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Annual Review of Plant Biology May 2022Proteins are intimately involved in executing and controlling virtually all cellular processes. To understand the molecular mechanisms that underlie plant phenotypes, it... (Review)
Review
Proteins are intimately involved in executing and controlling virtually all cellular processes. To understand the molecular mechanisms that underlie plant phenotypes, it is essential to investigate protein expression, interactions, and modifications, to name a few. The proteome is highly dynamic in time and space, and a plethora of protein modifications, protein interactions, and network constellations are at play under specific conditions and developmental stages. Analysis of proteomes aims to characterize the entire protein complement of a particular cell type, tissue, or organism-a challenging task, given the dynamic nature of the proteome. Modern mass spectrometry-based proteomics technology can be used to address this complexity at a system-wide scale by the global identification and quantification of thousands of proteins. In this review, we present current methods and technologies employed in mass spectrometry-based proteomics and provide examples of dynamic changes in the plant proteome elucidated by proteomic approaches.
Topics: Mass Spectrometry; Plants; Protein Processing, Post-Translational; Proteome; Proteomics
PubMed: 35138880
DOI: 10.1146/annurev-arplant-102620-031308 -
Molecular Systems Biology Mar 2022Single-cell technologies are revolutionizing biology but are today mainly limited to imaging and deep sequencing. However, proteins are the main drivers of cellular...
Single-cell technologies are revolutionizing biology but are today mainly limited to imaging and deep sequencing. However, proteins are the main drivers of cellular function and in-depth characterization of individual cells by mass spectrometry (MS)-based proteomics would thus be highly valuable and complementary. Here, we develop a robust workflow combining miniaturized sample preparation, very low flow-rate chromatography, and a novel trapped ion mobility mass spectrometer, resulting in a more than 10-fold improved sensitivity. We precisely and robustly quantify proteomes and their changes in single, FACS-isolated cells. Arresting cells at defined stages of the cell cycle by drug treatment retrieves expected key regulators. Furthermore, it highlights potential novel ones and allows cell phase prediction. Comparing the variability in more than 430 single-cell proteomes to transcriptome data revealed a stable-core proteome despite perturbation, while the transcriptome appears stochastic. Our technology can readily be applied to ultra-high sensitivity analyses of tissue material, posttranslational modifications, and small molecule studies from small cell counts to gain unprecedented insights into cellular heterogeneity in health and disease.
Topics: Mass Spectrometry; Protein Processing, Post-Translational; Proteome; Proteomics; Workflow
PubMed: 35226415
DOI: 10.15252/msb.202110798 -
Biochimica Et Biophysica Acta Aug 2016Although major advances have been made during the past 20 years in our understanding of the genetic and genomic consequences of polyploidy, our knowledge of polyploidy... (Review)
Review
Although major advances have been made during the past 20 years in our understanding of the genetic and genomic consequences of polyploidy, our knowledge of polyploidy and the proteome is in its infancy. One of our goals is to stimulate additional study, particularly broad-scale proteomic analyses of polyploids and their progenitors. Although it may be too early to generalize regarding the extent to which transcriptomic data are predictive of the proteome of polyploids, it is clear that the proteome does not always reflect the transcriptome. Despite limited data, important observations on the proteomes of polyploids are emerging. In some cases, proteomic profiles show qualitatively and/or quantitatively non-additive patterns, and proteomic novelty has been observed. Allopolyploids generally combine the parental contributions, but there is evidence of parental dominance of one contributing genome in some allopolyploids. Autopolyploids are typically qualitatively identical to but quantitatively different from their parents. There is also evidence of parental legacy at the proteomic level. Proteomes clearly provide insights into the consequences of genomic merger and doubling beyond what is obtained from genomic and/or transcriptomic data. Translating proteomic changes in polyploids to differences in morphology and physiology remains the holy grail of polyploidy--this daunting task of linking genotype to proteome to phenotype should emerge as a focus of polyploidy research in the next decade. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
Topics: Gene Expression Profiling; Plant Proteins; Plants; Polyploidy; Proteome; Proteomics
PubMed: 26993527
DOI: 10.1016/j.bbapap.2016.03.010 -
Current Opinion in Chemical Biology Feb 2015Advances in mass spectrometry (MS) have transformed the scope and impact of protein characterization efforts. Identifying hundreds of proteins from rather simple... (Review)
Review
Advances in mass spectrometry (MS) have transformed the scope and impact of protein characterization efforts. Identifying hundreds of proteins from rather simple biological matrices, such as yeast, was a daunting task just a few decades ago. Now, expression of more than half of the estimated ∼20,000 human protein coding genes can be confirmed in record time and from minute sample quantities. Access to proteomic information at such unprecedented depths has been fueled by strides in every stage of the shotgun proteomics workflow-from sample processing to data analysis-and promises to revolutionize our understanding of the causes and consequences of proteome variation.
Topics: Humans; Mass Spectrometry; Peptides; Proteome; Proteomics
PubMed: 25461719
DOI: 10.1016/j.cbpa.2014.10.017 -
Current Opinion in Hematology Sep 2009The proteome is the pool of proteins expressed at a given time and circumstance. The word 'proteomics' summarizes several technologies for visualization, quantitation... (Review)
Review
PURPOSE OF REVIEW
The proteome is the pool of proteins expressed at a given time and circumstance. The word 'proteomics' summarizes several technologies for visualization, quantitation and identification of these proteins. Recent advances in these techniques are helping to elucidate platelet processes which are relevant to bleeding and clotting disorders, transfusion medicine and regulation of angiogenesis.
RECENT FINDINGS
Over 1100 platelet proteins have been identified using proteomic techniques. Various subproteomes have been characterized, including platelet releasates (the 'secretome'), alpha and dense granules, membrane and cytoskeletal proteins, platelet-derived microparticles, and the platelet 'phosphoproteome'. Proteomic data about platelets have become increasingly available in integrated databases.
SUMMARY
Proteomic experiments in resting and activated platelets have identified novel signaling pathways and secreted proteins which may represent therapeutic targets, as well as potential cancer biomarkers.
Topics: Blood Platelets; Cell-Derived Microparticles; Humans; Platelet Activation; Proteome; Proteomics; Signal Transduction
PubMed: 19550320
DOI: 10.1097/MOH.0b013e32832e9dc6 -
Methods in Molecular Biology (Clifton,... 2021In recent decades, mass spectrometry has moved more than ever before into the front line of protein-centered research. After being established at the qualitative level,... (Review)
Review
In recent decades, mass spectrometry has moved more than ever before into the front line of protein-centered research. After being established at the qualitative level, the more challenging question of quantification of proteins and peptides using mass spectrometry has become a focus for further development. In this chapter, we discuss and review actual strategies and problems of the methods for the quantitative analysis of peptides, proteins, and finally proteomes by mass spectrometry. The common themes, the differences, and the potential pitfalls of the main approaches are presented in order to provide a survey of the emerging field of quantitative, mass spectrometry-based proteomics.
Topics: Animals; Humans; Mass Spectrometry; Proteins; Proteome; Proteomics
PubMed: 33950486
DOI: 10.1007/978-1-0716-1024-4_8 -
Briefings in Bioinformatics Jan 2021Empowered by the advancement of high-throughput bio technologies, recent research on body-fluid proteomes has led to the discoveries of numerous novel disease biomarkers... (Review)
Review
Empowered by the advancement of high-throughput bio technologies, recent research on body-fluid proteomes has led to the discoveries of numerous novel disease biomarkers and therapeutic drugs. In the meantime, a tremendous progress in disclosing the body-fluid proteomes was made, resulting in a collection of over 15 000 different proteins detected in major human body fluids. However, common challenges remain with current proteomics technologies about how to effectively handle the large variety of protein modifications in those fluids. To this end, computational effort utilizing statistical and machine-learning approaches has shown early successes in identifying biomarker proteins in specific human diseases. In this article, we first summarized the experimental progresses using a combination of conventional and high-throughput technologies, along with the major discoveries, and focused on current research status of 16 types of body-fluid proteins. Next, the emerging computational work on protein prediction based on support vector machine, ranking algorithm, and protein-protein interaction network were also surveyed, followed by algorithm and application discussion. At last, we discuss additional critical concerns about these topics and close the review by providing future perspectives especially toward the realization of clinical disease biomarker discovery.
Topics: Biomarkers; Body Fluids; Humans; Proteome; Proteomics
PubMed: 32020158
DOI: 10.1093/bib/bbz160 -
Molecular Cancer Feb 2022Alterations in DNAs could not reveal what happened in proteins. The accumulated alterations of DNAs would change the manifestation of proteins. Therefore, as is the case... (Review)
Review
Alterations in DNAs could not reveal what happened in proteins. The accumulated alterations of DNAs would change the manifestation of proteins. Therefore, as is the case in cancer liquid biopsies, deep proteome profiling will likely provide invaluable and clinically relevant information in real-time throughout all stages of cancer progression. However, due to the great complexity of proteomes in liquid biopsy samples and the limitations of proteomic technologies compared to high-plex sequencing technologies, proteomic discoveries have yet lagged behind their counterpart, genomic technologies. Therefore, novel protein technologies are in urgent demand to fulfill the goals set out for biomarker discovery in cancer liquid biopsies.Notably, conventional and innovative technologies are being rapidly developed for proteomic analysis in cancer liquid biopsies. These advances have greatly facilitated early detection, diagnosis, prognosis, and monitoring of cancer evolution, adapted or adopted in response to therapeutic interventions. In this paper, we review the high-plex proteomics technologies that are capable of measuring at least hundreds of proteins simultaneously from liquid biopsy samples, ranging from traditional technologies based on mass spectrometry (MS) and antibody/antigen arrays to innovative technologies based on aptamer, proximity extension assay (PEA), and reverse phase protein arrays (RPPA).
Topics: Early Detection of Cancer; Humans; Liquid Biopsy; Neoplasms; Proteome; Proteomics
PubMed: 35168611
DOI: 10.1186/s12943-022-01526-8 -
Cancer Cell Aug 2022The proteome provides unique insights into disease biology beyond the genome and transcriptome. A lack of large proteomic datasets has restricted the identification of...
The proteome provides unique insights into disease biology beyond the genome and transcriptome. A lack of large proteomic datasets has restricted the identification of new cancer biomarkers. Here, proteomes of 949 cancer cell lines across 28 tissue types are analyzed by mass spectrometry. Deploying a workflow to quantify 8,498 proteins, these data capture evidence of cell-type and post-transcriptional modifications. Integrating multi-omics, drug response, and CRISPR-Cas9 gene essentiality screens with a deep learning-based pipeline reveals thousands of protein biomarkers of cancer vulnerabilities that are not significant at the transcript level. The power of the proteome to predict drug response is very similar to that of the transcriptome. Further, random downsampling to only 1,500 proteins has limited impact on predictive power, consistent with protein networks being highly connected and co-regulated. This pan-cancer proteomic map (ProCan-DepMapSanger) is a comprehensive resource available at https://cellmodelpassports.sanger.ac.uk.
Topics: Biomarkers, Tumor; Cell Line; Humans; Neoplasms; Proteome; Proteomics
PubMed: 35839778
DOI: 10.1016/j.ccell.2022.06.010 -
Nucleic Acids Research Jan 2022Proteome-pI 2.0 is an update of an online database containing predicted isoelectric points and pKa dissociation constants of proteins and peptides. The isoelectric...
Proteome-pI 2.0 is an update of an online database containing predicted isoelectric points and pKa dissociation constants of proteins and peptides. The isoelectric point-the pH at which a particular molecule carries no net electrical charge-is an important parameter for many analytical biochemistry and proteomics techniques. Additionally, it can be obtained directly from the pKa values of individual charged residues of the protein. The Proteome-pI 2.0 database includes data for over 61 million protein sequences from 20 115 proteomes (three to four times more than the previous release). The isoelectric point for proteins is predicted by 21 methods, whereas pKa values are inferred by one method. To facilitate bottom-up proteomics analysis, individual proteomes were digested in silico with the five most commonly used proteases (trypsin, chymotrypsin, trypsin + LysC, LysN, ArgC), and the peptides' isoelectric point and molecular weights were calculated. The database enables the retrieval of virtual 2D-PAGE plots and customized fractions of a proteome based on the isoelectric point and molecular weight. In addition, isoelectric points for proteins in NCBI non-redundant (nr), UniProt, SwissProt, and Protein Data Bank are available in both CSV and FASTA formats. The database can be accessed at http://isoelectricpointdb2.org.
Topics: Amino Acid Sequence; Computational Biology; Databases, Protein; Electrophoresis, Gel, Two-Dimensional; Isoelectric Point; Molecular Weight; Peptides; Proteome; Proteomics
PubMed: 34718696
DOI: 10.1093/nar/gkab944