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List of works by Matthias Mann

1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data ⬇️

scientific article published on November 5, 2012

A "proteomic ruler" for protein copy number and concentration estimation without spike-in standards.

scientific article published on 15 September 2014

A Novel LC System Embeds Analytes in Pre-formed Gradients for Rapid, Ultra-robust Proteomics

scientific article published on 13 August 2018

A Systematic Investigation into the Nature of Tryptic HCD Spectra ⬇️

scientific article published on October 10, 2012

A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed.

scientific article published on 14 October 2009

A framework for intelligent data acquisition and real-time database searching for shotgun proteomics

scientific article

A human interactome in three quantitative dimensions organized by stoichiometries and abundances

scientific article

A knowledge graph to interpret clinical proteomics data

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

scientific article

A mass spectrometry guided approach for the identification of novel vaccine candidates in gram-negative pathogens

scientific article published on 22 November 2019

A mass spectrometry–friendly database for cSNP identification

scholarly article by Søren Schandorff et al published June 2007 in Nature Methods

A novel chromatographic method allows on-line reanalysis of the proteome

scientific article published on 29 April 2008

A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics

scientific article published on January 2009

A protein-interaction network of interferon-stimulated genes extends the innate immune system landscape

scientific article published on 04 March 2019

A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles

scientific article (publication date: October 2011)

A proteomic atlas of insulin signalling reveals tissue-specific mechanisms of longevity assurance.

scientific article published on 15 September 2017

Accurate MS-based Rab10 phosphorylation stoichiometry determination as readout for LRRK2 activity in Parkinson's disease

scientific article published on 29 June 2020

Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ.

scientific article

Acetylation site specificities of lysine deacetylase inhibitors in human cells

scientific article (publication date: 9 March 2015)

AlphaMap: an open-source Python package for the visual annotation of proteomics data with sequence-specific knowledge

scientific article published in 2021

AlphaTims: Indexing Trapped Ion Mobility Spectrometry–TOF Data for Fast and Easy Accession and Visualization

scientific article published on 17 September 2021

An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics

scientific article published on 27 February 2019

Analysis of the mouse liver proteome using advanced mass spectrometry.

scientific article published on 3 July 2007

Andromeda: a peptide search engine integrated into the MaxQuant environment

scientific article (publication date: April 2011)

Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry

scientific article published on 15 June 2020

Author Correction: Gel-like inclusions of C-terminal fragments of TDP-43 sequester stalled proteasomes in neurons

scientific article published on 7 June 2024

BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes

scientific article published on 07 May 2018

Cell-type-resolved quantitative proteomics of murine liver

scientific article published on December 2014

Cloning of a novel signaling molecule, AMSH-2, that potentiates transforming growth factor beta signaling

scientific article

Combined use of RNAi and quantitative proteomics to study gene function in Drosophila

scientific article published in September 2008

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

scientific article published on 28 September 2008

Computational principles of determining and improving mass precision and accuracy for proteome measurements in an Orbitrap

scientific article published on 20 May 2009

Correction to Feasibility of Large-Scale Phosphoproteomics with Higher Energy Collisional Dissociation Fragmentation

scholarly article published in Journal of Proteome Research

Cortical circuit alterations precede motor impairments in Huntington's disease mice

scientific article published on 29 April 2019

Cotranslational N-degron masking by acetylation promotes proteome stability in plants

scientific article published on 10 February 2022

Cryo-EM structures of Gid12-bound GID E3 reveal steric blockade as a mechanism inhibiting substrate ubiquitylation

scientific article published on 01 June 2022

DIA-based systems biology approach unveils E3 ubiquitin ligase-dependent responses to a metabolic shift

scientific article published on 07 December 2020

DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links

scientific article

Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology

scientific article published on 11 January 2021

Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation.

scientific article published on 17 May 2011

Deep learning the collisional cross sections of the peptide universe from a million experimental values

scientific article published on 20 February 2021

Deep muscle-proteomic analysis of freeze-dried human muscle biopsies reveals fiber type-specific adaptations to exercise training ⬇️

scientific article published on 12 January 2021

Deep proteome and transcriptome mapping of a human cancer cell line

scientific article

Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways, and transcription factors

scientific article

Defining the RBPome of primary T helper cells to elucidate higher-order Roquin-mediated mRNA regulation

scientific article published on 01 September 2021

Democratising Knowledge Representation with BioCypher

scientific article published on 27 December 2022

Democratizing knowledge representation with BioCypher

Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry

scientific article published on 21 November 2016

Dynamic human liver proteome atlas reveals functional insights into disease pathways

scientific article published on 01 May 2022

Dynamics in protein translation sustaining T cell preparedness

scientific article published on 06 July 2020

EASI-tag enables accurate multiplexed and interference-free MS2-based proteome quantification

scientific article published on 18 June 2018

Effective representation and storage of mass spectrometry-based proteomic data sets for the scientific community

scientific article

Efficient mitotic checkpoint signaling depends on integrated activities of Bub1 and the RZZ complex

scientific article published on 19 February 2019

Epigenetic control over the cell-intrinsic immune response antagonizes self-renewal in acute myeloid leukemia

scientific article published in 2024

Ethical Principles, Constraints, and Opportunities in Clinical Proteomics

scientific article published on 14 January 2021

Ethical principles, opportunities and constraints in clinical proteomics

scientific article published on 04 January 2021

Expert System for Computer-assisted Annotation of MS/MS Spectra ⬇️

scientific article published on August 10, 2012

FAM111 protease activity undermines cellular fitness and is amplified by gain-of-function mutations in human disease

scientific article published on 09 August 2020

Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation.

scientific article published on 26 October 2010

FoxK1 and FoxK2 in insulin regulation of cellular and mitochondrial metabolism

scientific article published on 05 April 2019

Functional characterization of Rad18 domains for Rad6, ubiquitin, DNA binding and PCNA modification

scientific article

Functional identity of hypothalamic melanocortin neurons depends on Tbx3

scientific article published on 28 January 2019

Gel‐like inclusions of C‐terminal fragments of TDP‐43 sequester stalled proteasomes in neurons

scientific article published on 19 April 2022

Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells.

scientific article published on January 2012

Global and site-specific quantitative phosphoproteomics: principles and applications

scientific article published on January 2009

Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics

scientific article published on 3 August 2009

Global, in vivo, and site-specific phosphorylation dynamics in signaling networks

scientific article

Glucose-regulated and drug-perturbed phosphoproteome reveals molecular mechanisms controlling insulin secretion

scientific article published on 14 November 2016

Hepatic Rab24 controls blood glucose homeostasis via improving mitochondrial plasticity

scientific article published on 14 October 2019

High performance computational analysis of large-scale proteome data sets to assess incremental contribution to coverage of the human genome

scientific article

High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast

scientific article published in October 2009

High-resolution serum proteome trajectories in COVID-19 reveal patient-specific seroconversion

scientific article published on 07 July 2021

High-throughput and high-sensitivity phosphoproteomics with the EasyPhos platform

scientific article published on 01 September 2018

Higher-energy C-trap dissociation for peptide modification analysis.

scientific article

Homology-driven assembly of NOn-redundant protEin sequence sets (NOmESS) for mass spectrometry

scientific article published on 6 January 2016

How much peptide sequence information is contained in ion trap tandem mass spectra?

scientific article

HysTag--a novel proteomic quantification tool applied to differential display analysis of membrane proteins from distinct areas of mouse brain

scientific article published on 10 November 2003

IKAP: A heuristic framework for inference of kinase activities from Phosphoproteomics data

scientific article

Identification of 491 proteins in the tear fluid proteome reveals a large number of proteases and protease inhibitors

scientific article

Identification of covalent modifications regulating immune signaling complex composition and phenotype

scientific article published on 01 July 2021

Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation

scholarly article

In vivo SILAC-based proteomics reveals phosphoproteome changes during mouse skin carcinogenesis

scientific article published on 31 January 2013

In vivo brain GPCR signaling elucidated by phosphoproteomics.

scientific article published in June 2018

In-gel digestion for mass spectrometric characterization of proteins and proteomes

scientific article (publication date: 2006)

In-vivo quantitative proteomics reveals a key contribution of post-transcriptional mechanisms to the circadian regulation of liver metabolism.

scientific article

Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria

scientific journal article

Integrated single cell analysis of human lung fibrosis resolves cellular origins of predictive protein signatures in body fluids ⬇️

journal article from 'medRxiv' published in 2020

Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers

scientific article published on 02 March 2021

Integrative proteomics reveals principles of dynamic phosphosignaling networks in human erythropoiesis

scientific article published on 01 December 2020

Interaction of 7SK with the Smn complex modulates snRNP production

scientific article published on 24 February 2021

Investigation of protein-tyrosine phosphatase 1B function by quantitative proteomics

scientific article

Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry

scientific article published in June 2008

Is proteomics the new genomics?

scientific article

Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle

scientific article published in August 2008

Large-scale proteomics analysis of the human kinome

scientific article published on 15 April 2009

Linkage-specific ubiquitin chain formation depends on a lysine hydrocarbon ruler

scientific article published on 07 December 2020

List of Contributors

Loss of full-length hnRNP R isoform impairs DNA damage response in motoneurons by inhibiting Yb1 recruitment to chromatin

scientific article published on 01 December 2021

Lysine acetylation targets protein complexes and co-regulates major cellular functions

scientific article (publication date: 14 August 2009)

Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in Arabidopsis

scientific article published on 23 October 2017

MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes

scientific article published on 7 November 2006

MSQuant, an open source platform for mass spectrometry-based quantitative proteomics

scientific article published on January 2010

Machine Learning-based Classification of Diffuse Large B-cell Lymphoma Patients by Their Protein Expression Profiles

scientific article

Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer.

scientific article

MaxQuant for in-depth analysis of large SILAC datasets

scientific article published in January 2014

MaxQuant.Live Enables Global Targeting of More Than 25,000 Peptides

article

MiT/TFE factors control ER-phagy via transcriptional regulation of FAM134B

scientific article published on 27 July 2020

Mislocalized activation of oncogenic RTKs switches downstream signaling outcomes

scientific article published in October 2009

More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MS ⬇️

scientific article published on February 28, 2011

Multi-spectra peptide sequencing and its applications to multistage mass spectrometry

scientific article

Multivalent binding of PWWP2A to H2A.Z regulates mitosis and neural crest differentiation

scientific article

Myosin binding protein H-like (MYBPHL): a promising biomarker to predict atrial damage

scientific article published on 10 July 2019

N-linked glycosylation enrichment for in-depth cell surface proteomics of diffuse large B-cell lymphoma subtypes

scientific article

Nanoelectrospray peptide mapping revisited: Composite survey spectra allow high dynamic range protein characterization without LCMS on an orbitrap mass spectrometer

Noncanonical assembly, neddylation and chimeric cullin–RING/RBR ubiquitylation by the 1.8 MDa CUL9 E3 ligase complex

scientific article published in 2024

Noncovalent interaction between Ubc9 and SUMO promotes SUMO chain formation

scientific article

Noninvasive proteomic biomarkers for alcohol-related liver disease

scientific article published in 2022

Nucleolar proteome dynamics

scientific article

Online parallel accumulation - serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer

article

OpenCell: Endogenous tagging for the cartography of human cellular organization

scientific article published on 11 March 2022

Organellar Proteomics and Phospho-Proteomics Reveal Subcellular Reorganization in Diet-Induced Hepatic Steatosis

article

PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites

scientific article

PLEKHA7 Recruits PDZD11 to Adherens Junctions to Stabilize Nectins

scientific article

PWWP2A binds distinct chromatin moieties and interacts with an MTA1-specific core NuRD complex

scientific article published in Nature Communications

Pervasive functional translation of noncanonical human open reading frames

scientific article published on 01 March 2020

PhosphoSiteAnalyzer: a bioinformatic platform for deciphering phospho proteomes using kinase predictions retrieved from NetworKIN.

scientific article published on 23 May 2012

Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation

scientific article published on 15 October 2007

Phosphoproteome profiling uncovers a key role for CDKs in TNF signaling

scientific article published on 18 October 2021

Phosphorylation of histone H3 Thr-45 is linked to apoptosis

scientific article

Phosphorylation variation during the cell cycle scales with structural propensities of proteins

scientific article

Plasma Proteome Profiling to detect and avoid sample-related biases in biomarker studies

scientific article published on 30 September 2019

Plasma proteome profiling discovers novel proteins associated with non-alcoholic fatty liver disease

scientific article published on 01 March 2019

Plasma proteomic data can contain personally identifiable, sensitive information and incidental findings

scientific article published on 17 December 2020

Predicting post-translational lysine acetylation using support vector machines.

scientific article published on 26 May 2010

Proceedings of the Frontiers of Retrovirology Conference 2016.

scientific article published on 26 September 2016

Profiling the human intestinal environment under physiological conditions

scientific article published in 2023

Proteome profiling in cerebrospinal fluid reveals novel biomarkers of Alzheimer's disease

scientific article published on 01 June 2020

Proteomic Analysis of Cellular Systems

article

Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response

scientific article

Proteomic mapping of brain plasma membrane proteins.

scientific article

Proteomic maps of breast cancer subtypes

scientific article

Proteomic portrait of human breast cancer progression identifies novel prognostic markers

scientific article

Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation

scientific article published on 7 July 2010

Proteomics reveals the effects of sustained weight loss on the human plasma proteome

scientific article

Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers

scientific article

Quantitative phosphoproteome analysis of a mouse liver cell line reveals specificity of phosphatase inhibitors

scientific article published on November 2008

Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway

scientific article published on 22 January 2005

Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis

scientific article

Quantitative proteomic assessment of very early cellular signaling events

Quantitative proteomic profiling of membrane proteins from the mouse brain cortex, hippocampus, and cerebellum using the HysTag reagent: mapping of neurotransmitter receptors and ion channels

scientific article published on 17 January 2007

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

scientific article

Quantitative proteomics reveals subset-specific viral recognition in dendritic cells.

scientific article published on 18 February 2010

Quantitative proteomics reveals that Hsp90 inhibition preferentially targets kinases and the DNA damage response

scientific article

Quantitative, high-resolution proteomics for data-driven systems biology

scientific article

Rapid and In-Depth Coverage of the (Phospho-)Proteome With Deep Libraries and Optimal Window Design for dia-PASEF

scientific article published in 2022

Region and cell-type resolved quantitative proteomic map of the human heart.

scientific article published on 13 November 2017

Reply to “Quality control requirements for the correct annotation of lipidomics data”

scientific article published in 2021

Response to Raaijmakers & Medema

scientific article published on 22 October 2019

Revisiting biomarker discovery by plasma proteomics.

scientific article published on 26 September 2017

Role for ribosome-associated quality control in sampling proteins for MHC class I-mediated antigen presentation

scientific article published on 11 February 2020

STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer

scientific article published on 01 April 2020

Secretome Analysis of Lipid-Induced Insulin Resistance in Skeletal Muscle Cells by a Combined Experimental and Bioinformatics Workflow

scientific article (publication date: 6 November 2015)

Signaling initiated by overexpression of the fibroblast growth factor receptor-1 investigated by mass spectrometry

scientific article (publication date: 2003)

Sleep-wake cycles drive daily dynamics of synaptic phosphorylation

scientific article

Software lock mass by two-dimensional minimization of peptide mass errors

scientific article published on 22 April 2011

Solid tumor proteome and phosphoproteome analysis by high resolution mass spectrometry

scientific article published on December 2008

Spatially and cell-type resolved quantitative proteomic atlas of healthy human skin

scientific article published on 05 November 2020

Spatiotemporal Proteomic Profiling of Huntington's Disease Inclusions Reveals Widespread Loss of Protein Function.

scientific article published in November 2017

Splicing factor YBX1 mediates persistence of JAK2-mutated neoplasms

scientific article published on 25 November 2020

Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins

scientific article published on 28 November 2007

Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system

scientific article published on January 2006

Status of large-scale analysis of post-translational modifications by mass spectrometry

scientific article

Super-SILAC Allows Classification of Diffuse Large B-cell Lymphoma Subtypes by Their Protein Expression Profiles ⬇️

scientific article published on March 21, 2012

Super-SILAC mix for quantitative proteomics of human tumor tissue

scientific article published on 4 April 2010

System-wide changes to SUMO modifications in response to heat shock

scientific article

System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap

scientific article published on 20 October 2011

System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation

scientific article published on 15 March 2011

Systematic proteomic analysis of LRRK2-mediated Rab GTPase phosphorylation establishes a connection to ciliogenesis.

scientific article published on 10 November 2017

The Coming Age of Complete, Accurate, and Ubiquitous Proteomes ⬇️

scientific article published on February 21, 2013

The Hippo pathway controls myofibril assembly and muscle fiber growth by regulating sarcomeric gene expression

scientific article published on 06 January 2021

The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics.

scientific article

The Perseus computational platform for comprehensive analysis of (prote)omics data

scientific article

The Proteome of Primary Prostate Cancer

scientific article

The Proteome of Prostate Cancer Bone Metastasis Reveals Heterogeneity with Prognostic Implications

scientific article published on 24 July 2018

The SH2 domain interaction landscape

scientific article

The Serine/Threonine/Tyrosine Phosphoproteome of the Model BacteriumBacillus subtilis

article

The ever expanding scope of electrospray mass spectrometry-a 30 year journey

scientific article published on 09 September 2019

The forebrain synaptic transcriptome is organized by clocks but its proteome is driven by sleep

scientific article

The hemicellulose-degrading enzyme system of the thermophilic bacterium : comparative characterisation and addition of new hemicellulolytic glycoside hydrolases

article

The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins

scientific article published in January 2006

The low molecular weight proteome of Halobacterium salinarum

scientific article

The non-classical nuclear import carrier Transportin 1 modulates circadian rhythms through its effect on PER1 nuclear localization.

scientific article

The phosphoproteome of toll-like receptor-activated macrophages

scientific article published on June 2010

The proteome landscape of the kingdoms of life

scientific article published on 17 June 2020

The tumor suppressor kinase DAPK3 drives tumor-intrinsic immunity through the STING-IFN-β pathway

scientific article published on 25 March 2021

The ubiquitin-proteasome system is a key component of the SUMO-2/3 cycle

scientific article published on 18 June 2008

Tissue-specific modulation of gene expression in response to lowered insulin signalling in <i>Drosophila</i>

scientific article published on 21 April 2021

Top-down protein sequencing and MS3 on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer

scientific article published on 13 February 2006

Trapped ion mobility spectrometry and PASEF enable in-depth lipidomics from minimal sample amounts

scientific article published on 16 January 2020

Trypsin cleaves exclusively C-terminal to arginine and lysine residues

scientific article published on 19 March 2004

Tyrosine phosphoproteomics of fibroblast growth factor signaling: a role for insulin receptor substrate-4.

scientific article

UBL3 modification influences protein sorting to small extracellular vesicles

scientific article published in Nature Communications

Ubc9 sumoylation regulates SUMO target discrimination

scientific article

Ultra High Resolution Linear Ion Trap Orbitrap Mass Spectrometer (Orbitrap Elite) Facilitates Top Down LC MS/MS and Versatile Peptide Fragmentation Modes ⬇️

scientific article published on December 9, 2011

Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling

scientific article published on 21 August 2014

Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation

scientific article published on 28 February 2022

Urinary proteome profiling for stratifying patients with familial Parkinson's disease

scientific article published on 22 January 2021

Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics

scientific article published on 01 February 2011

Yeast Expression Proteomics by High-Resolution Mass Spectrometry

scientific article published on 01 March 2010

diaPASEF: parallel accumulation-serial fragmentation combined with data-independent acquisition

scientific article published on 30 November 2020

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