Author details

Full Name

Markus MÃ¼ller

Affiliation

ORCID

Career Start Year

1999

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
33845167	Sensitive Immunopeptidomics by Leveraging Available Large-Scale Multi-HLA Spectral Libraries, Data-Independent Acquisition, and MS/MS Prediction.	Molecular and Cellular Proteomics	2021
33226770	Automatic Annotation and Dereplication of Tandem Mass Spectra of Peptidic Natural Products.	Analytical Chemistry	2020
31848261	Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands.	Molecular and Cellular Proteomics	2020
32102971	Chemical Genetics of AGC-kinases Reveals Shared Targets of Ypk1, Protein Kinase A and Sch9.	Mol Cell Proteomics	2020
32157095	Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes.	Nat Commun	2020
32983136	Biogenesis of HLA Ligand Presentation in Immune Cells Upon Activation Reveals Changes in Peptide Length Preference.	Frontiers in Immunology	2020
32909745	Kinetic Pathways of Block Copolymer Directed Self-Assembly: Insights from Efficient Continuum Modeling.	ACS Nano	2020
30737579	rBAN: retro-biosynthetic analysis of nonribosomal peptides.	Journal of Cheminformatics	2019
30980325	Detection of Unknown Chemical Adduct Modifications on Proteins: From Wet to Dry Laboratory.	Methods in Molecular Biology	2019
31482698	Controlled Spacing between Nanopatterned Regions in Block Copolymer Films Obtained by Utilizing Substrate Topography for Local Film Thickness Differentiation.	ACS applied materials & interfaces	2019
31420320	Comment on "A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands".	Sci Immunol	2019
30802063	Correction to "Large-Scale Reanalysis of Publicly Available HeLa Cell Proteomics Data in the Context of the Human Proteome Project".	J Proteome Res	2019
29791771	Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE).	Proteomics	2018
30171158	Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome.	Mol Cell Proteomics	2018
30175587	Large-Scale Reanalysis of Publicly Available HeLa Cell Proteomics Data in the Context of the Human Proteome Project.	J Proteome Res	2018
29242379	High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound InterferonÎ³-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome.	Molecular and Cellular Proteomics	2018
28199054	Optimization by infusion of multiple reaction monitoring transitions for sensitive quantification of peptides by liquid chromatography/mass spectrometry.	Rapid Communications in Mass Spectrometry	2017
28901741	Glycoforest 1.0.	Analytical Chemistry	2017
29104575	'Hotspots' of Antigen Presentation Revealed by Human Leukocyte Antigen Ligandomics for Neoantigen Prioritization.	Frontiers in Immunology	2017
27599297	Detection of busulfan adducts on proteins.	Rapid Communications in Mass Spectrometry	2016
26656212	Response profiles of murine spiral ganglion neurons on multi-electrode arrays.		2016
26653734	Mining Large Scale Tandem Mass Spectrometry Data for Protein Modifications Using Spectral Libraries.	Journal of Proteome Research	2016
27599736	EIGER detector: application in macromolecular crystallography.	Acta Crystallographica Section D: Structural Biology	2016
26691135	Comparative Proteomic Profiling of Ehrlichia ruminantium Pathogenic Strain and Its High-Passaged Attenuated Strain Reveals Virulence and Attenuation-Associated Proteins.	PLoS ONE	2015
25825003	Unrestricted modification search reveals lysine methylation as major modification induced by tissue formalin fixation and paraffin embedding.	Proteomics	2015
25430050	Processing strategies and software solutions for data-independent acquisition in mass spectrometry.	Proteomics	2015
26141507	MzJava: An open source library for mass spectrometry data processing.	Journal of Proteomics	2015
23467006	Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.	Biochim Biophys Acta	2014
23277275	EasyProt--an easy-to-use graphical platform for proteomics data analysis.	Journal of Proteomics	2013
24006250	Clustering and filtering tandem mass spectra acquired in data-independent mode.	Journal of the American Society for Mass Spectrometry	2013
22194332	Optimal fine Ï¿-slicing for single-photon-counting pixel detectors.		2012
22326964	Isoelectric point optimization using peptide descriptors and support vector machines.	J Proteomics	2012
21898822	An improved method for the construction of decoy peptide MS/MS spectra suitable for the accurate estimation of false discovery rates.	Proteomics	2011
21063961	LC/MS data processing for label-free quantitative analysis.	Methods in Molecular Biology	2011
21414208	pROC: an open-source package for R and S+ to analyze and compare ROC curves.	BMC Bioinformatics	2011
20958893	Matrix metalloproteinase-9 and intercellular adhesion molecule 1 are powerful staging markers for human African trypanosomiasis.	Tropical Medicine and International Health	2011
21500769	QuickMod: A tool for open modification spectrum library searches.	Journal of Proteome Research	2011
21630644	Human hemolysate glycated proteome.	Analytical Chemistry	2011
21658481	In silico analysis of accurate proteomics, complemented by selective isolation of peptides.	J Proteomics	2011
20655473	Enhanced SnapShot: Pore-forming toxins.	Cell	2010
19760205	A multiparameter panel method for outcome prediction following aneurysmal subarachnoid hemorrhage.	Intensive Care Medicine	2010
20029840	Unrestricted identification of modified proteins using MS/MS.	Proteomics	2010
19955080	Glycation isotopic labeling with 13C-reducing sugars for quantitative analysis of glycated proteins in human plasma.	Molecular and Cellular Proteomics	2010
19929612	Bioinformatics for protein biomarker panel classification: what is needed to bring biomarker panels into in vitro diagnostics?	Expert Review of Proteomics	2009
19554086	A combined CXCL10, CXCL8 and H-FABP panel for the staging of human African trypanosomiasis patients.	PLoS Neglected Tropical Diseases	2009
19036722	Analysis of cell surface proteome changes via label-free, quantitative mass spectrometry.	Mol Cell Proteomics	2009
19421192	The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism.	Nature	2009
19235171	A simple workflow to increase MS2 identification rate by subsequent spectral library search.	Proteomics	2009
18327264	Identification of cross-linked peptides from large sequence databases.	Nat Methods	2008
17956857	Quantitative proteomic analysis of protein complexes: concurrent identification of interactors and their state of phosphorylation.	Mol Cell Proteomics	2008