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Inference of Predictive Phospho-regulatory Networks from LC-MS/MS Phosphoproteomics Data

Sebastian Vlaic, Robert Altwasser, Peter Kupfer, Carol L. Nilsson, Mark Emmett, Anke Meyer-Baese, Reinhard Guthke
<span title="">2016</span> <i title="SCITEPRESS - Science and and Technology Publications"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lxwop3qtazexrkwj5xfe7k3uqm" style="color: black;">Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies</a> </i> &nbsp;
In the field of transcriptomics data the automated inference of predictive gene regulatory networks from highthroughput data is a common approach for the identification of novel genes with potential therapeutic  ...  In this study we conceptually adapt the TILAR network inference algorithm for the inference of a phospho-regulatory network.  ...  ACKNOWLEDGEMENTS This work was supported by the BMBF (Virtual Liver Network, FKZ: 0315736) and the excellence graduate school Jena School for Microbial Communication (JSMC).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5220/0005743000850091">doi:10.5220/0005743000850091</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/biostec/VlaicAKNEMG16.html">dblp:conf/biostec/VlaicAKNEMG16</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qkz4vtgk6fdt3fvnl7vwb2bto4">fatcat:qkz4vtgk6fdt3fvnl7vwb2bto4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190219052442/http://pdfs.semanticscholar.org/164a/4255f02fe3c996d005f37b843642f3bc21e5.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/16/4a/164a4255f02fe3c996d005f37b843642f3bc21e5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5220/0005743000850091"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data [article]

Ali Sinan Köksal, Kirsten Beck, Dylan R. Cronin, Aaron McKenna, Nathan D. Camp, Saurabh Srivastava, Matthew E. MacGilvray, Rastislav Bodík, Alejandro Wolf-Yadlin, Ernest Fraenkel, Jasmin Fisher, Anthony Gitter
<span title="2017-10-26">2017</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We present a computational method, the Temporal Pathway Synthesizer (TPS), to discover missing pathway elements by modeling temporal phosphoproteomic data.  ...  Our mass spectrometry study of the dynamic epidermal growth factor (EGF) response demonstrates that over 89% of significantly (de)phosphorylated proteins are excluded from individual EGF signaling maps  ...  The phosphotyrosine-rich fraction is analyzed by 1D-LC-MS/MS. The more complex phosphoserine/threonine rich fraction is analyzed by 2D-LC-MS/MS.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/209676">doi:10.1101/209676</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7fs5thjaevd2bcar545av6r5yu">fatcat:7fs5thjaevd2bcar545av6r5yu</a> </span>
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Kinase activity ranking using phosphoproteomics data (KARP) quantifies the contribution of protein kinases to the regulation of cell viability

Edmund H. Wilkes, Pedro Casado, Vinothini Rajeeve, Pedro R. Cutillas
<span title="2017-07-03">2017</span> <i title="American Society for Biochemistry &amp; Molecular Biology (ASBMB)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/63atlvwyorhorfip35rcvk6bey" style="color: black;">Molecular &amp; Cellular Proteomics</a> </i> &nbsp;
We found that the scores returned by this algorithm, which we have termed kinase activity ranking using phosphoproteomics data (KARP), were a quantitative measure of the contribution that individual kinases  ...  Thus, our study exemplifies KARP as an untargeted approach to empirically and systematically identify regulatory kinases within signaling networks.  ...  of multiomics data (17, 42) , whereas KARP uses data obtained from a single-shot LC-MS/MS run and does not require referencing to other omics datasets.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/mcp.o116.064360">doi:10.1074/mcp.o116.064360</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28674151">pmid:28674151</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5587867/">pmcid:PMC5587867</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4lodz5ep2fetvjqebbjbwptfiy">fatcat:4lodz5ep2fetvjqebbjbwptfiy</a> </span>
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PhosR enables processing and functional analysis of phosphoproteomic data [article]

Jieun Hani Kim, Taiyun Kim, Nolan Hoffman, Di Xiao, David E James, Sean Humphrey, Pengyi Yang
<span title="2020-09-01">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Together, our data and findings demonstrate the utility of PhosR in processing and generating novel biological knowledge from MS-based phosphoproteomic data.  ...  analysis of phosphoproteomic data.  ...  were enriched and analysed by LC-MS/MS as described previously (Hoffman et al., 2015) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.08.31.276329">doi:10.1101/2020.08.31.276329</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3kdd2v43dbbbdn5z4n2g3csrcu">fatcat:3kdd2v43dbbbdn5z4n2g3csrcu</a> </span>
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LC-MS/MS analysis of the dog serum phosphoproteome reveals novel and conserved phosphorylation sites: Phosphoprotein patterns in babesiosis caused by Babesia canis, a case study

Asier Galán, Anita Horvatić, Josipa Kuleš, Petra Bilić, Jelena Gotić, Vladimir Mrljak, Mauro Salvi
<span title="2018-11-28">2018</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
We compared serum from 10 healthy dogs and 10 dogs affected by B. canis-caused babesiosis with no organ dysfunctions by employing gel-free LC-MS/MS analysis of individual samples and tandem mass tag (TMT  ...  To the best of our knowledge the present study represents the first attempt to characterize canine serum phosphoproteome.  ...  Acknowledgments We thank Blanka Beer Ljubić for clinical analysis of dog serum samples.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0207245">doi:10.1371/journal.pone.0207245</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30485286">pmid:30485286</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6261647/">pmcid:PMC6261647</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2qceewk2njdi3n5ptoneqrr6ky">fatcat:2qceewk2njdi3n5ptoneqrr6ky</a> </span>
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The Coming of Age of Phosphoproteomics—from Large Data Sets to Inference of Protein Functions

Philippe P. Roux, Pierre Thibault
<span title="2013-09-13">2013</span> <i title="American Society for Biochemistry &amp; Molecular Biology (ASBMB)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/63atlvwyorhorfip35rcvk6bey" style="color: black;">Molecular &amp; Cellular Proteomics</a> </i> &nbsp;
This modification is finely coordinated by a network of kinases and phosphatases that recognize unique sequence motifs and/or mediate their functions through scaffold and adaptor proteins.  ...  In this review, we present meaningful technical details for MS-based phosphoproteomic analyses and describe important considerations for the selection of model systems and the functional characterization  ...  This is mostly due to recent advances in LC-MS/MS and phosphopeptide enrichment strategies that now allow the rapid identification of phosphorylation sites with precision and sensitivity.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/mcp.r113.032862">doi:10.1074/mcp.r113.032862</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24037665">pmid:24037665</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3861699/">pmcid:PMC3861699</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bklckou6snfpfawissuz3bgoce">fatcat:bklckou6snfpfawissuz3bgoce</a> </span>
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Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data

Alexander Schäfer, Enio Gjerga, Richard WD Welford, Imke Renz, Francois Lehembre, Peter MA Groenen, Julio Saez-Rodriguez, Ruedi Aebersold, Matthias Gstaiger
<span title="">2019</span> <i title="EMBO"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/oayrvwhnr5a2jm4pbva2dvz3ui" style="color: black;">Molecular Systems Biology</a> </i> &nbsp;
We investigated phosphoproteomic changes caused by endothelin B receptor (ENDRB) activation in the melanoma cell lines UACC257 and A2058 and built an integrated model of EDNRB signalling from the phosphoproteomics  ...  data.  ...  Samples were processed according to the digestion and phospho-enrichment protocol and LC-MS/ MS data-dependent acquisition workflow described in the Materials and Methods section.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.15252/msb.20198828">doi:10.15252/msb.20198828</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31464372">pmid:31464372</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6683863/">pmcid:PMC6683863</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dcszrdqhnndgvknbdkx7kavc6y">fatcat:dcszrdqhnndgvknbdkx7kavc6y</a> </span>
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Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis

Mukesh Bansal, Jing He, Michael Peyton, Manjunath Kustagi, Archana Iyer, Michael Comb, Michael White, John D. Minna, Andrea Califano, Srikumar Chellappan
<span title="2019-01-07">2019</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
To address this challenge, we introduce a novel algorithm for the systematic inference of protein kinase pathways, and applied it to published mass spectrometry-based phosphotyrosine profile data from  ...  Previously, such signaling pathway models are largely based on the compilation of literature data from heterogeneous cellular contexts.  ...  .), NIH, Office of the Director, Shared Instrumentation Grants (S10OD012351 and S10OD 021764) to AC, NCI SPORE in Lung Cancer (P50CA70907 to JDM), and CPRIT (Award RP110708 to JDM).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0208646">doi:10.1371/journal.pone.0208646</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30615629">pmid:30615629</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6322741/">pmcid:PMC6322741</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/73xsxhy35zhq7f2lkxakzibbly">fatcat:73xsxhy35zhq7f2lkxakzibbly</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190504014911/https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0208646&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/df/36/df366bfedb4dde13f4cf25220d353343e0f6cb93.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0208646"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6322741" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis [article]

Mukesh Bansal, Jing He, Michael Peyton, Manjunath Kaustagi, Archana Iyer, Michael Comb, Michael White, John Minna, Andrea Califano
<span title="2018-03-29">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Availability of the network allowed prediction of drug response in individual samples, including accurate prediction of synergistic EGFR and c-MET inhibitor activity in cells lacking mutations in either  ...  peptides from 250 samples representative of lung adenocarcinoma.  ...  (C). 676 Workflow of pARACNe from LC-MS/MS data normalization, IQD process, MI calculation, DPI 677 process, bootstrapping to network consolidation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/289603">doi:10.1101/289603</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nv7n6rionrdp3eqjcpw4jrpiby">fatcat:nv7n6rionrdp3eqjcpw4jrpiby</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190504121150/https://www.biorxiv.org/content/biorxiv/early/2018/04/03/289603.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a5/9e/a59e6fc2a7e1d19b1b1b440e9f75a21406b50a21.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/289603"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Computational methods and opportunities for phosphorylation network medicine

Yian Ann Chen, Steven A Eschrich
<span title="2014-06-01">2014</span> <i title="AME Publishing Company"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/7qfgvhekxvasbh2mducvro7c4y" style="color: black;">Translational Cancer Research</a> </i> &nbsp;
We review existing database resources, computational tools, methods for phosphorylation network inference, and ultimately demonstrate the connection to therapeutics.  ...  This therapeutic paradigm shift in cancer research is partly due to the generation and availability of high-dimensional proteomics data.  ...  Special thanks to the phosphoproteomics research group at the Moffitt Cancer Center: Eric Haura, John Koomen, Uwe Rix, and Keiran Smalley. We also thank Alvaro  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25530950">pmid:25530950</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4271781/">pmcid:PMC4271781</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bbfxl2kggzcvfowfn6fmlvrqnu">fatcat:bbfxl2kggzcvfowfn6fmlvrqnu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200320014314/http://tcr.amegroups.com/article/download/2594/3109" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ff/1e/ff1eae11b14e37678a768acf4de7661338b15ec5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271781" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes [article]

Brett Warren Engelmann, Chiaowen Joyce Hsiao, John D Blischak, Yannick Fourne, Michael Ford, Yoav Gilad
<span title="2018-02-26">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
phosphoproteome variation.  ...  Interestingly, we found evidence that is consistent with a phosphopeptide variability buffering effect endowed from properties enriched within longer proteins.  ...  Recent advances in liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) technology have enabled such surveys [5, 14, 15] , and multiple studies have reported the analysis of LC-MS/MS phosphoproteomic  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/271650">doi:10.1101/271650</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xvfnqq2tpffd5oeexjgfzx5epq">fatcat:xvfnqq2tpffd5oeexjgfzx5epq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430162917/https://www.biorxiv.org/content/biorxiv/early/2018/02/26/271650.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/44/e2/44e29de1141d6155778e04788b2ba97ab7444666.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/271650"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Kinase Inhibitor Treatment of Patients with Advanced Cancer Results in High Tumor Drug Concentrations and in Specific Alterations of the Tumor Phosphoproteome

Labots, Pham, Honeywell, Knol, Beekhof, de Goeij-de Haas, Dekker, Neerincx, Piersma, van der Mijn, van der Peet, Meijerink (+4 others)
<span title="2020-02-01">2020</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2zwku6u6nfdcri773tpisi6ldi" style="color: black;">Cancers</a> </i> &nbsp;
Tumor concentrations were determined by LC-MS/MS. pTyr-phosphoproteomics was performed by pTyr-immunoprecipitation followed by LC-MS/MS.  ...  Identification of predictive biomarkers for targeted therapies requires information on drug exposure at the target site as well as its effect on the signaling context of a tumor.  ...  Acknowledgments: We thank Maria Rovithi for her support to the collection of patient samples and Evan Henneberry for his contribution to the analysis of the phosphoproteomic data. Conflicts of  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/cancers12020330">doi:10.3390/cancers12020330</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32024067">pmid:32024067</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7072422/">pmcid:PMC7072422</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uncijp3p4rc5zjydyms6hlmvxe">fatcat:uncijp3p4rc5zjydyms6hlmvxe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201105131122/https://repository.ubn.ru.nl/bitstream/handle/2066/218883/218883.pdf;jsessionid=A3FD3B5383452F32156ECD65059CB628?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/aa/0a/aa0a1dff21d76df9f6f2e809bbc187c9d12579ee.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/cancers12020330"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7072422" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Deep phosphoproteome analysis of Schistosoma mansoni leads development of a kinomic array that highlights sex-biased differences in adult worm protein phosphorylation

Natasha L. Hirst, Jean-Christophe Nebel, Scott P. Lawton, Anthony J. Walker, Geoffrey M. Attardo
<span title="2020-03-23">2020</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/23nqq3odsjhmbi5tqavvcn7cfm" style="color: black;">PLoS Neglected Tropical Diseases</a> </i> &nbsp;
Herein, we report a deep phosphoproteome exploration of adult Schistosoma mansoni, providing one of the richest phosphoprotein resources for any parasite so far, and employ the data to build the first  ...  Analysis of putative protein kinase-phosphoprotein interactions revealed canonical networks but also novel interactions between signalling partners.  ...  Acknowledgments We are grateful to Matthew Stokes of CST and Daniel Maisch of Intavis Peptide Services for helpful discussion and insight concerning the phosphoproteomics and the CelluSpots array.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pntd.0008115">doi:10.1371/journal.pntd.0008115</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32203512">pmid:32203512</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qwptzeufvjbjpm4mym66tm6ypy">fatcat:qwptzeufvjbjpm4mym66tm6ypy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200325200036/https://journals.plos.org/plosntds/article/file?id=10.1371%2Fjournal.pntd.0008115&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/80/45/8045b1a95d3ae851de11347e3acb9bc2e33aaff5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pntd.0008115"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a>

Phosphoproteomic Analysis of Protein Phosphorylation Networks inTetrahymena thermophila, a Model Single-celled Organism

Miao Tian, Xiulan Chen, Qian Xiong, Jie Xiong, Chuanle Xiao, Feng Ge, Fuquan Yang, Wei Miao
<span title="2013-11-07">2013</span> <i title="American Society for Biochemistry &amp; Molecular Biology (ASBMB)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/63atlvwyorhorfip35rcvk6bey" style="color: black;">Molecular &amp; Cellular Proteomics</a> </i> &nbsp;
LC-MS/MS analysis.  ...  Our data provide the first global survey of phosphorylation in T. thermophila using a phosphoproteomic approach and suggest a wideranging regulatory scope of this modification.  ...  LC-MS/MS analysis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/mcp.m112.026575">doi:10.1074/mcp.m112.026575</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24200585">pmid:24200585</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3916650/">pmcid:PMC3916650</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/l3zhii6p4rbzzcbx2npevcyuhe">fatcat:l3zhii6p4rbzzcbx2npevcyuhe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720055016/http://www.mcponline.org/content/13/2/503.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e4/7c/e47c1e1ec00657bf4322c551b7f66d6861218e49.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/mcp.m112.026575"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3916650" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Mass-Spectrometry-Based Functional Proteomic and Phosphoproteomic Technologies and Their Application for Analyzing Ex Vivo and In Vitro Models of Hypertrophic Cardiomyopathy

Jarrod Moore, Andrew Emili
<span title="2021-12-20">2021</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3loumxx7kzamnlu4h6x3xoz6ay" style="color: black;">International Journal of Molecular Sciences</a> </i> &nbsp;
Cardiac research is poised to benefit enormously from the application of this toolkit to cardiac tissue models, which recapitulate key aspects of pathogenesis.  ...  In this review, we evaluate state-of-the-art mass-spectrometry-based proteomic and phosphoproteomic technologies and their application to in vitro and ex vivo models of HCM for global mapping of macromolecular  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms222413644">doi:10.3390/ijms222413644</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34948439">pmid:34948439</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8709159/">pmcid:PMC8709159</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ypheenvfkjcx3dx23q5rfeumyi">fatcat:ypheenvfkjcx3dx23q5rfeumyi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220202131154/https://mdpi-res.com/d_attachment/ijms/ijms-22-13644/article_deploy/ijms-22-13644.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/13/13/13136a5842244b3604256cbbd7eab819bbc818b3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms222413644"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8709159" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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