conditions of microorganisms. This requires detailed understanding of underlying metabolic pathways involved in the production of the targeted substances, and how the cellular processes or grow ...
DOI:
10.1016/j.mec.2020.e00149

17. Late-stage functionalization of peptides via a palladium-catalyzed C(sp³)–H activation strategy

Author:
Zhan, Bei-Bei; Jiang, Meng-Xue; Shi, Bing-Feng
Source:
Chemical communications 2020 v.56 no.90 pp. 13950-13958
ISSN:
1364-548X
Subject:
proteomics,   etc   ; diagnostic techniques; drugs; peptides; therapeutics;     Show all 5 Subjects
Abstract:
... Peptides hold great promise in proteomics, diagnostics and drug discovery. While natural peptides continue to be of key importance, chemically modified unnatural peptides have been found to show enhanced biological activities and improved therapeutic capabilities compared to their natural counterparts. Therefore, the development of efficient and versatile strategies to enable easy access to unnatu ...
DOI:
10.1039/d0cc06133f

18. Enhanced Validation of Antibodies Enables the Discovery of Missing Proteins

Author:
Sivertsson, Åsa; Lindström, Emil; Oksvold, Per; Katona, Borbala; Hikmet, Feria; Vuu, Jimmy; Gustavsson, Jonas; Sjöstedt, Evelina; von Feilitzen, Kalle; Kampf, Caroline; Schwenk, Jochen M.; Uhlén, Mathias; Lindskog, Cecilia
Source:
Journal of proteome research 2020 v.19 no.12 pp. 4766-4781
ISSN:
1535-3907
Subject:
proteomics,   etc   ; humans; immunohistochemistry; proteome; research; spatial data;     Show all 6 Subjects
Abstract:
... The localization of proteins at a tissue- or cell-type-specific level is tightly linked to the protein function. To better understand each protein’s role in cellular systems, spatial information constitutes an important complement to quantitative data. The standard methods for determining the spatial distribution of proteins in single cells of complex tissue samples make use of antibodies. For a s ...
DOI:
10.1021/acs.jproteome.0c00486

19. Identification of phostensin in association with Eps 15 homology domain-containing protein 1 (EHD1) and EHD4

Author:
Lin, Yu-Shan; Huang, Kuang-Yung; Yu, Hui-Chun; Lu, Ming-Chi; Fan, Cheng-Jhong; Huang Tseng, Hsien-Yu; Jhuang, Bi-Yao; Liu, Su-Qin; Lai, Ning-Sheng; Lin, Ta-Hsien; Huang, Hsien-Bin
Source:
Biochemical and biophysical research communications 2020 v.531 no.2 pp. 236-241
ISSN:
0006-291X
Subject:
proteomics,   etc   ; fluorescence microscopy; precipitin tests; research; transferrin;     Show all 5 Subjects
Abstract:
... Phostensin (PTS) encoded by KIAA1949 is a protein phosphatase 1 (PP1)-binding protein. In order to explore the cellular functions of PTS, we have searched PTS-binding proteins by using co-immunoprecipitation in combination with shotgun proteomics. Here, we report two novel PTS-binding proteins, Eps 15 homology domain-containing protein 1 (EHD1) and EHD4. PTS associated with EHD proteins was also o ...
DOI:
10.1016/j.bbrc.2020.07.030

20. Improved Sensitivity of Ultralow Flow LC–MS-Based Proteomic Profiling of Limited Samples Using Monolithic Capillary Columns and FAIMS Technology

Author:
Greguš, Michal; Kostas, James C.; Ray, Somak; Abbatiello, Susan E.; Ivanov, Alexander R.
Source:
Analytical chemistry 2020 v.92 no.21 pp. 14702-14712
ISSN:
1520-6882
Subject:
proteomics,   etc   ; analytical chemistry; myeloid leukemia; peptides;     Show all 4 Subjects
Abstract:
... In this work, we pioneered a combination of ultralow flow (ULF) high-efficiency ultranarrow bore monolithic LC columns coupled to MS via a high-field asymmetric waveform ion mobility spectrometry (FAIMS) interface to evaluate the potential applicability for high sensitivity, robust, and reproducible proteomic profiling of low nanogram-level complex biological samples. As a result, ULF LC-FAIMS-MS ...
DOI:
10.1021/acs.analchem.0c03262