Molecular & cellular proteomics : MCP最新文献

{"title":"Decoding Post-Translational Modification Crosstalk With Proteomics.","authors":"Mario Leutert,&nbsp;Samuel W Entwisle,&nbsp;Judit Villén","doi":"10.1016/j.mcpro.2021.100129","DOIUrl":"https://doi.org/10.1016/j.mcpro.2021.100129","url":null,"abstract":"<p><p>Post-translational modification (PTM) of proteins allows cells to regulate protein functions, transduce signals and respond to perturbations. PTMs expand protein functionality and diversity, which leads to increased proteome complexity. PTM crosstalk describes the combinatorial action of multiple PTMs on the same or on different proteins for higher order regulation. Here we review how recent advances in proteomic technologies, mass spectrometry instrumentation, and bioinformatics spurred the proteome-wide identification of PTM crosstalk through measurements of PTM sites. We provide an overview of the basic modes of PTM crosstalk, the proteomic methods to elucidate PTM crosstalk, and approaches that can inform about the functional consequences of PTM crosstalk.</p>","PeriodicalId":519518,"journal":{"name":"Molecular & cellular proteomics : MCP","volume":" ","pages":"100129"},"PeriodicalIF":7.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.mcpro.2021.100129","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39268659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantitative Ubiquitylome Analysis Reveals the Specificity of RNF111/Arkadia E3 Ubiquitin Ligase for its Degradative Substrates SKI and SKIL/SnoN in TGF-β Signaling Pathway.","authors":"Victor Laigle,&nbsp;Florent Dingli,&nbsp;Sadek Amhaz,&nbsp;Tiphaine Perron,&nbsp;Mouna Chouchène,&nbsp;Sabrina Colasse,&nbsp;Isabelle Petit,&nbsp;Patrick Poullet,&nbsp;Damarys Loew,&nbsp;Céline Prunier,&nbsp;Laurence Levy","doi":"10.1016/j.mcpro.2021.100173","DOIUrl":"https://doi.org/10.1016/j.mcpro.2021.100173","url":null,"abstract":"<p><p>RNF111/Arkadia is an E3 ubiquitin ligase that activates the transforming growth factor-β (TGF-β) pathway by degrading transcriptional repressors SKIL/SnoN and SKI. Truncations of the RING C-terminal domain of RNF111 that abolish its E3 function and subsequently activate TGF-β signaling are observed in some cancers. In the present study, we sought to perform a comprehensive analysis of RNF111 endogenous substrates upon TGF-β signaling activation using an integrative proteomic approach. In that aim, we carried out label-free quantitative proteomics after the enrichment of ubiquitylated proteins (ubiquitylome) in parental U2OS cell line compared with U2OS CRISPR engineered clones expressing a truncated form of RNF111 devoid of its C-terminal RING domain. We compared two methods of enrichment for ubiquitylated proteins before proteomics analysis by mass spectrometry, the diGlycine (diGly) remnant peptide immunoprecipitation with a K-ε-GG antibody, and a novel approach using protein immunoprecipitation with a ubiquitin pan nanobody that recognizes all ubiquitin chains and monoubiquitylation. Although we detected SKIL ubiquitylation among 108 potential RNF111 substrates with the diGly method, we found that the ubiquitin pan nanobody method also constitutes a powerful approach because it enabled the detection of 52 potential RNF111 substrates including SKI, SKIL, and RNF111. Integrative comparison of the RNF111-dependent proteome and ubiquitylomes enabled the identification of SKI and SKIL as the only targets ubiquitylated and degraded by RNF111 E3 ligase function in the presence of TGF-β. Our results indicate that lysine 343 localized in the SAND domain of SKIL constitutes a target for RNF111 ubiquitylation and demonstrate that RNF111 E3 ubiquitin ligase function specifically targets SKI and SKIL ubiquitylation and degradation upon TGF-β pathway activation.</p>","PeriodicalId":519518,"journal":{"name":"Molecular & cellular proteomics : MCP","volume":" ","pages":"100173"},"PeriodicalIF":7.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8665411/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39847755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chromatin Proteomics to Study Epigenetics - Challenges and Opportunities.","authors":"Guido van Mierlo,&nbsp;Michiel Vermeulen","doi":"10.1074/mcp.R120.002208","DOIUrl":"https://doi.org/10.1074/mcp.R120.002208","url":null,"abstract":"<p><p>Regulation of gene expression is essential for the functioning of all eukaryotic organisms. Understanding gene expression regulation requires determining which proteins interact with regulatory elements in chromatin. MS-based analysis of chromatin has emerged as a powerful tool to identify proteins associated with gene regulation, as it allows studying protein function and protein complex formation in their in vivo chromatin-bound context. Total chromatin isolated from cells can be directly analyzed using MS or further fractionated into transcriptionally active and inactive chromatin prior to MS-based analysis. Newly formed chromatin that is assembled during DNA replication can also be specifically isolated and analyzed. Furthermore, capturing specific chromatin domains facilitates the identification of previously unknown transcription factors interacting with these domains. Finally, in recent years, advances have been made toward identifying proteins that interact with a single genomic locus of interest. In this review, we highlight the power of chromatin proteomics approaches and how these provide complementary alternatives compared with conventional affinity purification methods. Furthermore, we discuss the biochemical challenges that should be addressed to consolidate and expand the role of chromatin proteomics as a key technology in the context of gene expression regulation and epigenetics research in health and disease.</p>","PeriodicalId":519518,"journal":{"name":"Molecular & cellular proteomics : MCP","volume":" ","pages":"100056"},"PeriodicalIF":7.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1074/mcp.R120.002208","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25344560","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantitative Proteomics Reveals Association of Neuron Projection Development Genes ARF4, KIF5B, and RAB8A With Hirschsprung Disease.","authors":"Qin Zhang,&nbsp;Lihua Wu,&nbsp;Baoling Bai,&nbsp;Dan Li,&nbsp;Ping Xiao,&nbsp;Qi Li,&nbsp;Zhen Zhang,&nbsp;Hui Wang,&nbsp;Long Li,&nbsp;Qian Jiang","doi":"10.1074/mcp.RA120.002325","DOIUrl":"https://doi.org/10.1074/mcp.RA120.002325","url":null,"abstract":"<p><p>Hirschsprung disease (HSCR) is a heterogeneous group of neurocristopathy characterized by the absence of the enteric ganglia along a variable length of the intestine. Genetic defects play a major role in the pathogenesis of HSCR, whereas family studies of pathogenic variants in all the known genes (loci) only demonstrate incomplete penetrance and variable expressivity for unknown reasons. Here, we applied large-scale, quantitative proteomics of human colon tissues from 21 patients using isobaric tags for relative and absolute quantification. method followed by bioinformatics analysis. Selected findings were confirmed by parallel reaction monitoring verification. At last, the interesting differentially expressed proteins were confirmed by Western blot. A total of 5341 proteins in human colon tissues were identified. Among them, 664 proteins with >1.2-fold difference were identified in six groups: groups A1 and A2 pooled protein from the ganglionic and aganglionic colon of male, long-segment HSCR patients (n = 7); groups B1 and B2 pooled protein from the ganglionic and aganglionic colon of male, short-segment HSCR patients (n = 7); and groups C1 and C2 pooled protein from the ganglionic and aganglionic colon of female, short-segment HSCR patients (n = 7). Based on these analyses, 49 proteins from five pathways were selected for parallel reaction monitoring verification, including ribosome, endocytosis, spliceosome, oxidative phosphorylation, and cell adhesion. The downregulation of three neuron projection development genes ARF4, KIF5B, and RAB8A in the aganglionic part of the colon was verified in 15 paired colon samples using Western blot. The findings of this study will shed new light on the pathogenesis of HSCR and facilitate the development of therapeutic targets.</p>","PeriodicalId":519518,"journal":{"name":"Molecular & cellular proteomics : MCP","volume":" ","pages":"100007"},"PeriodicalIF":7.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1074/mcp.RA120.002325","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25351701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantitative Proteomics and Phosphoproteomics Support a Role for Mut9-Like Kinases in Multiple Metabolic and Signaling Pathways in Arabidopsis.","authors":"Margaret E Wilson,&nbsp;Shin-Cheng Tzeng,&nbsp;Megan M Augustin,&nbsp;Matthew Meyer,&nbsp;Xiaoyue Jiang,&nbsp;Jae H Choi,&nbsp;John C Rogers,&nbsp;Bradley S Evans,&nbsp;Toni M Kutchan,&nbsp;Dmitri A Nusinow","doi":"10.1016/j.mcpro.2021.100063","DOIUrl":"https://doi.org/10.1016/j.mcpro.2021.100063","url":null,"abstract":"<p><p>Protein phosphorylation is one of the most prevalent posttranslational modifications found in eukaryotic systems. It serves as a key molecular mechanism that regulates protein function in response to environmental stimuli. The Mut9-like kinases (MLKs) are a plant-specific family of Ser/Thr kinases linked to light, circadian, and abiotic stress signaling. Here we use quantitative phosphoproteomics in conjunction with global proteomic analysis to explore the role of the MLKs in daily protein dynamics. Proteins involved in light, circadian, and hormone signaling, as well as several chromatin-modifying enzymes and DNA damage response factors, were found to have altered phosphorylation profiles in the absence of MLK family kinases. In addition to altered phosphorylation levels, mlk mutant seedlings have an increase in glucosinolate metabolism enzymes. Subsequently, we show that a functional consequence of the changes to the proteome and phosphoproteome in mlk mutant plants is elevated glucosinolate accumulation and increased sensitivity to DNA damaging agents. Combined with previous reports, this work supports the involvement of MLKs in a diverse set of stress responses and developmental processes, suggesting that the MLKs serve as key regulators linking environmental inputs to developmental outputs.</p>","PeriodicalId":519518,"journal":{"name":"Molecular & cellular proteomics : MCP","volume":" ","pages":"100063"},"PeriodicalIF":7.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.mcpro.2021.100063","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25442498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enabling Photoactivated Cross-Linking Mass Spectrometric Analysis of Protein Complexes by Novel MS-Cleavable Cross-Linkers.","authors":"Craig Gutierrez,&nbsp;Leah J Salituro,&nbsp;Clinton Yu,&nbsp;Xiaorong Wang,&nbsp;Sadie F DePeter,&nbsp;Scott D Rychnovsky,&nbsp;Lan Huang","doi":"10.1016/j.mcpro.2021.100084","DOIUrl":"https://doi.org/10.1016/j.mcpro.2021.100084","url":null,"abstract":"<p><p>Cross-linking mass spectrometry (XL-MS) is a powerful tool for studying protein-protein interactions and elucidating architectures of protein complexes. While residue-specific XL-MS studies have been very successful, accessibility of interaction regions nontargetable by specific chemistries remain difficult. Photochemistry has shown great potential in capturing those regions because of nonspecific reactivity, but low yields and high complexities of photocross-linked products have hindered their identification, limiting current studies predominantly to single proteins. Here, we describe the development of three novel MS-cleavable heterobifunctional cross-linkers, namely SDASO (Succinimidyl diazirine sulfoxide), to enable fast and accurate identification of photocross-linked peptides by MSⁿ. The MSⁿ-based workflow allowed SDASO XL-MS analysis of the yeast 26S proteasome, demonstrating the feasibility of photocross-linking of large protein complexes for the first time. Comparative analyses have revealed that SDASO cross-linking is robust and captures interactions complementary to residue-specific reagents, providing the foundation for future applications of photocross-linking in complex XL-MS studies.</p>","PeriodicalId":519518,"journal":{"name":"Molecular & cellular proteomics : MCP","volume":" ","pages":"100084"},"PeriodicalIF":7.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.mcpro.2021.100084","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38841936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Slight Deuterium Enrichment in Water Acts as an Antioxidant: Is Deuterium a Cell Growth Regulator?","authors":"Xuepei Zhang,&nbsp;Jin Wang,&nbsp;Roman A Zubarev","doi":"10.1074/mcp.RA120.002231","DOIUrl":"https://doi.org/10.1074/mcp.RA120.002231","url":null,"abstract":"<p><p>Small admixtures in water, <i>e.g.</i> of metal ions, often act as cell growth regulators. Here we report that enrichment of deuterium content in water, normally found at 8 mm concentration, two-three folds increases cell proliferation and lowers the oxidative stress level as well. Acting as an anti-oxidant, deuterium-enriched water prevents the toxic effect of such oxidative agents as hydrogen peroxide and auranofin. This action is opposite to that of deuterium depletion that is known to suppress cell growth and induce oxidative stress in mitochondria. We thus hypothesize that deuterium may be a natural cell growth regulator that controls mitochondrial oxidation-reduction balance. Because growth acceleration is reduced approximately by half by addition to water a minute amount (0.15%) of ¹⁸O isotope, at least part of the deuterium effect on cell growth can be explained by the isotopic resonance phenomenon. A slight (≈2-fold) enrichment of deuterium in water accelerates human cell growth. Quantitative MS based proteomics determined changes in protein abundances and redox states and found that deuterium-enriched water acts mainly through decreasing ROS production in mitochondria. This action is opposite to that of deuterium depletion that suppresses cell growth by inducing oxidative stress. Thus deuterium may be a natural cell growth regulator that controls mitochondrial oxidation-reduction balance. The role of isotopic resonance in this effect was validated by further experiments on bacteria.</p>","PeriodicalId":519518,"journal":{"name":"Molecular & cellular proteomics : MCP","volume":" ","pages":"1790-1804"},"PeriodicalIF":7.0,"publicationDate":"2020-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1074/mcp.RA120.002231","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40453401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomics of Galápagos Marine Iguanas Links Function of Femoral Gland Proteins to the Immune System.","authors":"Frederik Tellkamp,&nbsp;Franziska Lang,&nbsp;Alejandro Ibáñez,&nbsp;Lena Abraham,&nbsp;Galo Quezada,&nbsp;Stefan Günther,&nbsp;Mario Looso,&nbsp;Fabian Jannik Tann,&nbsp;Daniela Müller,&nbsp;Franz Cemic,&nbsp;Jürgen Hemberger,&nbsp;Sebastian Steinfartz,&nbsp;Marcus Krüger","doi":"10.1074/mcp.RA120.001947","DOIUrl":"https://doi.org/10.1074/mcp.RA120.001947","url":null,"abstract":"<p><p>Communication between individuals via molecules, termed chemosignaling, is widespread among animal and plant species. However, we lack knowledge on the specific functions of the substances involved for most systems. The femoral gland is an organ that secretes a waxy substance involved in chemical communication in lizards. Although the lipids and volatile substances secreted by the femoral glands have been investigated in several biochemical studies, the protein composition and functions of secretions remain completely unknown. Applying a proteomic approach, we provide the first attempt to comprehensively characterize the protein composition of femoral gland secretions from the Galápagos marine iguana. Using samples from several organs, the marine iguana proteome was assembled by next-generation sequencing and MS, resulting in 7513 proteins. Of these, 4305 proteins were present in the femoral gland, including keratins, small serum proteins, and fatty acid-binding proteins. Surprisingly, no proteins with discernible roles in partner recognition or inter-species communication could be identified. However, we did find several proteins with direct associations to the innate immune system, including lysozyme C, antileukoproteinase (ALP), pulmonary surfactant protein (SFTPD), and galectin (LGALS1) suggesting that the femoral glands function as an important barrier to infection. Furthermore, we report several novel anti-microbial peptides from the femoral glands that show similar action against <i>Escherichia coli</i> and <i>Bacillus subtilis</i> such as oncocin, a peptide known for its effectiveness against Gram-negative pathogens. This proteomics data set is a valuable resource for future functional protein analysis and demonstrates that femoral gland secretions also perform functions of the innate immune system.</p>","PeriodicalId":519518,"journal":{"name":"Molecular & cellular proteomics : MCP","volume":" ","pages":"1523-1532"},"PeriodicalIF":7.0,"publicationDate":"2020-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1074/mcp.RA120.001947","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38080917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of Lysine Acetylation Sites on MERS-CoV Replicase pp1ab.","authors":"Lin Zhu,&nbsp;Sin-Yee Fung,&nbsp;Guangshan Xie,&nbsp;Lok-Yin Roy Wong,&nbsp;Dong-Yan Jin,&nbsp;Zongwei Cai","doi":"10.1074/mcp.RA119.001897","DOIUrl":"https://doi.org/10.1074/mcp.RA119.001897","url":null,"abstract":"<p><p>MERS is a life-threatening disease and MERS-CoV has the potential to cause the next pandemic. Protein acetylation is known to play a crucial role in host response to viral infection. Acetylation of viral proteins encoded by other RNA viruses have been reported to affect viral replication. It is therefore of interest to see whether MERS-CoV proteins are also acetylated. Viral proteins obtained from infected cells were trypsin-digested into peptides. Acetylated peptides were enriched by immunoprecipitation and subject to nano-LC-Orbitrap analysis. Bioinformatic analysis was performed to assess the conservation level of identified acetylation sites and to predict the upstream regulatory factors. A total of 12 acetylation sites were identified from 7 peptides, which all belong to the replicase polyprotein pp1ab. All identified acetylation sites were found to be highly conserved across MERS-CoV sequences in NCBI database. Upstream factors, including deacetylases of the SIRT1 and HDAC families as well as acetyltransferases of the TIP60 family, were predicted to be responsible for regulating the acetylation events identified. Western blotting confirms that acetylation events indeed occur on pp1ab protein by expressing NSP4 in HEK293 cells. Acetylation events on MERS-CoV viral protein pp1ab were identified for the first time, which indicate that MERS-CoV might use the host acetylation machinery to regulate its enzyme activity and to achieve optimal replication. Upstream factors were predicted, which might facilitate further analysis of the regulatory mechanism of MERS-CoV replication.</p>","PeriodicalId":519518,"journal":{"name":"Molecular & cellular proteomics : MCP","volume":" ","pages":"1303-1309"},"PeriodicalIF":7.0,"publicationDate":"2020-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1074/mcp.RA119.001897","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37950834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Virtual Issue: Technological Innovations.","authors":"Anne-Claude Gingras,&nbsp;Steven A Carr,&nbsp;Alma L Burlingame","doi":"10.1074/mcp.E120.002042","DOIUrl":"https://doi.org/10.1074/mcp.E120.002042","url":null,"abstract":"The mission of Molecular and Cellular Proteomics since its creation in 2002 has been to “foster the development and applications of proteomics in both basic and translational research.” Our mission statement mandates that Research Articles “report significant new biological or clinical discoveries underpinned by proteomic observations across all kingdoms of life” and that “manuscripts must define the biological roles played by the proteins investigated or their mechanisms of action.” This governing principle still forms the basis of a Research Article’s acceptance in the journal. However, the Editors have also long realized that these achievements in proteomics discoveries are only possible in the context of advances in enabling technologies. As such, the journal has always welcomed—but has recently reemphasized its interest in—important “new computational methods and technological advancements that will enable future discoveries.” In contrast to standard MCP Research Articles, “manuscripts describing such approaches do not have to include a solution to a biological problem, but must demonstrate that the technology works as described, is reproducible and is appropriate to uncover yet unknown protein/proteome function or properties using relevant model systems or publicly available data.” Since our Editorial of January 2018 titled “Your technological advances belong here,” we have seen an increase in the submission of excellent experimental and computational technology papers. Those that we published have in turn garnered high interest from the community, both in terms of page access, Mendeley saves, online attention and even (despite their young age) citations. This virtual issue celebrates some of the Technological Innovation manuscripts published in MCP since January 2018. We have selected several papers that represent the trends in improving the sensitivity in sample preparation, notably by coupling mass spectrometric analysis to laser microdissection (1) or Fluorescence Activated Cell Sorting (2), by developing streamlined and cost effective isobaric labeling protocols for multiplexing (3), and by developing new protein capture strategies for global proteome profiling (4). Some of the selected papers focus on sample analysis for specific applications, notably by overcoming common contaminants in phosphopeptide enrichment (5), systematically investigating post-translationally modified spectra (6), expanding the acetyl proteome in plants (7) and enabling proximity dependent biotinylation across multiple cell types (8), and permitting multiplex protein profiling with DNA barcoded antibodies (9). Papers improving liquid chromatography (10, 11), adapting ion mobility workflows (12, 13), expanding Data Independent Acquisition (14) or defining new real-time quality control measurements (15) also exemplify the type of manuscripts that have been frequently accessed and/or cited. Lastly, a clear trend consistent with the need for new computational work","PeriodicalId":519518,"journal":{"name":"Molecular & cellular proteomics : MCP","volume":" ","pages":"572-573"},"PeriodicalIF":7.0,"publicationDate":"2020-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1074/mcp.E120.002042","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37747203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}