@article{Molina2013,
author = {Molina, Daniel Martinez and Jafari, Rozbeh and Ignatushchenko, Marina and Seki, Takahiro and Larsson, E. Andreas and Dan, Chen and Sreekumar, Lekshmy and Cao, Yihai and Nordlund, P{\"{a}}r},
journal = {Science},
number = {July},
pages = {84--88},
title = {{Monitoring Drug Target Engagement in Cells and Tissues Using the Cellular Thermal Shift Assay}},
volume = {341},
year = {2013}
}

@article{Savitski2014,
abstract = {The thermal stability of proteins can be used to assess ligand binding in living cells. We have generalized this concept by determining the thermal profiles of more than 7000 proteins in human cells by means of mass spectrometry. Monitoring the effects of small-molecule ligands on the profiles delineated more than 50 targets for the kinase inhibitor staurosporine. We identified the heme biosynthesis enzyme ferrochelatase as a target of kinase inhibitors and suggest that its inhibition causes the phototoxicity observed with vemurafenib and alectinib. Thermal shifts were also observed for downstream effectors of drug treatment. In live cells, dasatinib induced shifts in BCR-ABL pathway proteins, including CRK/CRKL. Thermal proteome profiling provides an unbiased measure of drug-target engagement and facilitates identification of markers for drug efficacy and toxicity.},
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {Savitski, M. M. and Reinhard, F. B. M. and Franken, H. and Werner, Thilo and Savitski, Maria F{\"{a}}lth and Eberhard, Dirk and {Martinez Molina}, Daniel and Jafari, Rozbeh and Dovega, Rebecca Bakszt and Klaeger, Susan and Kuster, Bernhard and Nordlund, P{\"{a}}r and Bantscheff, Marcus and Drewes, Gerard},
doi = {10.1126/science.1255784},
eprint = {arXiv:1011.1669v3},
isbn = {1095-9203 (Electronic)$\backslash$r0036-8075 (Linking)},
issn = {1095-9203},
journal = {Science},
number = {6205},
pages = {1255784},
pmid = {25278616},
title = {{Tracking cancer drugs in living cells by thermal profiling of the proteome.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25278616},
volume = {346},
year = {2014}
}
@article{Becher2016,
abstract = {We describe a two-dimensional thermal proteome profiling strategy that can be combined with an orthogonal chemoproteomics approach to enable comprehensive target profiling of the marketed histone deacetylase inhibitor panobinostat. The N-hydroxycinnamide moiety is identified as critical for potent and tetrahydrobiopterin-competitive inhibition of phenylalanine hydroxylase leading to increases in phenylalanine and decreases in tyrosine levels. These findings provide a rationale for adverse clinical observations and suggest repurposing of the drug for treatment of tyrosinemia.},
author = {Becher, Isabelle and Werner, Thilo and Doce, Carola and Zaal, Esther A and T{\"{o}}gel, Ina and Khan, Crystal A and Rueger, Anne and Muelbaier, Marcel and Salzer, Elsa and Berkers, Celia R and Fitzpatrick, Paul F and Bantscheff, Marcus and Savitski, Mikhail M},
doi = {10.1038/nchembio.2185},
issn = {1552-4450},
journal = {Nature Chemical Biology},
number = {11},
pages = {908--910},
pmid = {27669419},
title = {{Thermal profiling reveals phenylalanine hydroxylase as an off-target of panobinostat}},
url = {http://www.nature.com/doifinder/10.1038/nchembio.2185},
volume = {12},
year = {2016}
}
@article{Franken2015,
abstract = {The direct detection of drug-protein interactions in living cells is a major challenge in drug discovery research. Recently, we introduced an approach termed thermal proteome profiling (TPP), which enables the monitoring of changes in protein thermal stability across the proteome using quantitative mass spectrometry. We determined the intracellular thermal profiles for up to 7,000 proteins, and by comparing profiles derived from cultured mammalian cells in the presence or absence of a drug we showed that it was possible to identify direct and indirect targets of drugs in living cells in an unbiased manner. Here we demonstrate the complete workflow using the histone deacetylase inhibitor panobinostat. The key to this approach is the use of isobaric tandem mass tag 10-plex (TMT10) reagents to label digested protein samples corresponding to each temperature point in the melting curve so that the samples can be analyzed by multiplexed quantitative mass spectrometry. Important steps in the bioinformatic analysis include data normalization, melting curve fitting and statistical significance determination of compound concentration-dependent changes in protein stability. All analysis tools are made freely available as R and Python packages. The workflow can be completed in 2 weeks.},
author = {Franken, Holger and Mathieson, Toby and Childs, Dorothee and Sweetman, Gavain M A and Werner, Thilo and T{\"{o}}gel, Ina and Doce, Carola and Gade, Stephan and Bantscheff, Marcus and Drewes, Gerard and Reinhard, Friedrich B M and Huber, Wolfgang and Savitski, Mikhail M},
doi = {10.1038/nprot.2015.101},
isbn = {1754-2189},
issn = {1754-2189},
journal = {Nature Protocols},
number = {10},
pages = {1567--1593},
pmid = {26379230},
title = {{Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry}},
url = {http://www.nature.com/doifinder/10.1038/nprot.2015.101},
volume = {10},
year = {2015}
}
@article{Perrin2018,
abstract = {},
author = {Perrin, Jessica and Werner, Thilo and Kurzawa, Nils and Childs, Dorothee and Kalxdorf, Mathias and Rutkowska, Anna and Poeckel, Daniel and Sevin, Daniel C. and Stonehouse, Eugenia and Strohmer, Katrin and Heller, Bianca and Thomson, Douglas W. and Vappiani, Johanna and Krause, Jana and Eberl, H. Christian and Rau, Christina and Franken, Holger and Huber, Wolfgang and Faelth-Savitski, Maria and Savitski, Mikhail M. and Bantscheff, Marcus and Bergamini, Giovanna},
doi = {},
isbn = {},
issn = {},
journal = {submitted},
number = {},
pages = {},
pmid = {},
title = {{Proteome thermal stability reflects organ physiology and identifies drug- target engagement in vivo}},
url = {},
volume = {},
year = {2018}
}
@article{Sridharan2018,
abstract = {},
author = {Sridharan, Sindhuja and Kurzawa, Nils and Werner, Thilo and Günther, Ina and Helm, Dominic and Huber, Wolfgang and Bantscheff, Marcus and Savitski, Mikhail M.},
doi = {},
isbn = {},
issn = {},
journal = {submitted},
number = {},
pages = {},
pmid = {},
title = {{Proteome-wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP}},
url = {},
volume = {},
year = {2018}
}
@article{Childs2018,
abstract = {Determining the interaction partners of small molecules in the intact cellular context remains a key challenge in drug research. Thermal proteome profiling (TPP) addresses this need by inferring target engagement from changes in temperature-dependent protein denaturation at a proteome-wide scale. Existing approaches to TPP data analysis have been centered around a single parameter, the melting point. Target engagement is then identified from a compound induced change in this parameter. However, for a substantial number of proteins the melting point shift does not reflect the treatment effect well, or cannot be confidently estimated at all. To overcome these limitations, we present a non-parametric analysis of response curves (NPARC), a functional approach that compares entire curves instead of summary parameters. NPARC projects the data to a space of smooth functions and infers treatment effects by an F-statistic with degrees of freedom estimated from the data. We show that our method outperforms the currently used melting point-centric approach with regard to specificity and sensitivity on five independent datasets. NPARC reliably detected known cancer drug targets for which ligand binding was not reflected by melting point shifts. The proposed method works with arbitrary numbers of replicates, and comparisons can be defined in a flexible manner. We hope that the proposed approach will aid in the detection of novel targets and off-targets for drugs with to date unexplained mechanisms of action or side effects.},
author = {Childs, Dorothee and Bach, Karsten and Franken, Holger and Anders, Simon and Kurzawa, Nils and Bantscheff, Marcus and Savitski, Mikhail and Huber, Wolfgang},
doi = {10.1101/373845},
journal = {bioRxiv},
mendeley-groups = {TppLm},
pages = {1--20},
title = {{Non-Parametric Analysis of Thermal Proteome Profiles Reveals Novel Drug-Binding Proteins}},
url = {http://biorxiv.org/cgi/content/short/373845v1},
year = {2018}
}
@article{Storey2005,
abstract = {Characterizing the genome-wide dynamic regulation of gene expression is important and will be of much interest in the future. However, there is currently no established method for identifying differentially expressed genes in a time course study. Here we propose a significance method for analyzing time course microarray studies that can be applied to the typical types of comparisons and sampling schemes. This method is applied to two studies on humans. In one study, genes are identified that show differential expression over time in response to in vivo endotoxin administration. By using our method, 7,409 genes are called significant at a 1{\%} false-discovery rate level, whereas several existing approaches fail to identify any genes. In another study, 417 genes are identified at a 10{\%} false-discovery rate level that show expression changing with age in the kidney cortex. Here it is also shown that as many as 47{\%} of the genes change with age in a manner more complex than simple exponential growth or decay. The methodology proposed here has been implemented in the freely distributed and open-source edge software package.},
author = {Storey, John D and Xiao, Wenzhong and Leek, Jeffrey T and Tompkins, Ronald G and Davis, Ronald W},
doi = {10.1073/pnas.0504609102},
isbn = {0027-8424 (Print)$\backslash$r0027-8424 (Linking)},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Adult,Aged,Aged, 80 and over,Aging,Aging: genetics,Gene Expression Profiling,Gene Expression Profiling: methods,Gene Expression Regulation,Gene Expression Regulation: drug effects,Humans,Inflammation,Inflammation: chemically induced,Inflammation: genetics,Kidney Cortex,Kidney Cortex: metabolism,Lipopolysaccharides,Lipopolysaccharides: pharmacology,Middle Aged,Oligonucleotide Array Sequence Analysis,Oligonucleotide Array Sequence Analysis: methods,Software,Time Factors},
number = {36},
pages = {12837--42},
pmid = {16141318},
title = {{Significance analysis of time course microarray experiments.}},
url = {http://www.pnas.org/content/102/36/12837.abstract},
volume = {102},
year = {2005}
}
@article{Becher2018,
abstract = {{\textless}h2{\textgreater}Summary{\textless}/h2{\textgreater}{\textless}p{\textgreater}Quantitative mass spectrometry has established proteome-wide regulation of protein abundance and post-translational modifications in various biological processes. Here, we used quantitative mass spectrometry to systematically analyze the thermal stability and solubility of proteins on a proteome-wide scale during the eukaryotic cell cycle. We demonstrate pervasive variation of these biophysical parameters with most changes occurring in mitosis and G1. Various cellular pathways and components vary in thermal stability, such as cell-cycle factors, polymerases, and chromatin remodelers. We demonstrate that protein thermal stability serves as a proxy for enzyme activity, DNA binding, and complex formation {\textless}i{\textgreater}in situ{\textless}/i{\textgreater}. Strikingly, a large cohort of intrinsically disordered and mitotically phosphorylated proteins is stabilized and solubilized in mitosis, suggesting a fundamental remodeling of the biophysical environment of the mitotic cell. Our data represent a rich resource for cell, structural, and systems biologists interested in proteome regulation during biological transitions.{\textless}/p{\textgreater}},
author = {Becher, Isabelle and Andr{\'{e}}s-Pons, Amparo and Romanov, Natalie and Stein, Frank and Schramm, Maike and Baudin, Florence and Helm, Dominic and Kurzawa, Nils and Mateus, Andr{\'{e}} and Mackmull, Marie-Therese and Typas, Athanasios and M{\"{u}}ller, Christoph W and Bork, Peer and Beck, Martin and Savitski, Mikhail M},
doi = {10.1016/j.cell.2018.03.053},
issn = {00928674},
journal = {Cell},
pages = {1--13},
title = {{Pervasive Protein Thermal Stability Variation during the Cell Cycle}},
url = {https://www.cell.com/cell/fulltext/S0092-8674(18)30385-4},
year = {2018}
}
@article{Mateus2020,
title = {Thermal proteome profiling for interrogating protein interactions.},
author = {Mateus, André and Kurzawa, Nils and Becher, Isabelle and Sridharan, Sindhuja and Helm, Dominic and Stein, Frank and Typas, Athanasios and Savitski, Mikhail M},
pages = {e9232},
url = {http://dx.doi.org/10.15252/msb.20199232},
year = {2020},
urldate = {2020-03-09},
journal = {Molecular Systems Biology},
volume = {16},
number = {3},
doi = {10.15252/msb.20199232},
pmid = {32133759},
pmcid = {PMC7057112},
abstract = {Thermal proteome profiling ({TPP}) is based on the principle that, when subjected to heat, proteins denature and become insoluble. Proteins can change their thermal stability upon interactions with small molecules (such as drugs or metabolites), nucleic acids or other proteins, or upon post-translational modifications. {TPP} uses multiplexed quantitative mass spectrometry-based proteomics to monitor the melting profile of thousands of expressed proteins. Importantly, this approach can be performed in vitro, in situ, or in vivo. It has been successfully applied to identify targets and off-targets of drugs, or to study protein-metabolite and protein-protein interactions. Therefore, {TPP} provides a unique insight into protein state and interactions in their native context and at a proteome-wide level, allowing to study basic biological processes and their underlying mechanisms. \copyright 2020 The Authors. Published under the terms of the {CC} {BY} 4.0 license.}
}


