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1. SWATH-MS-Based Proteomics: Strategies and Applications in Plants

Author:
Chen, Mo-Xian; Zhang, Youjun; Fernie, Alisdair R.; Liu, Ying-Gao; Zhu, Fu-Yuan
Source:
Trends in biotechnology 2021 v.39 no.5 pp. 433-437
ISSN:
0167-7799
Subject:
proteomics,   etc   ; animals; biotechnology;     Show all 3 Subjects
Abstract:
... Most applied proteomic approaches require labeling steps. Recent technological advances provide an alternative label-free proteomics approach: SWATH-MS. This powerful tool is now widely used in animal studies but has drawn far less attention in plants. Here we summarize how this promising technology can be applied to facilitate functional analysis in plant research. ...
DOI:
10.1016/j.tibtech.2020.09.002

2. Discovery of post-translational modifications in immunometabolism by chemical proteomics

Author:
Zhang, Yanling; Qin, Wei; Wang, Chu
Source:
Current opinion in biotechnology 2021 v.68 pp. 37-43
ISSN:
0958-1669
Subject:
proteomics,   etc   ; biotechnology; macrophages; metabolites;     Show all 4 Subjects
Abstract:
... Metabolic reprogramming of macrophages during immune activation can generate diversified types of small molecule metabolites, which in turn induce post-translational modifications (PTMs) on proteins. Understanding the functional implications of these modifications requires precise identification of them from complex biological samples. We herein review recent progress in systematic discovery of im ...
DOI:
10.1016/j.copbio.2020.09.013

3. The earless monitor lizard Lanthanotus borneensis – A venomous animal?

Author:
Mebs, Dietrich; Lomonte, Bruno; Fernández, Julián; Calvete, Juan J.; Sanz, Libia; Mahlow, Kristin; Müller, Johannes; Köhler, Gunther; Zollweg, Michael
Source:
Toxicon 2021 v.189 pp. 73-78
ISSN:
0041-0101
Subject:
proteomics,   etc   ; Heloderma; lizards; secretion;     Show all 4 Subjects
Abstract:
... Based on its mandibular gland secretion, the earless monitor lizard, Lanthanotus borneensis, has been considered a venomous animal like other members of the Toxicofera group, including Heloderma. In the present study, the gland structure and teeth of L. borneensis were examined by micro-tomography (μCT) and scanning electron microscopy (SEM), respectively, and proteomic analysis of the gland extra ...
DOI:
10.1016/j.toxicon.2020.11.013

4. Metaproteomic sample preparation methods bias the recovery of host and microbial proteins according to taxa and cellular compartment

Author:
Gavin, Patrick G.; Wong, Justin; Loo, Dorothy; Zipris, Danny; Hill, Michelle M.; Hamilton-Williams, Emma E.
Source:
Journal of proteomics 2021 v.240 pp. 104219
ISSN:
1874-3919
Subject:
proteomics,   etc   ; Bacteroidales; centrifugation; fractionation; intestines;     Show all 5 Subjects
Abstract:
... Faecal proteomics studies have focussed on identification of microbial proteins, however; stool represents a valuable resource to interrogate the host interactions with the microbiota without the need for invasive intestinal biopsies. As the widely used enrichment method (differential centrifugation, DC) enriches for microbial proteins, we compared two other methods for enrichment of host proteins ...
DOI:
10.1016/j.jprot.2021.104219

5. Systematically defining selective autophagy receptor-specific cargo using autophagosome content profiling

Author:
Zellner, Susanne; Schifferer, Martina; Behrends, Christian
Source:
Molecular cell 2021 v.81 no.6 pp. 1337-1354.e8
ISSN:
1097-2765
Subject:
proteomics,   etc   ; autophagosomes; dissection; humans; macroautophagy;     Show all 5 Subjects
Abstract:
... Autophagy deficiency in fed conditions leads to the formation of protein inclusions highlighting the contribution of this lysosomal delivery route to cellular proteostasis. Selective autophagy pathways exist that clear accumulated and aggregated ubiquitinated proteins. Receptors for this type of autophagy (aggrephagy) include p62, NBR1, TOLLIP, and OPTN, which possess LC3-interacting regions and u ...
DOI:
10.1016/j.molcel.2021.01.009

6. A Second Look at FAIR in Proteomic Investigations

Author:
Caufield, J. Harry; Fu, John; Wang, Ding; Guevara-Gonzalez, Vladimir; Wang, Wei; Ping, Peipei
Source:
Journal of proteome research 2021 v.20 no.5 pp. 2182-2186
ISSN:
1535-3907
Subject:
proteomics,   etc   ; phenotype; proteome; research; stakeholders;     Show all 5 Subjects
Abstract:
... Proteomics is, by definition, comprehensive and large-scale, seeking to unravel ome-level protein features with phenotypic information on an entire system, an organ, cells, or organisms. This scope consistently involves and extends beyond single experiments. Multitudinous resources now exist to assist in making the results of proteomics experiments more findable, accessible, interoperable, and reu ...
DOI:
10.1021/acs.jproteome.1c00177

7. Inflect: Optimizing Computational Workflows for Thermal Proteome Profiling Data Analysis

Author:
McCracken, Neil A.; Peck Justice, Sarah A.; Wijeratne, Aruna B.; Mosley, Amber L.
Source:
Journal of proteome research 2021 v.20 no.4 pp. 1874-1888
ISSN:
1535-3907
Subject:
proteomics,   etc   ; data analysis; proteome; research;     Show all 4 Subjects
Abstract:
... The CETSA and Thermal Proteome Profiling (TPP) analytical methods are invaluable for the study of protein–ligand interactions and protein stability in a cellular context. These tools have increasingly been leveraged in work ranging from understanding signaling paradigms to drug discovery. Consequently, there is an important need to optimize the data analysis pipeline that is used to calculate prot ...
DOI:
10.1021/acs.jproteome.0c00872

8. mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection

Author:
Fondrie, William E.; Noble, William S.
Source:
Journal of proteome research 2021 v.20 no.4 pp. 1966-1971
ISSN:
1535-3907
Subject:
proteomics,   etc   ; algorithms; peptides; proteome; research;     Show all 5 Subjects
Abstract:
... Proteomics studies rely on the accurate assignment of peptides to the acquired tandem mass spectra—a task where machine learning algorithms have proven invaluable. We describe mokapot, which provides a flexible semisupervised learning algorithm that allows for highly customized analyses. We demonstrate some of the unique features of mokapot by improving the detection of RNA-cross-linked peptides f ...
DOI:
10.1021/acs.jproteome.0c01010

9. Dissecting the Structural Dynamics of the Nuclear Pore Complex

Author:
Hakhverdyan, Zhanna; Molloy, Kelly R.; Keegan, Sarah; Herricks, Thurston; Lepore, Dante M.; Munson, Mary; Subbotin, Roman I.; Fenyö, David; Aitchison, John D.; Fernandez-Martinez, Javier; Chait, Brian T.; Rout, Michael P.
Source:
Molecular cell 2021 v.81 no.1 pp. 153-165.e7
ISSN:
1097-2765
Subject:
proteomics,   etc   ; cytoplasm; nuclear pore; yeasts;     Show all 4 Subjects
Abstract:
... Cellular processes are largely carried out by macromolecular assemblies, most of which are dynamic, having components that are in constant flux. One such assembly is the nuclear pore complex (NPC), an ∼50 MDa assembly comprised of ∼30 different proteins called Nups that mediates selective macromolecular transport between the nucleus and cytoplasm. We developed a proteomics method to provide a comp ...
DOI:
10.1016/j.molcel.2020.11.032

10. Diagenetiforms: A new term to explain protein changes as a result of diagenesis in paleoproteomics

Author:
Cleland, Timothy P.; Schroeter, Elena R.; Colleary, Caitlin
Source:
Journal of proteomics 2021 v.230 pp. 103992
ISSN:
1874-3919
Subject:
proteomics,   etc   ; archaeology; diagenesis; proteins; proteome;     Show all 5 Subjects
Abstract:
... The term proteoform describes all combinations of change in a protein, as elucidated through intact mass proteomics. Paleoproteomic studies have begun using digestion-free and top-down techniques to access information from ancient and historical remains. However, to discuss protein changes that uniquely occur to archaeological and paleontological proteomes as the result of diagenesis (i.e., physic ...
DOI:
10.1016/j.jprot.2020.103992

11. Giotto: a toolbox for integrative analysis and visualization of spatial expression data

Author:
Dries, Ruben; Zhu, Qian; Dong, Rui; Eng, Chee-Huat Linus; Li, Huipeng; Liu, Kan; Fu, Yuntian; Zhao, Tianxiao; Sarkar, Arpan; Bao, Feng; George, Rani E.; Pierson, Nico; Cai, Long; Yuan, Guo-Cheng
Source:
Genome biology 2021 v.22 no.1 pp. 78
ISSN:
1474-760X
Subject:
proteomics,   etc   ; data collection; genome; spatial data; transcriptomics;     Show all 5 Subjects
Abstract:
... Spatial transcriptomic and proteomic technologies have provided new opportunities to investigate cells in their native microenvironment. Here we present Giotto, a comprehensive and open-source toolbox for spatial data analysis and visualization. The analysis module provides end-to-end analysis by implementing a wide range of algorithms for characterizing tissue composition, spatial expression patt ...
DOI:
10.1186/s13059-021-02286-2

12. Advances in functional proteomics to study plant-pathogen interactions

Author:
Elmore, James M.; Griffin, Brianna D.; Walley, Justin W.
Source:
Current opinion in plant biology 2021 v.63 pp. 102061
ISSN:
1369-5266
Subject:
proteomics,   etc   ; enzymes; pathogens; plant biology; proteome;     Show all 5 Subjects
Abstract:
... Pathogen infection triggers complex signaling networks in plant cells that ultimately result in either susceptibility or resistance. We have made substantial progress in dissecting many of these signaling events, and it is becoming clear that changes in proteome composition and protein activity are major drivers of plant-microbe interactions. Here, we highlight different approaches to analyze the ...
DOI:
10.1016/j.pbi.2021.102061

13. Constrained Standardization of Count Data from Massive Parallel Sequencing

Author:
Van Houtven, Joris; Cuypers, Bart; Meysman, Pieter; Hooyberghs, Jef; Laukens, Kris; Valkenborg, Dirk
Source:
Journal of molecular biology 2021 v.433 no.11 pp. 166966
ISSN:
0022-2836
Subject:
proteomics,   etc   ; molecular biology; multiomics; statistical analysis; transcriptomics;     Show all 5 Subjects
Abstract:
... In high-throughput omics disciplines like transcriptomics, researchers face a need to assess the quality of an experiment prior to an in-depth statistical analysis. To efficiently analyze such voluminous collections of data, researchers need triage methods that are both quick and easy to use. Such a normalization method for relative quantitation, CONSTANd, was recently introduced for isobarically- ...
DOI:
10.1016/j.jmb.2021.166966

14. Proteomic profile of eps-urine through fasp digestion and data-independent analysis

Author:
Prestagiacomo, Licia E.; Gabriele, Caterina; Morelli, Paola; Rota, Maria Antonietta; Alba, Stefano; Cuda, Giovanni; Damiano, Rocco; Gaspari, Marco
Source:
Journal of visualized experiments 2021 no.171 pp. e62512
ISSN:
1940-087X
Subject:
proteomics,   etc   ; biomarkers; digestion; prostatic neoplasms; proteome;     Show all 5 Subjects
Abstract:
... Filter-aided sample protocol (FASP) is widely used for proteomics sample preparation because it allows to concentrate diluted samples and it is compatible with a wide variety of detergents. Bottom-up proteomics workflows like FASP increasingly rely on LC-MS/MS methods performed in data-independent analysis (DIA) mode, a scanning method that allows deep proteome coverage and low incidence of missin ...
DOI:
10.3791/62512

15. Cross‐linking mass spectrometry reveals the structural topology of peripheral NuRD subunits relative to the core complex

Author:
Spruijt, Cornelia G.; Gräwe, Cathrin; Kleinendorst, Simone C.; Baltissen, Marijke P. A.; Vermeulen, Michiel
Source:
TheFEBS journal 2021 v.288 no.10 pp. 3231-3245
ISSN:
1742-464X
Subject:
proteomics,   etc   ; crosslinking; databases; mass spectrometry; nucleosomes; topology;     Show all 6 Subjects
Abstract:
... The multi‐subunit nucleosome remodeling and deacetylase (NuRD) complex consists of seven subunits, each of which comprises two or three paralogs in vertebrates. These paralogs define mutually exclusive and functionally distinct complexes. In addition, several proteins in the complex are multimeric, which complicates structural studies. Attempts to purify sufficient amounts of endogenous complex or ...
DOI:
10.1111/febs.15650

16. Chemical Proteomics Approach for Profiling the NAD Interactome

Author:
Šileikytė, Justina; Sundalam, Sunil; David, Larry L.; Cohen, Michael S.
Source:
Journal of the American Chemical Society 2021 v.143 no.18 pp. 6787-6791
ISSN:
1520-5126
Subject:
proteomics,   etc   ; NAD (coenzyme); post-translational modification;     Show all 3 Subjects
Abstract:
... Nicotinamide adenine dinucleotide (NAD⁺) is a multifunctional molecule. Beyond redox metabolism, NAD⁺ has an equally important function as a substrate for post-translational modification enzymes, the largest family being the poly-ADP–ribose polymerases (PARPs, 17 family members in humans). The recent surprising discoveries of noncanonical NAD (NAD⁺/NADH)-binding proteins suggests that the NAD inte ...
DOI:
10.1021/jacs.1c01302

17. Theoretical Considerations for Next-Generation Proteomics

Author:
Palmblad, Magnus
Source:
Journal of proteome research 2021 v.20 no.6 pp. 3395-3399
ISSN:
1535-3907
Subject:
proteomics,   etc   ; humans; mass spectrometry; peptides; proteome; research;     Show all 6 Subjects
Abstract:
... While mass spectrometry still dominates proteomics research, alternative and potentially disruptive, next-generation technologies are receiving increased investment and attention. Most of these technologies aim at the sequencing of single peptide or protein molecules, typically labeling or otherwise distinguishing a subset of the proteinogenic amino acids. This note considers some theoretical aspe ...
DOI:
10.1021/acs.jproteome.1c00136

18. Discovery of Novel Protein Biomarkers in Urine for Diagnosis of Urothelial Cancer Using iTRAQ Proteomics

Author:
Chen, Chao-Jung; Chou, Che-Yi; Shu, Kuo-Hsiung; Chen, Hung-Chun; Wang, Ming-Cheng; Chang, Chia-Chu; Hsu, Bang-Gee; Wu, Mai-Szu; Yang, Yuan-Lung; Liao, Wen-Ling; Yang, Chieh; Hsiao, Yu-Tien; Huang, Chiu-Ching
Source:
Journal of proteome research 2021 v.20 no.5 pp. 2953-2963
ISSN:
1535-3907
Subject:
proteomics,   etc   ; biomarkers; carcinoma; monitoring; proteome; research; urine;     Show all 7 Subjects
Abstract:
... Urothelial carcinoma (UC) is the ninth most prevalent malignancy worldwide. Noninvasive and efficient biomarkers with high accuracy are imperative for the surveillance and diagnosis of UC. CKD patients were enrolled as a control group in this study for the discovery of highly specific urinary protein markers of UC. An iTRAQ-labeled quantitative proteomic approach was used to discover novel potenti ...
DOI:
10.1021/acs.jproteome.1c00164

19. Proteomics Software in bio.tools: Coverage and Annotations

Author:
Schwämmle, Veit; Harrow, Jennifer; Ienasescu, Hans
Source:
Journal of proteome research 2021 v.20 no.4 pp. 1821-1825
ISSN:
1535-3907
Subject:
proteomics,   etc   ; bioinformatics; biomedical research; computer software; proteome;     Show all 5 Subjects
Abstract:
... The large diversity of experimental methods in proteomics as well as their increasing usage across biological and clinical research has led to the development of hundreds if not thousands of software tools to aid in the analysis and interpretation of the resulting data. Detailed information about these tools needs to be collected, categorized, and validated to guarantee their optimal utilization. ...
DOI:
10.1021/acs.jproteome.0c00978

20. leapR: An R Package for Multiomic Pathway Analysis

Author:
Danna, Vincent; Mitchell, Hugh; Anderson, Lindsey; Godinez, Iobani; Gosline, Sara J. C.; Teeguarden, Justin; McDermott, Jason E.
Source:
Journal of proteome research 2021 v.20 no.4 pp. 2116-2121
ISSN:
1535-3907
Subject:
proteomics,   etc   ; genomics; metabolomics; proteome; research; transcriptomics;     Show all 6 Subjects
Abstract:
... A generalized goal of many high-throughput data studies is to identify functional mechanisms that underlie observed biological phenomena, whether they be disease outcomes or metabolic output. Increasingly, studies that rely on multiple sources of high-throughput data (genomic, transcriptomic, proteomic, metabolomic) are faced with a challenge of summarizing the data to generate testable hypotheses ...
DOI:
10.1021/acs.jproteome.0c00963