S. Mohammed

发表

Protease bias in absolute protein quantitation

M. Peng, N. Taouatas, Salvatore Cappadona, 2012, Nature Methods.

Applications of stable isotope dimethyl labeling in quantitative proteomics

Salvatore Cappadona, S. Mohammed, A. Scholten, 2012, Analytical and Bioanalytical Chemistry.

Collaboration of AMPK and PKC to induce phosphorylation of Ser413 on PIP5K1B resulting in decreased kinase activity and reduced PtdIns(4,5)P2 synthesis in response to oxidative stress and energy restriction.

S. Mohammed, Z. Shah, Iman van den Bout, 2013, The Biochemical journal.

Proteome adaptation of Saccharomyces cerevisiae to severe calorie restriction in Retentostat cultures.

J. Pronk, P. Daran-Lapujade, S. Mohammed, 2014, Journal of proteome research.

Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics

Reinout Raijmakers, Albert J R Heck, Shabaz Mohammed, 2009, Nature Protocols.

Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.

Jeroen Krijgsveld, Albert J R Heck, Andreas O Helbig, 2009, Analytical chemistry.

Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium

Arne G. Schmeisky, P. Bork, A. Gavin, 2012, Molecular systems biology.

Nicotinamide Cofactors Suppress Active-Site Labeling of Aldehyde Dehydrogenases.

S. Mohammed, D. Bartels, R. V. D. van der Hoorn, 2016, ACS chemical biology.

A large synthetic peptide and phosphopeptide reference library for mass spectrometry–based proteomics

M. Mann, J. Cox, B. Kuster, 2013, Nature Biotechnology.

Robust phosphoproteome enrichment using monodisperse microsphere–based immobilized titanium (IV) ion affinity chromatography

S. Mohammed, A. Heck, H. Zou, 2013, Nature Protocols.

Strong Cation Exchange-based Fractionation of Lys-N-generated Peptides Facilitates the Targeted Analysis of Post-translational Modifications*

Madalina M. Drugan, N. Taouatas, S. Mohammed, 2009, Molecular & Cellular Proteomics.

Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC and ZIC-cHILIC) provide high resolution separation and increase sensitivity in proteome analysis.

S. Mohammed, A. Heck, Serena Di Palma, 2011, Analytical chemistry.

Improved identification of endogenous peptides from murine nervous tissue by multiplexed peptide extraction methods and multiplexed mass spectrometric analysis.

S. Mohammed, A. Heck, M. Brans, 2009, Journal of proteome research.

The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search*

P. Pevzner, S. Mohammed, A. Heck, 2010, Molecular & Cellular Proteomics.

Phosphopeptide Fragmentation and Analysis by Mass Spectrometry

S. Mohammed, A. Heck, P. Boersema, 2010 .

Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos.

S. Mohammed, A. Heck, A. Altelaar, 2011, Journal of proteome research.

University of Groningen Quantitative and Qualitative Proteome Characteristics Extracted from In-Depth Integrated Genomics and Proteomics Analysis

S. V. Heesch, E. Cuppen, S. Mohammed, 2018 .

Targeted analysis of protein termini.

B. V. Breukelen, S. Mohammed, A. Heck, 2007, Journal of proteome research.

Phosphopeptide fragmentation and analysis by mass spectrometry.

S. Mohammed, A. Heck, P. Boersema, 2009, Journal of mass spectrometry : JMS.

Universal quantitative kinase assay based on diagonal SCX chromatography and stable isotope dimethyl labeling provides high-definition kinase consensus motifs for PKA and human Mps1.

S. Mohammed, A. Heck, G. Kops, 2013, Journal of proteome research.

Exploring the human leukocyte phosphoproteome using a microfluidic reversed-phase-TiO2-reversed-phase high-performance liquid chromatography phosphochip coupled to a quadrupole time-of-flight mass spectrometer.

S. Mohammed, A. Heck, R. Raijmakers, 2010, Analytical chemistry.

Quantitative Phosphoproteomics of Early Elicitor Signaling in Arabidopsis*S

Albert J R Heck, Shabaz Mohammed, J. Benschop, 2007, Molecular & Cellular Proteomics.

Multiplexed proteomics mapping of yeast RNA polymerase II and III allows near-complete sequence coverage and reveals several novel phosphorylation sites.

P. Cramer, S. Mohammed, A. Heck, 2008, Analytical chemistry.

Highly sensitive proteome analysis of FACS-sorted adult colon stem cells.

H. Clevers, S. Mohammed, A. Heck, 2011, Journal of proteome research.

Posttranslational mutagenesis: A chemical strategy for exploring protein side-chain diversity

Gonçalo J. L. Bernardes, Shabaz Mohammed, Timothy D. W. Claridge, 2016, Science.

Quantitative Phosphoproteomics after Auxin-stimulated Lateral Root Induction Identifies an SNX1 Protein Phosphorylation Site Required for Growth*

S. Mohammed, A. Heck, B. Scheres, 2013, Molecular & Cellular Proteomics.

Structural characterization of KKT4, an unconventional microtubule-binding kinetochore protein

S. Mohammed, E. Lowe, C. Redfield, 2020, bioRxiv.

Toward an Optimized Workflow for Middle-Down Proteomics

Henk W. P. van den Toorn, S. Mohammed, A. Heck, 2017, Analytical chemistry.

Sampling From the Proteome to the Human Leukocyte Antigen-DR (HLA-DR) Ligandome Proceeds Via High Specificity*

Shabaz Mohammed, Albert J. R. Heck, Fabio Marino, 2016, Molecular & Cellular Proteomics.

A systems-wide screen identifies substrates of the SCFβTrCP ubiquitin ligase

M. Peng, S. Mohammed, D. Guardavaccaro, 2014, Science Signaling.

A systems-wide screen identifies substrates of the SCF ubiquitin ligase

M. Peng, S. Mohammed, A. Heck, 2014 .

Identification of salt-tolerant Sinorhizobium sp. strain BL3 membrane proteins based on proteomics.

S. Mohammed, O. Jensen, R. Matthiesen, 2010, Microbes and environments.

Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection

S. Mohammed, Alfredo Castello, R. Bartenschlager, 2020, bioRxiv.

In-house construction of a UHPLC system enabling the identification of over 4000 protein groups in a single analysis.

S. Mohammed, A. Heck, P. Giansanti, 2012, The Analyst.

Quantitative Proteomics for Differential Protein Expression Profiling

S. Mohammed, A. Heck, H. W. van den Toorn, 2019, Proteomics for Biological Discovery.

Proteasome-dependent Degradation of Transcription Factor Activating Enhancer-binding Protein 4 (TFAP4) Controls Mitotic Division*

S. Mohammed, A. Heck, D. Guardavaccaro, 2014, The Journal of Biological Chemistry.

Acetylation and phosphorylation control both local and global stability of the chloroplast F1 ATP synthase

S. Mohammed, C. Robinson, Carla Schmidt, 2017, Scientific Reports.

Database independent proteomics analysis of the ostrich and human proteome

B. Snel, S. Mohammed, A. Heck, 2011, Proceedings of the National Academy of Sciences.

LysNDeNovo: An algorithm enabling de novo sequencing of Lys‐N generated peptides fragmented by electron transfer dissociation

Madalina M. Drugan, N. Taouatas, S. Mohammed, 2010, Proteomics.

Running title: Analysis of phosphate group rearrangement in a phosphoproteomics dataset

S. Mohammed, J. D. Navarro, N. Mischerikow, 2010 .

Light-driven post-translational installation of reactive protein side chains

S. Mohammed, A. Baldwin, B. G. Davis, 2020, Nature.

Monitoring the Disassembly of Virus-like Particles by 19F-NMR

S. Mohammed, A. Baldwin, Brian Lyons, 2017, Journal of the American Chemical Society.

Improving depth in phosphoproteomics by using a strong cation exchange-weak anion exchange-reversed phase multidimensional separation approach.

S. Mohammed, A. Heck, G. Kops, 2011, Analytical chemistry.

The tyrosine phosphatase Shp2 interacts with NPM-ALK and regulates anaplastic lymphoma cell growth and migration.

S. Mohammed, G. Inghirami, O. Jensen, 2007, Cancer research.

p130Cas mediates the transforming properties of the anaplastic lymphoma kinase.

S. Mohammed, G. Inghirami, E. Hirsch, 2005, Blood.

Signal Transduction Reaction Monitoring Deciphers Site-Specific PI3K-mTOR/MAPK Pathway Dynamics in Oncogene-Induced Senescence.

S. Mohammed, A. Heck, D. Peeper, 2015, Journal of proteome research.

Exploitation of an iron transporter for bacterial protein antibiotic import

S. Mohammed, C. Kleanthous, P. White, 2017, Proceedings of the National Academy of Sciences.

Interdomain conformational flexibility underpins the activity of UGGT, the eukaryotic glycoprotein secretion checkpoint

S. Mohammed, P. Roversi, N. Zitzmann, 2017, Proceedings of the National Academy of Sciences.

Quantitative Map of Proteome Dynamics during Neuronal Differentiation

C. Hoogenraad, S. Mohammed, A. Heck, 2017, Cell reports.

Effect of chemical modifications on peptide fragmentation behavior upon electron transfer induced dissociation.

S. Mohammed, A. Heck, P. Boersema, 2009, Analytical chemistry.

Characterization of HSP27 phosphorylation sites in human atherosclerotic plaque secretome.

S. Mohammed, O. Jensen, J. Egido, 2007, Methods in molecular biology.

The Leukemia-Associated Mllt10/Af10-Dot1l Are Tcf4/β-Catenin Coactivators Essential for Intestinal Homeostasis

T. Mahmoudi, H. Clevers, N. Taouatas, 2010, PLoS biology.

Dimer interface of bovine cytochrome c oxidase is influenced by local posttranslational modifications and lipid binding

S. Mohammed, C. Robinson, S. Yoshikawa, 2016, Proceedings of the National Academy of Sciences.

Atorvastatin modulates the profile of proteins released by human atherosclerotic plaques.

S. Mohammed, O. Jensen, J. Egido, 2007, European journal of pharmacology.

A unique residue in rab3c determines the interaction with novel binding protein Zwint‐1

C. Hoogenraad, S. Mohammed, A. Heck, 2008, FEBS letters.

Stereoretentive Post-Translational Protein Editing

S. Mohammed, B. G. Davis, Jack Ren, 2022, bioRxiv.

Threonine phosphorylation of IκBζ mediates inhibition of pro-inflammatory target genes

Daniela, S. Mohammed, F. Essmann, 2019 .

A Role for PtdIns(4,5)P 2 and PIP5Kα in Regulating Stress-Induced Apoptosis

S. Mohammed, A. Heck, K. Jalink, 2006, Current Biology.

SIGNAL TRANSDUCTION REACTION MONITORING DECIPHERS SITE-SPECIFIC PI 3 K-mTOR / MAPK PATHWAY DYNAMICS

S. Mohammed, A. Heck, D. Peeper, 2014 .

De novo sequencing of two novel peptides homologous to calcitonin-like peptides, from skin secretion of the Chinese Frog, Odorrana schmackeri

S. Mohammed, A. Heck, P. Verhaert, 2015 .

Protein Syndesmos is a novel RNA-binding protein that regulates primary cilia formation

P. Zoppoli, S. Mohammed, Alfredo Castello, 2018, Nucleic acids research.

Regulation of retromer recruitment to endosomes by sequential action of Rab5 and Rab7

J. Bonifacino, S. Mohammed, A. Heck, 2008, The Journal of cell biology.

Ubiquitin-based pathway acts inside chloroplasts to regulate photosynthesis

S. Mohammed, Marjorie Fournier, Yonghong Hu, 2022, bioRxiv.

Protein Phosphatase 2A (B55α) Prevents Premature Activation of Forkhead Transcription Factor FoxM1 by Antagonizing Cyclin A/Cyclin-dependent Kinase-mediated Phosphorylation*

S. Mohammed, R. Medema, V. Halim, 2011, The Journal of Biological Chemistry.

Recovery from a DNA‐damage‐induced G2 arrest requires Cdk‐dependent activation of FoxM1

S. Mohammed, A. Heck, R. Medema, 2010, EMBO reports.

USP17- and SCF (cid:2) TrCP -Regulated Degradation of DEC1 Controls the DNA Damage Response

S. Mohammed, A. Heck, R. Medema, 2014 .

Regulated Degradation of DEC 1 Controls the DNA Damage 1 Response 2 3

S. Mohammed, A. Heck, R. Medema, 2014 .

Broad‐range metalloprotease profiling in plants uncovers immunity provided by defence‐related metalloenzyme

S. Mohammed, B. Cravatt, S. Sieber, 2022, The New phytologist.

Activation of FoxM1 during G2 Requires Cyclin A/Cdk-Dependent Relief of Autorepression by the FoxM1 N-Terminal Domain

S. Mohammed, A. Heck, R. Medema, 2008, Molecular and Cellular Biology.

Lipids mediate supramolecular outer membrane protein assembly in bacteria

S. Mohammed, C. Robinson, S. Khalid, 2022, Science advances.

Post-translational mutagenesis: a chemical synthetic strategy for exploration of protein side-chain diversity

Rafal P. Wiewiora, S. Gerstberger, S. Mohammed, 2016 .

Activation of FoxM 1 during G 2 Requires Cyclin A / Cdk-Dependent Relief of Autorepression by the FoxM 1 N-Terminal Domain †

S. Mohammed, A. Heck, R. Medema, 2008 .

Comparative Phosphoproteomic Analysis of Checkpoint Recovery Identifies New Regulators of the DNA Damage Response

Shabaz Mohammed, Albert J. R. Heck, Henk W. P. van den Toorn, 2013, Science Signaling.

Protein phosphatase 2A (B55α) prevents premature activation of forkhead transcription factor FoxM1 by antagonizing cyclin A/cyclin-dependent kinase-mediated phosphorylation.

S. Mohammed, R. Medema, J. Laoukili, 2011, The Journal of Biological Chemistry.

Post-translational insertion of boron in proteins to probe and modulate function

S. Mohammed, A. Baldwin, B. G. Davis, 2021, Nature Chemical Biology.

Synthetic post-translational modification of histones.

Benjamin G Davis, Shabaz Mohammed, S. Mohammed, 2018, Current opinion in chemical biology.

Evaluation and optimization of ZIC-HILIC-RP as an alternative MudPIT strategy.

S. Mohammed, A. Heck, P. Boersema, 2007, Journal of proteome research.

Elongation/Termination Factor Exchange Mediated by PP1 Phosphatase Orchestrates Transcription Termination

S. Mohammed, C. Robinson, K. Kuś, 2018, Cell reports.

The CRAPome: a Contaminant Repository for Affinity Purification Mass Spectrometry Data

Amber L. Couzens, Mihaela E. Sardiu, Wade H. Dunham, 2013, Nature Methods.

Recent advances in peptide separation by multidimensional liquid chromatography for proteome analysis.

Albert J R Heck, Shabaz Mohammed, S. Mohammed, 2012, Journal of proteomics.

Personalized Proteome Profiles of Healthy and Tumor Human Colon Organoids Reveal Both Individual Diversity and Basic Features of Colorectal Cancer.

Hans Clevers, Albert J R Heck, Shabaz Mohammed, 2017, Cell reports.

Tumour suppressor RNF43 is a stem-cell E3 ligase that induces endocytosis of Wnt receptors

H. Clevers, S. Mohammed, A. Heck, 2012, Nature.

Lgr5 homologues associate with Wnt receptors and mediate R-spondin signalling

Hans Clevers, Bon-Kyoung Koo, Marc van de Wetering, 2011, Nature.

Chemical Proteomics and Phenotypic Profiling Identifies the Aryl Hydrocarbon Receptor as a Molecular Target of the Utrophin Modulator Ezutromid

G. Wynne, K. Davies, S. Mohammed, 2019, Angewandte Chemie.

Genetic Incorporation of Olefin Cross-Metathesis Reaction Tags for Protein Modification.

S. Mohammed, B. G. Davis, M. Bak, 2018, Journal of the American Chemical Society.

Genetic Incorporation of Ole fi n Cross-Metathesis Reaction Tags for Protein Modi fi cation

S. Mohammed, B. G. Davis, M. Bak, 2018 .

Optimal Synthetic Glycosylation of a Therapeutic Antibody

S. Mohammed, C. Robinson, J. Benesch, 2016, Angewandte Chemie.

Exploring new proteome space: combining Lys-N proteolytic digestion and strong cation exchange (SCX) separation in peptide-centric MS-driven proteomics.

N. Taouatas, S. Mohammed, A. Heck, 2011, Methods in molecular biology.

Straightforward and de Novo Peptide Sequencing by MALDI-MS/MS Using a Lys-N Metalloendopeptidase*S

N. Taouatas, S. Mohammed, A. Heck, 2009, Molecular & Cellular Proteomics.

Polyamines Control eIF5A Hypusination, TFEB Translation, and Autophagy to Reverse B Cell Senescence

A. Ballabio, S. Mohammed, S. Balabanov, 2019, Molecular cell.

The Lgr 5 intestinal stem cell signature : robust expression of proposed quiescent ‘ þ 4 ’ cell markers

Alexander van Oudenaarden, Hans Clevers, Jan Koster, 2012 .

hnRNPK Recruits PCGF3/5-PRC1 to the Xist RNA B-Repeat to Establish Polycomb-Mediated Chromosomal Silencing

N. Brockdorff, S. Mohammed, Alfredo Castello, 2017, Molecular cell.

The kinase TNIK is an essential activator of Wnt target genes

Hans Clevers, Shabaz Mohammed, S. Ng, 2009, The EMBO journal.

System-wide Profiling of RNA-Binding Proteins Uncovers Key Regulators of Virus Infection

Luis Carrasco, S. Mohammed, Alfredo Castello, 2019, Molecular cell.

Wnt Signaling through Inhibition of β-Catenin Degradation in an Intact Axin1 Complex

Hans Clevers, Shabaz Mohammed, S. Ng, 2012, Cell.

LanCLs add glutathione to dehydroamino acids generated at phosphorylated sites in the proteome

K. P. Chooi, S. Mohammed, G. Hutchings, 2021, Cell.

Nuclear phosphorylated Dicer processes double-stranded RNA in response to DNA damage

S. Mohammed, M. Gullerová, Margarita Schlackow, 2017, The Journal of cell biology.

Identification of ischemia-regulated phosphorylation sites in connexin43: A possible target for the antiarrhythmic peptide analogue rotigaptide (ZP123).

S. Mohammed, O. Jensen, N. Holstein-Rathlou, 2006, Journal of molecular and cellular cardiology.

Ordered dephosphorylation initiated by the selective proteolysis of cyclin B drives mitotic exit

S. Mohammed, F. Barr, James Holder, 2020, bioRxiv.

Coupled Activation and Degradation of eEF2K Regulates Protein Synthesis in Response to Genotoxic Stress

Michele Pagano, Teck Yew Low, Shabaz Mohammed, 2012, Science Signaling.

Highly efficient depletion strategy for the two most abundant erythrocyte soluble proteins improves proteome coverage dramatically.

S. Mohammed, A. Heck, M. Slijper, 2008, Journal of proteome research.

Doxorubicin-induced DNA Damage Causes Extensive Ubiquitination of Ribosomal Proteins Associated with a Decrease in Protein Translation*

S. Mohammed, A. Heck, R. Medema, 2018, Molecular & Cellular Proteomics.

Unambiguous Phosphosite Localization using Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)

Karl Mechtler, Shabaz Mohammed, Albert J. R. Heck, 2013, Journal of proteome research.

Enhancing the Identification of Phosphopeptides from Putative Basophilic Kinase Substrates Using Ti (IV) Based IMAC Enrichment*

Albert J R Heck, Hanfa Zou, Shabaz Mohammed, 2011, Molecular & Cellular Proteomics.

Quantitative Phosphoproteomics Applied to the Yeast Pheromone Signaling Pathway*S

M. Mann, A. Gruhler, P. Mortensen, 2005, Molecular & Cellular Proteomics.

A systematic approach to modeling, capturing, and disseminating proteomics experimental data

Chris F. Taylor, Norman W. Paton, Douglas B. Kell, 2003, Nature Biotechnology.

MAP3K1 functionally interacts with Axin1 in the canonical Wnt signalling pathway

T. Mahmoudi, H. Clevers, S. Mohammed, 2010, Biological chemistry.

Comparative poly(A)+ RNA interactome capture of fission yeast RNA exosome mutants reveals insights into RNA biogenesis

S. Mohammed, Alfredo Castello, K. Kuś, 2020, bioRxiv.

Probing Genuine Strong Interactions and Post-translational Modifications in the Heterogeneous Yeast Exosome Protein Complex*S

S. Mohammed, A. Heck, R. V. D. van den Heuvel, 2006, Molecular & Cellular Proteomics.

Highly robust, automated, and sensitive online TiO2-based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster.

Joost W Gouw, Albert J R Heck, Shabaz Mohammed, 2008, Journal of proteome research.

Rapid analyses of proteomes and interactomes using an integrated solid-phase extraction-liquid chromatography-MS/MS system.

N. Bache, S. Mohammed, A. Heck, 2015, Journal of proteome research.

Modification-specific proteomics of plasma membrane proteins: identification and characterization of glycosylphosphatidylinositol-anchored proteins released upon phospholipase D treatment.

Jakob Bunkenborg, Ole N Jensen, Shabaz Mohammed, 2006, Journal of proteome research.

Hydrophilic interaction liquid chromatography (HILIC) in proteomics

S. Mohammed, A. Heck, P. Boersema, 2008, Analytical and bioanalytical chemistry.

Characterization of biases in phosphopeptide enrichment by Ti(4+)-immobilized metal affinity chromatography and TiO2 using a massive synthetic library and human cell digests.

Henk W. P. van den Toorn, S. Mohammed, A. Heck, 2014, Analytical chemistry.

Comparative Assessment of Site Assignments in CID and Electron Transfer Dissociation Spectra of Phosphopeptides Discloses Limited Relocation of Phosphate Groups*

Albert J R Heck, Shabaz Mohammed, J Daniel Navarro, 2010, Molecular & Cellular Proteomics.

Selective Metal-Site-Guided Arylation of Proteins.

Benjamin G Davis, Shabaz Mohammed, S. Mohammed, 2016, Journal of the American Chemical Society.

Synthetic Phosphorylation of p38α Recapitulates Protein Kinase Activity

K. P. Chooi, S. Mohammed, B. G. Davis, 2014, Journal of the American Chemical Society.

System-wide analyses of the fission yeast poly(A)+ RNA interactome reveal insights into organization and function of RNA–protein complexes

S. Mohammed, Alfredo Castello, K. Kuś, 2019, bioRxiv.

eIF2 interactions with initiator tRNA and eIF2B are regulated by post-translational modifications and conformational dynamics

S. Mohammed, C. Robinson, Y. Gordiyenko, 2015, Cell Discovery.

Toward a comprehensive characterization of a human cancer cell phosphoproteome.

M. Peng, S. Mohammed, A. Heck, 2013, Journal of proteome research.

Online automated in vivo zebrafish phosphoproteomics: from large-scale analysis down to a single embryo.

S. Lemeer, S. Mohammed, A. Heck, 2008, Journal of proteome research.

Chip-Based Enrichment and NanoLC-MS/MS Analysis of Phosphopeptides from Whole Lysates.

Albert J R Heck, Shabaz Mohammed, Simone Lemeer, 2008, Journal of proteome research.

A PP2A-B55 recognition signal controls substrate dephosphorylation kinetics during mitotic exit

B. Novák, S. Mohammed, F. Barr, 2016, The Journal of cell biology.

Discovering the RNA-Binding Proteome of Plant Leaves with an Improved RNA Interactome Capture Method

S. Mohammed, Alfredo Castello, M. Kaiser, 2020, Biomolecules.

Compositional analysis of Sindbis virus ribonucleoproteins reveals an extensive co-opting of key nuclear RNA-binding proteins

S. Mohammed, Alfredo Castello, Ilan Davis, 2021, bioRxiv.

Uncovering viral RNA–host cell interactions on a proteome-wide scale

P. Simmonds, S. Mohammed, Alfredo Castello, 2021, Trends in biochemical sciences.

Global analysis of RNA-binding protein dynamics by comparative and enhanced RNA interactome capture

M. Hentze, S. Mohammed, Alfredo Castello, 2020, Nature Protocols.

Global analysis of RNA-binding protein dynamics by comparative and enhanced RNA interactome capture

M. Hentze, S. Mohammed, Alfredo Castello, 2020, Nature Protocols.

Proteome-wide Profiling of RNA-Binding Protein Responses to flg22 Reveals Novel Components of Plant Immunity

S. Mohammed, Alfredo Castello, M. Kaiser, 2020, bioRxiv.

Comparative Poly(A)+ RNA Interactome Capture of RNA Surveillance Mutants.

S. Mohammed, Alfredo Castello, L. Vasiljeva, 2020, Methods in molecular biology.

Understanding RNP remodelling uncovers RBPs functionally required for viral replication

Luis Carrasco, S. Mohammed, Alfredo Castello, 2018, bioRxiv.

Threonine phosphorylation of IκBζ mediates inhibition of selective proinflammatory target genes.

S. Mohammed, K. Schulze-Osthoff, F. Essmann, 2020, The Journal of investigative dermatology.

Toward full peptide sequence coverage by dual fragmentation combining electron-transfer and higher-energy collision dissociation tandem mass spectrometry.

Albert J R Heck, Shabaz Mohammed, Henk van den Toorn, 2012, Analytical chemistry.

The role of the Xist 5’ m6A region and RBM15 in X chromosome inactivation

N. Brockdorff, S. Mohammed, T. Nesterova, 2020, Wellcome open research.

Profiling of diet-induced neuropeptide changes in rat brain by quantitative mass spectrometry.

Albert J R Heck, Shabaz Mohammed, S. Mohammed, 2013, Analytical chemistry.

RNA-binding protein Mub1 and the nuclear RNA exosome act to fine-tune environmental stress response

S. Mohammed, Alfredo Castello, K. Kuś, 2020, Life Science Alliance.

Assessing biological variation and protein processing in primary human leukocytes by automated multiplex stable isotope labeling coupled to 2 dimensional peptide separation.

S. Mohammed, A. Heck, R. Raijmakers, 2009, Molecular bioSystems.

An optimized protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry.

Andrew Hayes, Stephen G Oliver, Shabaz Mohammed, 2003, Phytochemistry.

USP17- and SCFβTrCP-Regulated Degradation of DEC1 Controls the DNA Damage Response

S. Mohammed, A. Heck, R. Medema, 2014, Molecular and Cellular Biology.

Improving SRM assay development: a global comparison between triple quadrupole, ion trap, and higher energy CID peptide fragmentation spectra.

Albert J R Heck, Shabaz Mohammed, Bas van Breukelen, 2011, Journal of proteome research.

Benchmarking stable isotope labeling based quantitative proteomics.

Albert J R Heck, Shabaz Mohammed, S. Mohammed, 2013, Journal of proteomics.

Phosphopeptide quantitation using amine-reactive isobaric tagging reagents and tandem mass spectrometry: application to proteins isolated by gel electrophoresis.

N. Bache, S. Mohammed, O. Jensen, 2006, Rapid communications in mass spectrometry : RCM.

Serum protein profiling by miniaturized solid-phase extraction and matrix-assisted laser desorption/ionization mass spectrometry.

W. Vach, S. Mohammed, J. Bunkenborg, 2005, Rapid communications in mass spectrometry : RCM.

Enhancing Phosphotyrosine Proteome Coverage Using a Combined ETD and CID Approach on a LTQ Orbitrap XL ETD

S. Lemeer, S. Mohammed, A. Heck, 2010 .

Quantitative MS‐Based Proteomics: Comparing the MCF‐7 Cellular Response to Hypoxia and a 2‐Oxoglutarate Analogue

S. Mohammed, C. Schofield, M. Chan, 2020, Chembiochem : a European journal of chemical biology.

YcfDRM is a thermophilic oxygen-dependent ribosomal protein uL16 oxygenase

S. Mohammed, M. Münzel, C. Schofield, 2018, Extremophiles.

The anti-sigma factor RsrA responds to oxidative stress by reburying its hydrophobic core

Konrad Zdanowski, Shabaz Mohammed, Connor Sharp, 2016, Nature Communications.

Combining Deep Sequencing, Proteomics, Phosphoproteomics, and Functional Screens To Discover Novel Regulators of Sphingolipid Homeostasis.

M. Schuldiner, S. Lemeer, S. Mohammed, 2017, Journal of proteome research.

Generation of a synthetic GlcNAcylated nucleosome reveals regulation of stability by H2A-Thr101 GlcNAcylation

S. Mohammed, C. Robinson, B. G. Davis, 2015, Nature Communications.

Synthetic Nucleosomes Reveal that GlcNAcylation Modulates Direct Interaction with the FACT Complex

S. Mohammed, B. G. Davis, L. Lercher, 2016, Angewandte Chemie.

Profiling of N-Acetylated Protein Termini Provides In-depth Insights into the N-terminal Nature of the Proteome*

S. Mohammed, A. Heck, M. Slijper, 2010, Molecular & Cellular Proteomics.

Comparative poly(A)+ RNA interactome capture reveals new proteins implicated in RNA regulation in fission yeast

S. Mohammed, Alfredo Castello, K. Kuś, 2021 .

Nuclear PtdIns5P as a transducer of stress signaling: an in vivo role for PIP4Kbeta.

S. Mohammed, A. Heck, David R. Jones, 2006, Molecular cell.

β2-Syntrophin Is a Cdk5 Substrate That Restrains the Motility of Insulin Secretory Granules

Yu. V. Bodrov, Y. Kalaidzidis, S. Mohammed, 2010, PloS one.

A three‐way proteomics strategy allows differential analysis of yeast mitochondrial membrane protein complexes under anaerobic and aerobic conditions

J. Pronk, P. Daran-Lapujade, S. Mohammed, 2009, Proteomics.

receptor for the complement regulator factor H increases transmission of trypanosomes to tsetse flies. Nature

S. Mohammed, N. Savill, R. Minter, 2020 .

Characterization and usage of the EASY-spray technology as part of an online 2D SCX-RP ultra-high pressure system.

N. Bache, S. Mohammed, A. Heck, 2014, The Analyst.

Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels

Andreas O Helbig, Shabaz Mohammed, Bas van Breukelen, 2010, BMC Genomics.

Light regulated SIK1 remodels the synaptic phosphoproteome to induce sleep

Philip R. Cohen, S. Mohammed, V. Vyazovskiy, 2021, bioRxiv.

Strong cation exchange (SCX) based analytical methods for the targeted analysis of protein post-translational modifications.

S. Mohammed, A. Heck, 2011, Current opinion in biotechnology.

Phosphorylation of Not4p Functions Parallel to BUR2 to Regulate Resistance to Cellular Stresses in Saccharomyces cerevisiae

S. Mohammed, A. Heck, K. Mulder, 2010, PloS one.

Translational control of TFEB and autophagy via eIF5A rejuvenates B cell immunity

S. Mohammed, S. Balabanov, J. Mellor, 2018 .

Ligand binding to a G protein–coupled receptor captured in a mass spectrometer

S. Mohammed, C. Robinson, T. Allison, 2017, Science Advances.

Peptide Orientation Affects Selectivity in Ion-Exchange Chromatography

Richard D. Smith, S. Mohammed, A. Heck, 2010, Analytical chemistry.

Triazine Probes Target Ascorbate Peroxidases in Plants1

S. Mohammed, K. Yamaguchi-Shinozaki, M. Kaiser, 2019, Plant Physiology.

Colicin-Mediated Transport of DNA through the Iron Transporter FepA

Jeffrey J. Gray, S. Mohammed, J. J. Gray, 2021, bioRxiv.

HGF signaling regulates Claudin-3 dynamics through its C-terminal tyrosine residues

S. Mohammed, J. de Rooij, L. Mathéron, 2013, Tissue barriers.

Cleavage specificities of the brother and sister proteases Lys-C and Lys-N.

S. Mohammed, A. Heck, R. Raijmakers, 2010, Chemical communications.

Evaluation of metalloendopeptidase Lys-N protease performance under different sample handling conditions.

N. Taouatas, S. Mohammed, A. Heck, 2010, Journal of proteome research.

Quantitative global phosphoproteomics of human umbilical vein endothelial cells after activation of the Rap signaling pathway.

S. Mohammed, A. Heck, J. Bos, 2013, Molecular bioSystems.

Ultra acidic strong cation exchange enabling the efficient enrichment of basic phosphopeptides.

Henk W. P. van den Toorn, S. Mohammed, A. Heck, 2012, Analytical chemistry.

Comparative Phosphoproteomics of Zebrafish Fyn/Yes Morpholino Knockdown Embryos*S

S. Lemeer, S. Mohammed, A. Heck, 2008, Molecular & Cellular Proteomics.

Quantitative proteomics identifies Gemin5, a scaffolding protein involved in ribonucleoprotein assembly, as a novel partner for eukaryotic initiation factor 4E.

S. Mohammed, P. Roepstorff, C. Proud, 2006, Journal of proteome research.

Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates

Albert J R Heck, Shabaz Mohammed, S. Mohammed, 2008, Proteomics.

ZIC-cHILIC as a fractionation method for sensitive and powerful shotgun proteomics

S. Mohammed, A. Heck, S. D. Palma, 2012, Nature Protocols.

Dimethyl isotope labeling assisted de novo peptide sequencing

S. Mohammed, A. Heck, A. Altelaar, 2010, Journal of the American Society for Mass Spectrometry.

Guanidination chemistry for qualitative and quantitative proteomics.

S. Mohammed, I. Cristea, S. Gaskell, 2006, Rapid communications in mass spectrometry : RCM.

Optimal Synthetic Glycosylation of a Therapeutic Antibody

S. Mohammed, C. Robinson, J. Benesch, 2016, Angewandte Chemie.

Automated Online Sequential Isotope Labeling for Protein Quantitation Applied to Proteasome Tissue-specific Diversity*S

S. Mohammed, A. Heck, H. Ovaa, 2008, Molecular & Cellular Proteomics.

purification–mass spectrometry data

Amber L. Couzens, Mihaela E. Sardiu, Wade H. Dunham, 2022 .

Incorporation of genome-bound cellular proteins into HIV-1 particles regulates viral infection

S. Mohammed, Alfredo Castello, Emiliano P. Ricci, 2023, bioRxiv.

Proteomics as a tool for live attenuated influenza vaccine characterisation.

S. Mohammed, E. Hutchinson, A. Hawksworth, 2019, Vaccine.

On the Statistical Significance of Compressed Ratios in Isobaric Labeling: A Cross-Platform Comparison.

Shabaz Mohammed, Isabel Ruppen, Fernando Garcia, 2016, Journal of proteome research.

Control of epithelial cell migration and invasion by the IKKβ- and CK1α-mediated degradation of RAPGEF2.

S. Mohammed, A. Heck, D. Guardavaccaro, 2013, Developmental cell.

Selectivity in Enrichment of cAMP-dependent Protein Kinase Regulatory Subunits Type I and Type II and Their Interactors Using Modified cAMP Affinity Resins*S

Henk W. P. van den Toorn, S. Mohammed, A. Scholten, 2009, Molecular & Cellular Proteomics.

Integrated Proteomics Unveils Nuclear PDE3A2 as a Regulator of Cardiac Myocyte Hypertrophy

M. Zaccolo, S. Mohammed, A. Scholten, 2023, Circulation research.

Characterization of Electron Transfer Dissociation in the Orbitrap Velos HCD Cell

S. Mohammed, A. Heck, A. Altelaar, 2013, Journal of The American Society for Mass Spectrometry.

Datasets from an interaction proteomics screen for substrates of the SCFβTrCP ubiquitin ligase

S. Mohammed, A. Heck, D. Guardavaccaro, 2015, Data in brief.

Deconvolution of overlapping isotopic clusters improves quantification of stable isotope-labeled peptides.

Javier Muñoz, Shabaz Mohammed, Bas van Breukelen, 2011, Journal of proteomics.

In-depth Quantitative Cardiac Proteomics Combining Electron Transfer Dissociation and the Metalloendopeptidase Lys-N with the SILAC Mouse*

S. Mohammed, A. Scholten, A. Heck, 2011, Molecular & Cellular Proteomics.

RockerBox: analysis and filtering of massive proteomics search results.

Reinout Raijmakers, Albert J R Heck, Javier Muñoz, 2011, Journal of proteome research.

Targeted SCX Based Peptide Fractionation for Optimal Sequencing by Collision Induced, and Electron Transfer Dissociation

B. V. Breukelen, S. Mohammed, A. Heck, 2008 .

A role for PtdIns(4,5)P2 and PIP5Kalpha in regulating stress-induced apoptosis.

S. Mohammed, A. Heck, J. van Rheenen, 2006, Current biology : CB.

Fyn/Yes morpholino knockdown embryos

S. Lemeer, S. Mohammed, M. Slijper, 2008 .

NeissLock provides an inducible protein anhydride for covalent targeting of endogenous proteins

S. Mohammed, M. Howarth, Sheryl Y. Lim, 2021, Nature Communications.

The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent ‘+4’ cell markers

S. Itzkovitz, A. van Oudenaarden, H. Clevers, 2022 .

A receptor for the complement regulator factor H increases transmission of trypanosomes to tsetse flies

S. Mohammed, N. Savill, R. Minter, 2020, Nature Communications.

System-wide Profiling of RNA-Binding Proteins Uncovers Key Regulators of Virus Infection

Luis Carrasco, S. Mohammed, Alfredo Castello, 2019, Molecular cell.

Straightforward ladder sequencing of peptides using a Lys-N metalloendopeptidase

Albert J R Heck, Shabaz Mohammed, N. Taouatas, 2008, Nature Methods.

Metabolic diversification in human retinal pigment epithelium cells induced by hyperglycemic and hypoxic conditions

Salvatore Cappadona, S. Mohammed, A. Heck, 2014 .

The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent ‘+4’ cell markers

S. Itzkovitz, A. van Oudenaarden, H. Clevers, 2012, The EMBO journal.

The tyrosine phosphatase Shp2 interacts with NPM-ALK and regulates anaplastic lymphoma cell growth and migration.

S. Mohammed, G. Inghirami, O. Jensen, 2007, Cancer research.

Enhancing the Identification of Phosphopeptides from Putative Basophilic Kinase Substrates Using Ti (IV) Based IMAC Enrichment*

S. Mohammed, A. Heck, Houjiang Zhou, 2011, Molecular & Cellular Proteomics.

Genetic Incorporation of Olefin Cross-Metathesis Reaction Tags for Protein Modification.

S. Mohammed, B. G. Davis, M. Bak, 2018, Journal of the American Chemical Society.

The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent ‘+4’ cell markers

S. Itzkovitz, A. van Oudenaarden, H. Clevers, 2012, The EMBO journal.

Regulation of retromer recruitment to endosomes by sequential action of Rab 5 and Rab 7

J. Bonifacino, S. Mohammed, P. Sluijs, 2022 .

Recent advances in peptide separation by multidimensional liquid chromatography for proteome analysis.

S. Mohammed, A. Heck, Serena Di Palma, 2012, Journal of proteomics.

Improving SRM assay development: a global comparison between triple quadrupole, ion trap, and higher energy CID peptide fragmentation spectra.

S. Mohammed, A. Heck, A. Altelaar, 2011, Journal of proteome research.

Reductive site-selective atypical C,Z-type/N2-C2 cleavage allows C-terminal protein amidation

S. Mohammed, A. Baldwin, D. Anthony, 2022, Science advances.

Quantitative Phosphoproteomics after Auxin-stimulated Lateral Root Induction Identifies an SNX1 Protein Phosphorylation Site Required for Growth*

S. Mohammed, A. Heck, B. Scheres, 2013, Molecular & Cellular Proteomics.

Selective Metal-Site-Guided Arylation of Proteins.

S. Mohammed, B. G. Davis, R. Raj, 2016, Journal of the American Chemical Society.

Characterization of an Omnitrap-Orbitrap Platform Equipped with Infrared Multiphoton Dissociation, Ultraviolet Photodissociation, and Electron Capture Dissociation for the Analysis of Peptides and Proteins

S. Mohammed, A. Makarov, D. Papanastasiou, 2023, bioRxiv.

MAP3K1 functionally interacts with Axin1 in the canonical Wnt signalling pathway

T. Mahmoudi, H. Clevers, S. Mohammed, 2010, Biological chemistry.

Novel protein phosphorylation site identification in spinach stroma membranes by titanium dioxide microcolumns and tandem mass spectrometry.

S. Mohammed, M. Larsen, L. Zolla, 2006, Journal of proteome research.

Molecular Systems Biology Peer Review Process File Cross-talk between Phosphorylation and Lysine Acetylation in a Genome-reduced Bacterium Transaction Report

Arne G. Schmeisky, A. Gavin, V. Rybin, 2022 .

Automated online sequential isotope labeling for protein quan- titation applied to proteasome tissue-specific diversity

S. Mohammed, H. Ovaa, Albert J. R. Heck, 2010 .

Dimer interface of bovine cytochrome c oxidase is influenced by local posttranslational modifications and lipid binding

S. Mohammed, C. Robinson, S. Yoshikawa, 2016, Proceedings of the National Academy of Sciences.

Alphavirus infection triggers selective cytoplasmic translocation of nuclear RBPs with moonlighting antiviral roles

S. Mohammed, Alfredo Castello, Ilan Davis, 2021, bioRxiv.

Protein Phosphatase 2 A ( B 55 ) Prevents Premature Activation of Forkhead Transcription Factor FoxM 1 by Antagonizing Cyclin A / Cyclin-dependent Kinase-mediated Phosphorylation *

S. Mohammed, R. Medema, Vincentius A. Halim, 2011 .