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1. Full Text Mass-spectrometry-based draft of the human proteome
by Wilhelm, Mathias and Schlegl, Judith and Hahne, Hannes and Gholami, Amin Moghaddas and Lieberenz, Marcus and Savitski, Mikhail M and Ziegler, Emanuel and Butzmann, Lars and Gessulat, Siegfried and Marx, Harald and Mathieson, Toby and Lemeer, Simone and Schnatbaum, Karsten and Reimer, Ulf and Wenschuh, Holger and Mollenhauer, Martin and Slotta-Huspenina, Julia and Boese, Joos-Hendrik and Bantscheff, Marcus and Gerstmair, Anja and Faerber, Franz and Kuster, Bernhard
Nature, ISSN 0028-0836, 2014, Volume 509, Issue 7502, pp. 582 - 587
Proteomes are characterized by large protein-abundance differences, cell-type- and time-dependent expression patterns and post-translational modifications, all... 
GROWTH-FACTOR RECEPTOR | PROJECT | DATABASE | NONCODING RNAS | QUANTIFICATION | MULTIDISCIPLINARY SCIENCES | IDENTIFICATION | PROTEINS | EXPRESSION | PEPTIDE | REVEALS | Cell Line | Proteome - genetics | Humans | Molecular Sequence Annotation | RNA, Messenger - genetics | Body Fluids - chemistry | RNA, Messenger - analysis | Gene Expression Profiling | Proteome - analysis | Organ Specificity | Proteome - chemistry | Genome, Human - genetics | Body Fluids - metabolism | Databases, Protein | Mass Spectrometry | Proteomics | Proteome - metabolism | Usage | Genomes | Research | Mass spectrometry | Genomics | Proteins | Peptides | Experiments | Chromatography | Index Medicus
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2. Full Text Tracking cancer drugs in living cells by thermal profiling of the proteome
by Savitski, Mikhail M and Reinhard, Friedrich B. M and Franken, Holger and Werner, Thilo and Savitski, Maria Fälth and Eberhard, Dirk and Molina, Daniel Martinez and Jafari, Rozbeh and Dovega, Rebecca Bakszt and Klaeger, Snsan and Kuster, Bernhard and Nordlund, Pär and Bantscheff, Marcus and Drewes, Gerard
Science, ISSN 0036-8075, 10/2014, Volume 346, Issue 6205, pp. 55 - 55
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... 
CHRONIC MYELOGENOUS LEUKEMIA | KINOME | TARGET ENGAGEMENT | QUANTIFICATION | MULTIDISCIPLINARY SCIENCES | IMATINIB | RESISTANCE | SYSTEMS | PHOTOSENSITIVITY | KINASE INHIBITORS | IDENTIFICATION | Humans | K562 Cells | Protein Denaturation | Adenosine Triphosphatases - metabolism | Protein Binding | Proteome - drug effects | Ligands | Antineoplastic Agents - pharmacology | Hot Temperature | Protein Stability | Proteomics - methods | Pharmacology | Cellular biology | Proteomics | Cancer | Index Medicus | Proteins | Drugs | Binding | Melting | Profiling | Inhibitors | Kinases
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3. Full Text A scalable approach for protein false discovery rate estimation in large proteomic data sets
by Savitski, Mikhail M and Wilhelm, Mathias and Hahne, Hannes and Kuster, Bernhard and Bantscheff, Marcus
Molecular and Cellular Proteomics, ISSN 1535-9476, 09/2015, Volume 14, Issue 9, pp. 2394 - 2404
Calculating the number of confidently identified proteins and estimating false discovery rate (FDR) is a challenge when analyzing very large proteomic data... 
CELLS | PROJECT | PEPTIDES | SHOTGUN PROTEOMICS | SEARCH | PERFORMANCE | BIOCHEMICAL RESEARCH METHODS | QUADRUPOLE | TANDEM MASS-SPECTROMETRY | IDENTIFICATION | CONFIDENCE | Reproducibility of Results | Databases, Protein | Humans | Software | Proteomics - methods | Chromatography, Liquid - methods | False Positive Reactions | Tandem Mass Spectrometry - methods | Index Medicus | Special Issue
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4. Full Text Ion coalescence of neutron encoded TMT 10-plex reporter ions
by Werner, Thilo and Sweetman, Gavain and Savitski, Maria Fälth and Mathieson, Toby and Bantscheff, Marcus and Savitski, Mikhail M
Analytical Chemistry, ISSN 0003-2700, 04/2014, Volume 86, Issue 7, pp. 3594 - 3601
Isobaric mass tag-based quantitative proteomics strategies such as iTRAQ and TMT utilize reporter ions in the low mass range of tandem MS spectra for relative... 
CHEMISTRY, ANALYTICAL | KINOME | QUANTITATION | PROTEIN QUANTIFICATION | MECHANISMS | INHIBITORS | ABSOLUTE QUANTIFICATION | IDENTIFICATION | MASS-SPECTROMETRY | PROTEOMICS | ACCURACY | Neutrons | Ions | Tandem Mass Spectrometry - methods | Proteins | Usage | Analysis | Proteomics | Peptides | Mass spectrometry | Index Medicus | Coalescing | Mass spectrometers | Strategy | Spectra | Coalescence | Tags
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5. Full Text High-resolution enabled TMT 8-plexing
by Werner, Thilo and Becher, Isabelle and Sweetman, Gavain and Doce, Carola and Savitski, Mikhail M and Bantscheff, Marcus
Analytical Chemistry, ISSN 0003-2700, 08/2012, Volume 84, Issue 16, pp. 7188 - 7194
Isobaric mass tag-based quantitative proteomics strategies such as iTRAQ and TMT utilize reporter ions in the low-mass range of tandem MS spectra for relative... 
TANDEM MASS TAGS | CHEMISTRY, ANALYTICAL | BIOMARKER DISCOVERY | QUANTIFICATION | QUANTITATION | LTQ-ORBITRAP | IDENTIFICATION | EXPRESSION | CELL-LINE | ISOBARIC TAGS | PROTEOMICS | Dasatinib | Humans | Pyrimidines - pharmacology | Dose-Response Relationship, Drug | Pregnancy | Protein Kinase Inhibitors - analysis | HEK293 Cells | K562 Cells | Female | Protein Kinase Inhibitors - pharmacology | Thiazoles - pharmacology | Indicators and Reagents - chemistry | Tandem Mass Spectrometry - methods | Measurement | Usage | Chemical reaction, Rate of | Analysis | Chemical properties | Structure | Activation energy | Isotopes | Mass spectrometry | Ions | Kinases | Biological assays | Proteomics | Index Medicus
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6. Full Text Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia
by Dawson, Mark A and Prinjha, Rab K and Dittmann, Antje and Giotopoulos, George and Bantscheff, Marcus and Chan, Wai-In and Robson, Samuel C and Chung, Chun-Wa and Hopf, Carsten and Savitski, Mikhail M and Huthmacher, Carola and Gudgin, Emma and Lugo, Dave and Beinke, Soren and Chapman, Trevor D and Roberts, Emma J and Soden, Peter E and Auger, Kurt R and Mirguet, Olivier and Doehner, Konstanze and Delwel, Ruud and Burnett, Alan K and Jeffrey, Phillip and Drewes, Gerard and Lee, Kevin and Huntly, Brian J. P and Kouzarides, Tony
Nature, ISSN 0028-0836, 10/2011, Volume 478, Issue 7370, pp. 529 - 533
Recurrent chromosomal translocations involving the mixed lineage leukaemia (MLL) gene initiate aggressive forms of leukaemia, which are often refractory to... 
TARGET | CELLS | ELONGATION | MULTIDISCIPLINARY SCIENCES | TRANSCRIPTION | COMPONENT | BROMODOMAIN PROTEIN BRD4 | P-TEFB | Chromatin - metabolism | Transcription, Genetic - drug effects | Myeloid-Lymphoid Leukemia Protein - metabolism | Oncogene Proteins, Fusion - metabolism | Humans | Leukemia, Myeloid, Acute - metabolism | Gene Expression Profiling | Heterocyclic Compounds, 4 or More Rings - pharmacology | Multiprotein Complexes - metabolism | Chromatin Immunoprecipitation | Heterocyclic Compounds, 4 or More Rings - therapeutic use | Protein Binding - drug effects | Leukemia, Myeloid, Acute - drug therapy | Gene Expression Regulation, Neoplastic - drug effects | Disease Models, Animal | Leukemia, Myeloid, Acute - pathology | Models, Molecular | Transcription Factors - antagonists & inhibitors | Transcription Factors - metabolism | Multiprotein Complexes - chemistry | Animals | Proteomics | Cell Line, Tumor | Mice | Chromatin - genetics | Leukemia, Myeloid, Acute - genetics | Proteins | Competition | Cell cycle | Epigenetics | Clinical medicine | Kinases | Crystal structure | Apoptosis | Human | Therapy | Inhibitors | Genes | Elongation | Displacement | Leukaemia | Index Medicus
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7. Full Text Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes
by Ramsden, Nigel G and Schlegl, Judith and Becher, Isabelle and Bantscheff, Marcus and Savitski, Mikhail M and Strunk, Katja and Mathieson, Toby and Bergamini, Giovanna and Dittmann, Antje and Grandi, Paola and Delling, Manja and Neubauer, Gitte and Drewes, Gerard and Reader, Valérie and Sweetman, Gavain and Eberhard, Dirk and Michon, Anne-Marie and Abraham, Yann and Dümpelfeld, Birgit and Boesche, Markus and Hopf, Carsten and Kruse, Ulrich and Huthmacher, Carola and Poeckel, Daniel
Nature Biotechnology, ISSN 1087-0156, 03/2011, Volume 29, Issue 3, pp. 255 - 265
The development of selective histone deacetylase (HDAC) inhibitors with anti-cancer and anti-inflammatory properties remains challenging in large part owing to... 
SIN3 COMPLEX | CHROMATIN | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | PROTEIN COMPLEXES | HISTONE DEACETYLASE INHIBITORS | ORBITRAP MASS-SPECTROMETER | LYSINE ACETYLATION | CATALYTIC-ACTIVITY | IDENTIFICATION | CELL | PROTEOMICS | Protein Interaction Mapping - methods | Histone Deacetylases - metabolism | Peptide Mapping - methods | Proteomics - methods | Mass Spectrometry - methods | Histone Deacetylases - chemistry | Antimitotic agents | Enzymes | Enzyme inhibitors | Physiological aspects | Hydrolases | Research | Antineoplastic agents | Health aspects | Phylogenetics | Biotechnology | Protein folding | Proteomics | Index Medicus
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8. Full Text Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present
by Bantscheff, Marcus and Lemeer, Simone and Savitski, Mikhail M and Kuster, Bernhard
Analytical and Bioanalytical Chemistry, ISSN 1618-2642, 09/2012, Volume 404, Issue 4, p. 939
Mass-spectrometry-based proteomics is continuing to make major contributions to the discovery of fundamental biological processes and, more recently, has also... 
Usage | Analysis | Proteomics | Liquid chromatography | Mass spectrometry
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9. Full Text Confident phosphorylation site localization using the mascot delta score
by Savitski, Mikhail M and Lemeer, Simone and Boesche, Markus and Lang, Manja and Mathieson, Toby and Bantscheff, Marcus and Kuster, Bernhard
Molecular and Cellular Proteomics, ISSN 1535-9476, 02/2011, Volume 10, Issue 2, pp. M110.003830 - M110.003830
Large scale phosphorylation analysis is more and more getting into focus of proteomic research. Although it is now possible to identify thousands of... 
SPECTROMETRY DATA | TANDEM MASS-SPECTRA | TYROSINE PHOSPHORYLATION | PHOSPHOPEPTIDES | STRATEGY | BIOCHEMICAL RESEARCH METHODS | PHOSPHOPROTEINS | VALIDATION | FRAGMENTATION | IMPROVED PEPTIDE IDENTIFICATION | PROTEOMICS | Phosphopeptides - chemistry | Computational Biology - methods | Phosphorylation | Reproducibility of Results | Peptides - chemistry | Humans | Ions | Proteome | Algorithms | Protein Processing, Post-Translational | Software | Proteomics - methods | Chromatography, Liquid - methods | Binding Sites | Mass Spectrometry - methods | Index Medicus | Technological Innovation and Resources | Regular Issue
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10. Full Text Thermal proteome profiling monitors ligand interactions with cellular membrane proteins
by Reinhard, Friedrich B.M and Eberhard, Dirk and Werner, Thilo and Franken, Holger and Childs, Dorothee and Doce, Carola and Savitski, Maria Fälth and Huber, Wolfgang and Bantscheff, Marcus and Savitski, Mikhail M and Drewes, Gerard
Nature Methods, ISSN 1548-7091, 12/2015, Volume 12, Issue 12, pp. 1129 - 1131
We extended thermal proteome profiling to detect transmembrane protein-small molecule interactions in cultured human cells. When we assessed the effects of... 
CELLS | ACTIVATION | QUANTIFICATION | BIOCHEMICAL RESEARCH METHODS | RECEPTOR | KINASE INHIBITORS | TYROSINE-PHOSPHORYLATION | IDENTIFICATION | DRUG TARGETS | SHIFT ASSAY | REVEALS | Caco-2 Cells | Small Molecule Libraries - pharmacology | Receptors, Antigen, T-Cell - metabolism | Jurkat Cells | Humans | Hot Temperature | Proteome - analysis | Sodium-Potassium-Exchanging ATPase - metabolism | Vanadates - pharmacology | K562 Cells | ATP Binding Cassette Transporter, Sub-Family B - metabolism | Protein Binding | Ligands | Membrane Proteins - metabolism | Protein Stability | Proteomics - methods | Proteome - metabolism | Tandem Mass Spectrometry - methods | Physiological aspects | Ligands (Biochemistry) | Methods | Proteomics | Membrane proteins | Membranes | Scientific method | Cellular biology | Index Medicus
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11. Full Text Measuring and managing ratio compression for accurate iTRAQ/TMT quantification
by Savitski, Mikhail M and Mathieson, Toby and Zinn, Nico and Sweetman, Gavain and Doce, Carola and Becher, Isabelle and Pachl, Fiona and Kuster, Bernhard and Bantscheff, Marcus
Journal of Proteome Research, ISSN 1535-3893, 08/2013, Volume 12, Issue 8, pp. 3586 - 3598
Isobaric mass tagging (e.g., TMT and iTRAQ) is a precise and sensitive multiplexed peptide/protein quantification technique in mass spectrometry. However,... 
isobaric mass tagging | iTRAQ/TMT | peptide/protein quantification | Staining and Labeling - methods | Tandem Mass Spectrometry - standards | Molecular Weight | Jurkat Cells | Peptide Fragments - isolation & purification | Staining and Labeling - standards | Humans | Escherichia coli - chemistry | Peptide Fragments - chemistry | Algorithms | Proteomics - standards | K562 Cells | Proteomics - methods | Escherichia coli Proteins - chemistry | Index Medicus
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12. Full Text Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry
by Franken, Holger and Mathieson, Toby and Childs, Dorothee and Sweetman, Gavain M. A and Werner, Thilo and Tögel, 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
Nature Protocols, ISSN 1754-2189, 10/2015, Volume 10, Issue 10, pp. 1567 - 1593
The direct detection of drug-protein interactions in living cells is a major challenge in drug discovery research. Recently, we introduced an approach termed... 
CELLS | POLYPHARMACOLOGY | RELATIVE QUANTIFICATION | KINOME | PEPTIDE IDENTIFICATION | BIOCHEMICAL RESEARCH METHODS | HISTONE DEACETYLASE INHIBITORS | SHIFT ASSAY | DISCOVERY | ISOBARIC TAGS | ACCURACY | Proteome - genetics | Temperature | Humans | Mass Spectrometry | K562 Cells | Protein Array Analysis | Protein Stability | Drug Delivery Systems - methods | Drug targeting | Usage | Research | Mass spectrometry | Proteomics | Index Medicus
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13. Full Text Species-specific activity of antibacterial drug combinations
by Brochado, Ana Rita and Telzerow, Anja and Bobonis, Jacob and Banzhaf, Manuel and Mateus, André and Selkrig, Joel and Huth, Emily and Bassler, Stefan and Zamarreño Beas, Jordi and Zietek, Matylda and Ng, Natalie and Foerster, Sunniva and Ezraty, Benjamin and Py, Béatrice and Barras, Frédéric and Savitski, Mikhail M and Bork, Peer and Göttig, Stephan and Typas, Athanasios
Nature, ISSN 0028-0836, 07/2018, Volume 559, Issue 7713, pp. 259 - 263
The spread of antimicrobial resistance has become a serious public health concern, making once-treatable diseases deadly again and undermining the achievements... 
OUTER-MEMBRANE | AMINOGLYCOSIDES | BACTERIA | PSEUDOMONAS-AERUGINOSA | MULTIDISCIPLINARY SCIENCES | ESCHERICHIA-COLI | ANTIBIOTIC-RESISTANCE | INTERACTION NETWORKS | AZITHROMYCIN | ACCUMULATION | DISCOVERY | Pharmaceutical research | Drug resistance in microorganisms | Research | Antibiosis | Drug interactions | Drugs | Larvae | Salmonella | Additives | Colistin | Escherichia coli | Clinical isolates | Infections | Phylogeny | Drug resistance | Experiments | Proteins | E coli | Food additives | Bacteria | Pseudomonas aeruginosa | Drug dosages | Species | Public health | Food | Integrated approach | Bacterial infections | Antimicrobial agents | Gene expression | Antibiotics | Antimicrobial resistance | Vanillin | Drug additives | Index Medicus | Drug Synergism | Life Sciences | Microbiology and Parasitology | Species Specificity | Salmonella typhimurium/classification | Escherichia coli/drug effects | Anti-Bacterial Agents/pharmacology | Pseudomonas aeruginosa/drug effects | Pseudomonas aeruginosa/classification
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14. Full Text Proteome-wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP
by Sridharan, S and Kurzawa, N and Werner, T and Gunthner, I and Helm, D and Huber, W and Bantscheff, M and Savitski, MM
NATURE COMMUNICATIONS, ISSN 2041-1723, 03/2019, Volume 10, Issue 1, pp. 1155 - 13
Adenosine triphosphate (ATP) plays fundamental roles in cellular biochemistry and was recently discovered to function as a biological hydrotrope. Here, we use... 
DRUG | ACTIVATION | INHIBITION | PHOSPHORYLATION | DNA | MULTIDISCIPLINARY SCIENCES | KINASE | R PACKAGE | GRANULES | BINDING | DEHYDROGENASE | Profiling | Solubility | Mass spectroscopy | Solubilization | Organelles | Thermal stability | Substrates | Proteins | Allosteric properties | Localization | Mass spectrometry | Protein structure | ATP | Adenosine triphosphate | Index Medicus
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