Mass spectrometric technology for next generation proteomics in systems medicine

Deliverables

LCMS time-scale compatible peptide and protein sequencing using hybrid fragmentation methods, with special applications into multiply modified larger peptides

Benchmark the performance in peptide and protein identifications of EThcD versus HCD peptides from complex mixtures, whereby the Mw of the peptides is in the range between 2.5 and 10 kDa (middle-down proteomics)

Software module for comprehensive identification of PTMs, mutations and splice variants

Implement genome-informed proteomics platform that incorporates knowledge on human natural variations, disease mutations and alternative splicing. Ensure efficiency of search algorithm in huge protein/peptide spaces further inflated by multiple PTMs.

Software module for multiplexed quantification of clinical samples

Develop and test software module that enables low variance quantification in body fluid and tissue samples for MS1 and MS2 label and label free quantification for hundreds of patients simultaneously.

Extension of software module to novel/hybrid fragmentation methods

Develop peptide identification algorithms for EThcD, UVPD and other novel techniques with competitive identification rates. Incorporation in the MaxQuant software.

Industrialized workflow with low CVs

Develop and test a workflow that enables robust analysis of hundreds of tissue and body fluid samples with minimal intervention and CVs in the smaller than 20% range for proteins of interest

Feasibility study in cancer tissue proteomics

Perform large-scale quantitative phosphoproteomics of patient samples from ovarian cancer, colon cancer and prostate cancer samples using the protocols and MS acquisition strategies established in D5.1

Construction/coupling of UVPD to the latest Orbitrap instruments

An UVPD laser will be coupled to the latest Q-Exactive mass analyzer and/or other Orbitrap instruments

Software modules implemented for MS/MS based analysis of unconven-tional peptide and protein sequences

Implementation and benchmarking of all algorithms needed for the identification of peptide and proteins measured with the novel and hybrid fragmentation techniques including top and middle down proteomics.

LCMS time-scale compatible top- and middle-down proteomics workflows using hybrid fragmentation methods

Benchmark the performance in protein identifications of HCD, ETD and EThcD for proteins in the range between 10 and 100 kDa (top-down proteomics)

Top- and middle-down software module

Further develop the MaxQuant platform in order to analyze and quality control the top and middle down data generated in this project.

Machine learning module for biomarker discovery and classification of clinical samples

Develop and benchmark a machine learning platform using support vector machines and deep learning networks for making robust decisions on patient treatment based on clinical samples.

LCMS time-scale compatible UV-PD peptide and protein sequencing

Benchmark the performance in peptide and protein identifications of UVPD versus HCD using a cellular lysate on a Q-Exactive instrument (bottom-up proteomics)

Ethics check

All relevant ethical approvals, consent forms and patient information sheets will be uploaded as deliverable 6.12. This will also include an up to date approval from The Central Denmark Region Committees on Health Research Ethics stating the ethical approvals for Aarhus University Hospital are also valid for project MSmed.

Catalogs of functional PTMs and their dynamics in normal and deregulated signaling pathways

Develop and implement high-performance offline high-pH reversed-phase chromatography prior to high-resolution mass spectrometry for parallel analysis of major PTMs without enrichment and apply this to cancer cell lines treated with chemotherapeutic agents.

MaxQuant summer school 2

The annual MaxQuant Summer School (host: MPIB, over 160 participants) provides an introduction into the MaxQuant software and application examples. Projeect results will be included into the School’s curriculum.

Data Management Plan

Describes the strategy for depositing and curating MSmed experimental data in publicly accessible proteomic data bases, the use of proteomic standard formats, and exceptions made as required to protect personal data and intellectual property to be patented

Robust and reproducible sample prepa¬ration protocols including MS instru¬mentation and acquisition strat-egies for large-scale, quantitative PTM analysis from primary tissue samples such as patient biopsy material

Establish tissue sample preparation protocol based on heat-inactivation of biopsies, efficient protein extraction by ceramic bead milling, in-solution digestion and optimized nanoflow LC-MS/MS acquisition strategies. Benchmark the performance versus established protocols.

MaxQuant summer school

Protocol for hyper-multiplexing

Develop labeling protocols and test them for multiplexing and analyzing) more than 10 patient samples at a time (goal is up to 20)

Scientific outreach meeting

International scientific outreach meeting on Next Generation Proteomics linked to an annual Progress Meeting of the Netherlands Proteomics Center. Dissemination of project results to the broader community of proteomics researchers in Europe.

Publications

Exploring ECD on a Benchtop Q Exactive Orbitrap Mass Spectrometer

Author(s): Kyle L. Fort, Christian N. Cramer, Valery G. Voinov, Yury V. Vasil’ev, Nathan I. Lopez, Joseph S. Beckman, Albert J. R. Heck
Published in: Journal of Proteome Research, Issue 17/2, 2018, Page(s) 926-933, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.7b00622

Toward an Optimized Workflow for Middle-Down Proteomics

Author(s): Alba Cristobal, Fabio Marino, Harm Post, Henk W. P. van den Toorn, Shabaz Mohammed, Albert J. R. Heck
Published in: Analytical Chemistry, Issue 89/6, 2017, Page(s) 3318-3325, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.6b03756

Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification

Author(s): Fan Liu, Philip Lössl, Richard Scheltema, Rosa Viner, Albert J. R. Heck
Published in: Nature Communications, Issue 8, 2017, Page(s) 15473, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/ncomms15473

The interactome of intact mitochondria by cross-linking mass spectrometry provides evidence for coexisting respiratory supercomplexes

Author(s): Fan Liu, Philip Lössl, Beverley M. Rabbitts, Robert S. Balaban, Albert J. R. Heck
Published in: Molecular & Cellular Proteomics, Issue 17/2, 2018, Page(s) 216-232, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.RA117.000470

Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer

Author(s): Chiara Francavilla, Michela Lupia, Kalliopi Tsafou, Alessandra Villa, Katarzyna Kowalczyk, Rosa Rakownikow Jersie-Christensen, Giovanni Bertalot, Stefano Confalonieri, Søren Brunak, Lars J. Jensen, Ugo Cavallaro, Jesper V. Olsen
Published in: Cell Reports, Issue 18/13, 2017, Page(s) 3242-3256, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2017.03.015

Resolving the micro-heterogeneity and structural integrity of monoclonal antibodies by hybrid mass spectrometric approaches

Author(s): Yang Yang, Guanbo Wang, Ting Song, Carlito B. Lebrilla, Albert J. R. Heck
Published in: mAbs, Issue 9/4, 2017, Page(s) 638-645, ISSN 1942-0870
Publisher: Landes Bioscience
DOI: 10.1080/19420862.2017.1290033

Direct Monitoring of Protein O-GlcNAcylation by High-Resolution Native Mass Spectrometry

Author(s): Aneika C. Leney, Karim Rafie, Daan M. F. van Aalten, Albert J. R. Heck
Published in: ACS Chemical Biology, Issue 12/8, 2017, Page(s) 2078-2084, ISSN 1554-8929
Publisher: American Chemical Society
DOI: 10.1021/acschembio.7b00371

Enhancing Accuracy in Molecular Weight Determination of Highly Heterogeneously Glycosylated Proteins by Native Tandem Mass Spectrometry

Author(s): Guanbo Wang, Rob N. de Jong, Ewald T. J. van den Bremer, Paul W. H. I. Parren, Albert J. R. Heck
Published in: Analytical Chemistry, Issue 89/9, 2017, Page(s) 4793-4797, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.6b05129

Opposite Electron-Transfer Dissociation and Higher-Energy Collisional Dissociation Fragmentation Characteristics of Proteolytic K/R(X) n and (X) n K/R Peptides Provide Benefits for Peptide Sequencing in Proteomics and Phosphoproteomics

Author(s): Liana Tsiatsiani, Piero Giansanti, Richard A. Scheltema, Henk van den Toorn, Christopher M. Overall, A.F. Maarten Altelaar, Albert J.R. Heck
Published in: Journal of Proteome Research, Issue 16/2, 2017, Page(s) 852-861, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.6b00825

An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes

Author(s): Dorte B. Bekker-Jensen, Christian D. Kelstrup, Tanveer S. Batth, Sara C. Larsen, Christa Haldrup, Jesper B. Bramsen, Karina D. Sørensen, Søren Høyer, Torben F. Ørntoft, Claus L. Andersen, Michael L. Nielsen, Jesper V. Olsen
Published in: Cell Systems, Issue 4/6, 2017, Page(s) 587-599.e4, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.cels.2017.05.009

Robust, Sensitive, and Automated Phosphopeptide Enrichment Optimized for Low Sample Amounts Applied to Primary Hippocampal Neurons

Author(s): Harm Post, Renske Penning, Martin A. Fitzpatrick, Luc B. Garrigues, W. Wu, Harold D. MacGillavry, Casper C. Hoogenraad, Albert J. R. Heck, A. F. Maarten Altelaar
Published in: Journal of Proteome Research, Issue 16/2, 2017, Page(s) 728-737, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.6b00753

Proteoform Profile Mapping of the Human Serum Complement Component C9 Revealing Unexpected New Features of N -, O -, and C -Glycosylation

Author(s): Vojtech Franc, Yang Yang, Albert J. R. Heck
Published in: Analytical Chemistry, Issue 89/6, 2017, Page(s) 3483-3491, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.6b04527

Proteomics insights into DNA damage response and translating this knowledge to clinical strategies

Author(s): Louise von Stechow, Jesper V. Olsen
Published in: PROTEOMICS, Issue 17/3-4, 2017, Page(s) 1600018, ISSN 1615-9853
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.201600018

A Molecular Basis for the Presentation of Phosphorylated Peptides by HLA-B Antigens

Author(s): Adán Alpízar, Fabio Marino, Antonio Ramos-Fernández, Manuel Lombardía, Anita Jeko, Florencio Pazos, Alberto Paradela, César Santiago, Albert J. R. Heck, Miguel Marcilla
Published in: Molecular & Cellular Proteomics, Issue 16/2, 2017, Page(s) 181-193, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.M116.063800

Proteomics Reveals Global Regulation of Protein SUMOylation by ATM and ATR Kinases during Replication Stress

Author(s): Stephanie Munk, Jón Otti Sigurðsson, Zhenyu Xiao, Tanveer Singh Batth, Giulia Franciosa, Louise von Stechow, Andres Joaquin Lopez-Contreras, Alfred Cornelis Otto Vertegaal, Jesper Velgaard Olsen
Published in: Cell Reports, Issue 21/2, 2017, Page(s) 546-558, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2017.09.059

Performance Evaluation of the Q Exactive HF-X for Shotgun Proteomics

Author(s): Christian D. Kelstrup, Dorte B. Bekker-Jensen, Tabiwang N. Arrey, Alexander Hogrebe, Alexander Harder, Jesper V. Olsen
Published in: Journal of Proteome Research, Issue 17/1, 2017, Page(s) 727-738, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.7b00602

Large-Scale Phosphoproteomics Reveals Shp-2 Phosphatase-Dependent Regulators of Pdgf Receptor Signaling

Author(s): Tanveer S. Batth, Moreno Papetti, Anamarija Pfeiffer, Maxim A.X. Tollenaere, Chiara Francavilla, Jesper V. Olsen
Published in: Cell Reports, Issue 22/10, 2018, Page(s) 2784-2796, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2018.02.038

Benchmarking common quantification strategies for large-scale phosphoproteomics

Author(s): Alexander Hogrebe, Louise von Stechow, Dorte B. Bekker-Jensen, Brian T. Weinert, Christian D. Kelstrup, Jesper V. Olsen
Published in: Nature Communications, Issue 9/1, 2018, Page(s) 1045, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-03309-6

Phosphate Transfer in Activated Protein Complexes Reveals Interaction Sites

Author(s): Sem Tamara, Richard A. Scheltema, Albert J. R. Heck, Aneika C. Leney
Published in: Angewandte Chemie International Edition, Issue 56/44, 2017, Page(s) 13641-13644, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201706749

High-fidelity mass analysis unveils heterogeneity in intact ribosomal particles

Author(s): Michiel van de Waterbeemd, Kyle L Fort, Dmitriy Boll, Maria Reinhardt-Szyba, Andrew Routh, Alexander Makarov, Albert J R Heck
Published in: Nature Methods, Issue 14/3, 2017, Page(s) 283-286, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/nmeth.4147

Glycoproteomics: A Balance between High-Throughput and In-Depth Analysis

Author(s): Yang Yang, Vojtech Franc, Albert J.R. Heck
Published in: Trends in Biotechnology, Issue 35/7, 2017, Page(s) 598-609, ISSN 0167-7799
Publisher: Elsevier BV
DOI: 10.1016/j.tibtech.2017.04.010

Expanding the structural analysis capabilities on an Orbitrap-based mass spectrometer for large macromolecular complexes

Author(s): Kyle L. Fort, Michiel van de Waterbeemd, Dmitriy Boll, Maria Reinhardt-Szyba, Mikhail E. Belov, Eita Sasaki, Reinhard Zschoche, Donald Hilvert, Alexander A. Makarov, Albert J. R. Heck
Published in: The Analyst, Issue 143/1, 2018, Page(s) 100-105, ISSN 0003-2654
Publisher: Royal Society of Chemistry
DOI: 10.1039/c7an01629h

Parsimonious Charge Deconvolution for Native Mass Spectrometry

Author(s): Marshall Bern, Tomislav Caval, Yong J. Kil, Wilfred Tang, Christopher Becker, Eric Carlson, Doron Kletter, K. Ilker Sen, Nicolas Galy, Dominique Hagemans, Vojtech Franc, Albert J. R. Heck
Published in: Journal of Proteome Research, Issue 17/3, 2018, Page(s) 1216-1226, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.7b00839

Determination of Collision Cross-Sections of Protein Ions in an Orbitrap Mass Analyzer

Author(s): James D. Sanders, Dmitry Grinfeld, Konstantin Aizikov, Alexander Makarov, Dustin D. Holden, Jennifer S. Brodbelt
Published in: Analytical Chemistry, Issue 90/9, 2018, Page(s) 5896-5902, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.8b00724

Ion traps in modern mass spectrometry

Author(s): Dirk Nolting, Robert Malek, Alexander Makarov
Published in: Mass Spectrometry Reviews, 2017, ISSN 0277-7037
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/mas.21549

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

Author(s): Sebastian Virreira Winter, Florian Meier, Christoph Wichmann, Juergen Cox, Matthias Mann, Felix Meissner
Published in: Nature Methods, Issue 15, 2018, Page(s) 527–530, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-018-0037-8

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

Author(s): Florian Meier, Philipp E. Geyer, Sebastian Virreira Winter, Juergen Cox, Matthias Mann
Published in: Nature Methods, Issue 15/6, 2018, Page(s) 440-448, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-018-0003-5

MaxQuant goes Linux

Author(s): Pavel Sinitcyn, Shivani Tiwary, Jan Rudolph, Petra Gutenbrunner, Christoph Wichmann, Şule Yılmaz, Hamid Hamzeiy, Favio Salinas, Jürgen Cox
Published in: Nature Methods, Issue 15/6, 2018, Page(s) 401-401, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-018-0018-y

What computational non-targeted mass spectrometry-based metabolomics can gain from shotgun proteomics

Author(s): Hamid Hamzeiy, Jürgen Cox
Published in: Current Opinion in Biotechnology, Issue 43, 2017, Page(s) 141-146, ISSN 0958-1669
Publisher: Elsevier BV
DOI: 10.1016/j.copbio.2016.11.014

TMEM59 potentiates Wnt signaling by promoting signalosome formation

Author(s): Jan P. Gerlach, Ingrid Jordens, Daniele V. F. Tauriello, Ineke van ‘t Land-Kuper, Jeroen M. Bugter, Ivar Noordstra, Johanneke van der Kooij, Teck Y. Low, Felipe X. Pimentel-Muiños, Despina Xanthakis, Nicola Fenderico, Catherine Rabouille, Albert J. R. Heck, David A. Egan, Madelon M. Maurice
Published in: Proceedings of the National Academy of Sciences, Issue 115/17, 2018, Page(s) E3996-E4005, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1721321115

Computational Methods for Understanding Mass Spectrometry–Based Shotgun Proteomics Data

Author(s): Pavel Sinitcyn, Jan Daniel Rudolph, Jürgen Cox
Published in: Annual Review of Biomedical Data Science, Issue 1/1, 2018, Page(s) 207-234, ISSN 2574-3414
Publisher: Annual Reviews
DOI: 10.1146/annurev-biodatasci-080917-013516

Comprehensive Proteoform Characterization of Plasma Complement Component C8αβγ by Hybrid Mass Spectrometry Approaches

Author(s): Vojtech Franc, Jing Zhu, Albert J. R. Heck
Published in: Journal of The American Society for Mass Spectrometry, Issue 29/6, 2018, Page(s) 1099-1110, ISSN 1044-0305
Publisher: Elsevier BV
DOI: 10.1007/s13361-018-1901-6

Dissecting ribosomal particles throughout the kingdoms of life using advanced hybrid mass spectrometry methods

Author(s): Michiel van de Waterbeemd, Sem Tamara, Kyle L. Fort, Eugen Damoc, Vojtech Franc, Philipp Bieri, Martin Itten, Alexander Makarov, Nenad Ban, Albert J. R. Heck
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-04853-x

Direct quality control of glycoengineered erythropoietin variants

Author(s): Tomislav Čaval, Weihua Tian, Zhang Yang, Henrik Clausen, Albert J. R. Heck
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-05536-3

Deciphering the Interplay among Multisite Phosphorylation, Interaction Dynamics, and Conformational Transitions in a Tripartite Protein System

Author(s): Philip Lössl, Andrea M. Brunner, Fan Liu, Aneika C. Leney, Masami Yamashita, Richard A. Scheltema, Albert J. R. Heck
Published in: ACS Central Science, Issue 2/7, 2016, Page(s) 445-455, ISSN 2374-7943
Publisher: ACS Publications
DOI: 10.1021/acscentsci.6b00053

Analytic framework for peptidomics applied to large-scale neuropeptide identification

Author(s): Anna Secher, Christian D. Kelstrup, Kilian W. Conde-Frieboes, Charles Pyke, Kirsten Raun, Birgitte S. Wulff, Jesper V. Olsen
Published in: Nature Communications, Issue 7, 2016, Page(s) 11436, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/ncomms11436

Implementation of Ultraviolet Photodissociation on a Benchtop Q Exactive Mass Spectrometer and Its Application to Phosphoproteomics

Author(s): Kyle L. Fort, Andrey Dyachenko, Clement M. Potel, Eleonora Corradini, Fabio Marino, Arjan Barendregt, Alexander A. Makarov, Richard A. Scheltema, Albert J. R. Heck
Published in: Analytical Chemistry, Issue 88/4, 2016, Page(s) 2303-2310, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.5b04162

Author(s): Yu-Hsien Lin, Vojtech Franc, Albert J. R. Heck
Published in: Journal of Proteome Research, Issue 17/8, 2018, Page(s) 2861-2869, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.8b00318

The dual methyltransferase METTL13 targets N terminus and Lys55 of eEF1A and modulates codon-specific translation rates

Author(s): Magnus E. Jakobsson, Jędrzej M. Małecki, Levon Halabelian, Benedikt S. Nilges, Rita Pinto, Srikanth Kudithipudi, Stephanie Munk, Erna Davydova, Fawzi R. Zuhairi, Cheryl H. Arrowsmith, Albert Jeltsch, Sebastian A. Leidel, Jesper V. Olsen, Pål Ø. Falnes
Published in: Nature Communications, Issue 9/1, 2018, Page(s) 3411, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-05646-y

Proteomics for blood biomarker exploration of severe mental illness: pitfalls of the past and potential for the future

Author(s): Ashley L. Comes, Sergi Papiol, Thorsten Mueller, Philipp E. Geyer, Matthias Mann, Thomas G. Schulze
Published in: Translational Psychiatry, Issue 8/1, 2018, Page(s) 160, ISSN 2158-3188
Publisher: Nature Publishing Group
DOI: 10.1038/s41398-018-0219-2

Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE)

Author(s): Jennie R. Lill, Peter A. van Veelen, Stefan Tenzer, Arie Admon, Etienne Caron, Joshua E. Elias, Albert J.R. Heck, Miguel Marcilla, Fabio Marino, Markus Müller, Bjoern Peters, Anthony Purcell, Alessandro Sette, Theo Sturm, Nicola Ternette, Juan Antonio Vizcaíno, Michal Bassani-Sternberg
Published in: PROTEOMICS, Issue 18/12, 2018, Page(s) 1800110, ISSN 1615-9853
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.201800110

Symmetry of Charge Partitioning in Collisional and UV Photon-Induced Dissociation of Protein Assemblies

Author(s): Sem Tamara, Andrey Dyachenko, Kyle L. Fort, Alexander A. Makarov, Richard A. Scheltema, Albert J. R. Heck
Published in: Journal of the American Chemical Society, Issue 138/34, 2016, Page(s) 10860-10868, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.6b05147

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

Author(s): Stefka Tyanova, Tikira Temu, Pavel Sinitcyn, Arthur Carlson, Marco Y Hein, Tamar Geiger, Matthias Mann, Jürgen Cox
Published in: Nature Methods, Issue 13/9, 2016, Page(s) 731-740, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/nmeth.3901

Hybrid mass spectrometry approaches in glycoprotein analysis and their usage in scoring biosimilarity

Author(s): Yang Yang, Fan Liu, Vojtech Franc, Liem Andhyk Halim, Huub Schellekens, Albert J. R. Heck
Published in: Nature Communications, Issue 7, 2016, Page(s) 13397, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/ncomms13397

The diverse and expanding role of mass spectrometry in structural and molecular biology

Author(s): Philip Lössl, Michiel van de Waterbeemd, Albert JR Heck
Published in: The EMBO Journal, Issue 35/24, 2016, Page(s) 2634-2657, ISSN 0261-4189
Publisher: Nature Publishing Group
DOI: 10.15252/embj.201694818

Multilayered proteomics reveals molecular switches dictating ligand-dependent EGFR trafficking

Author(s): Chiara Francavilla, Moreno Papetti, Kristoffer T G Rigbolt, Anna-Kathrine Pedersen, Jon O Sigurdsson, Giuseppe Cazzamali, Gopal Karemore, Blagoy Blagoev, Jesper V Olsen
Published in: Nature Structural & Molecular Biology, Issue 23/6, 2016, Page(s) 608-618, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/nsmb.3218

Phase-Constrained Spectrum Deconvolution for Fourier Transform Mass Spectrometry

Author(s): Dmitry Grinfeld, Konstantin Aizikov, Arne Kreutzmann, Eugen Damoc, Alexander Makarov
Published in: Analytical Chemistry, Issue 89/2, 2016, Page(s) 1202-1211, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.6b03636

Plasma Proteome Profiling Reveals Dynamics of Inflammatory and Lipid Homeostasis Markers after Roux-En-Y Gastric Bypass Surgery

Author(s): Nicolai J. Wewer Albrechtsen, Philipp E. Geyer, Sophia Doll, Peter V. Treit, Kirstine N. Bojsen-Møller, Christoffer Martinussen, Nils B. Jørgensen, Signe S. Torekov, Florian Meier, Lili Niu, Alberto Santos, Eva C. Keilhauer, Jens J. Holst, Sten Madsbad, Matthias Mann
Published in: Cell Systems, Issue 7/6, 2018, Page(s) 601-612.e3, ISSN 2405-4712
Publisher: Cell Press
DOI: 10.1016/j.cels.2018.10.012

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

Author(s): Nicolai Bache, Philipp E. Geyer, Dorte B. Bekker-Jensen, Ole Hoerning, Lasse Falkenby, Peter V. Treit, Sophia Doll, Igor Paron, Johannes B. Müller, Florian Meier, Jesper V. Olsen, Ole Vorm, Matthias Mann
Published in: Molecular & Cellular Proteomics, Issue 17/11, 2018, Page(s) 2284-2296, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.TIR118.000853

A Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis

Author(s): Jan Daniel Rudolph, Jürgen Cox
Published in: Journal of Proteome Research, Issue 18/5, 2019, Page(s) 2052-2064, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.8b00927

The PRIDE database and related tools and resources in 2019: improving support for quantification data

Author(s): Yasset Perez-Riverol, Attila Csordas, Jingwen Bai, Manuel Bernal-Llinares, Suresh Hewapathirana, Deepti J Kundu, Avinash Inuganti, Johannes Griss, Gerhard Mayer, Martin Eisenacher, Enrique Pérez, Julian Uszkoreit, Julianus Pfeuffer, Timo Sachsenberg, Şule Yılmaz, Shivani Tiwary, Jürgen Cox, Enrique Audain, Mathias Walzer, Andrew F Jarnuczak, Tobias Ternent, Alvis Brazma, Juan Antonio Vizcaíno
Published in: Nucleic Acids Research, Issue 47/D1, 2018, Page(s) D442-D450, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gky1106

Proteomics of Cytochrome c Oxidase-Negative versus -Positive Muscle Fiber Sections in Mitochondrial Myopathy

Author(s): Marta Murgia, Jing Tan, Philipp E. Geyer, Sophia Doll, Matthias Mann, Thomas Klopstock
Published in: Cell Reports, Issue 29/12, 2019, Page(s) 3825-3834.e4, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2019.11.055

A New Tool to Reveal Bacterial Signaling Mechanisms in Antibiotic Treatment and Resistance

Author(s): Miao-Hsia Lin, Clement M. Potel, Kamaleddin H. M. E. Tehrani, Albert J. R. Heck, Nathaniel I. Martin, Simone Lemeer
Published in: Molecular & Cellular Proteomics, Issue 17/12, 2018, Page(s) 2496-2507, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.ra118.000880

Rearrangement of the Protein Phosphatase 1 Interactome During Heart Failure Progression

Author(s): David Y. Chiang, Katherina M. Alsina, Eleonora Corradini, Martin Fitzpatrick, Li Ni, Satadru K. Lahiri, Julia O. Reynolds, Xiaolu Pan, Larry Scott, Albert J.R. Heck, Xander H.T. Wehrens
Published in: Circulation, Issue 138/15, 2018, Page(s) 1569-1581, ISSN 0009-7322
Publisher: Lippincott Williams & Wilkins Ltd.
DOI: 10.1161/circulationaha.118.034361

The benefits of hybrid fragmentation methods for glycoproteomics

Author(s): Karli R. Reiding, Albert Bondt, Vojtech Franc, Albert J.R. Heck
Published in: TrAC Trends in Analytical Chemistry, Issue 108, 2018, Page(s) 260-268, ISSN 0165-9936
Publisher: Elsevier BV
DOI: 10.1016/j.trac.2018.09.007

Mix and match of the tumor metastasis suppressor Nm23 protein isoforms in vitro and in vivo

Author(s): Clement M. Potel, Domenico Fasci, Albert J.R. Heck
Published in: The FEBS Journal, Issue 285/15, 2018, Page(s) 2856-2868, ISSN 1742-464X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/febs.14525

Defeating Major Contaminants in Fe 3+ - Immobilized Metal Ion Affinity Chromatography (IMAC) Phosphopeptide Enrichment

Author(s): Clement M. Potel, Miao-Hsia Lin, Albert J. R. Heck, Simone Lemeer
Published in: Molecular & Cellular Proteomics, Issue 17/5, 2018, Page(s) 1028-1034, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.tir117.000518

Widespread bacterial protein histidine phosphorylation revealed by mass spectrometry-based proteomics

Author(s): Clement M Potel, Miao-Hsia Lin, Albert J R Heck, Simone Lemeer
Published in: Nature Methods, Issue 15/3, 2018, Page(s) 187-190, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/nmeth.4580

Efficient and robust proteome-wide approaches for cross-linking mass spectrometry

Author(s): Oleg Klykov, Barbara Steigenberger, Sibel Pektaş, Domenico Fasci, Albert J. R. Heck, Richard A. Scheltema
Published in: Nature Protocols, Issue 13/12, 2018, Page(s) 2964-2990, ISSN 1754-2189
Publisher: Nature Publishing Group
DOI: 10.1038/s41596-018-0074-x

Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei

Author(s): Domenico Fasci, Hugo van Ingen, Richard A. Scheltema, Albert J. R. Heck
Published in: Molecular & Cellular Proteomics, Issue 17/10, 2018, Page(s) 2018-2033, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.ra118.000924

PhoX: An IMAC-Enrichable Cross-Linking Reagent

Author(s): Barbara Steigenberger, Roland J. Pieters, Albert J. R. Heck, Richard A. Scheltema
Published in: ACS Central Science, Issue 5/9, 2019, Page(s) 1514-1522, ISSN 2374-7943
Publisher: ACS Publications
DOI: 10.1021/acscentsci.9b00416

Simply Extending the Mass Range in Electron Transfer Higher Energy Collisional Dissociation Increases Confidence in N-Glycopeptide Identification

Author(s): Tomislav Čaval, Jing Zhu, Albert J.R. Heck
Published in: Analytical Chemistry, Issue 91/16, 2019, Page(s) 10401-10406, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.9b02125

Expanding the mass range for UVPD-based native top-down mass spectrometry

Author(s): Jean-François Greisch, Sem Tamara, Richard A. Scheltema, Howard W. R. Maxwell, Robert D. Fagerlund, Peter C. Fineran, Stephan Tetter, Donald Hilvert, Albert J. R. Heck
Published in: Chemical Science, Issue 10/30, 2019, Page(s) 7163-7171, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9sc01857c

Gaining Confidence in the Elusive Histidine Phosphoproteome

Author(s): Clement M. Potel, Miao-Hsia Lin, Nadine Prust, Henk W. P. van den Toorn, Albert J. R. Heck, Simone Lemeer
Published in: Analytical Chemistry, Issue 91/9, 2019, Page(s) 5542-5547, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.9b00734

Pre-fractionation Extends but also Creates a Bias in the Detectable HLA Class Ι Ligandome

Author(s): Laura C. Demmers, Albert J. R. Heck, Wei Wu
Published in: Journal of Proteome Research, Issue 18/4, 2019, Page(s) 1634-1643, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.8b00821

Toward an efficient workflow for the analysis of the human milk peptidome

Author(s): Kelly A. Dingess, Henk W. P. van den Toorn, Marko Mank, Bernd Stahl, Albert J. R. Heck
Published in: Analytical and Bioanalytical Chemistry, Issue 411/7, 2019, Page(s) 1351-1363, ISSN 1618-2642
Publisher: Springer Verlag
DOI: 10.1007/s00216-018-01566-4

Phosphopeptide Fragmentation and Site Localization by Mass Spectrometry: An Update

Author(s): Clement M. Potel, Simone Lemeer, Albert J. R. Heck
Published in: Analytical Chemistry, Issue 91/1, 2018, Page(s) 126-141, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.8b04746

Discovery and Quantification of Nonhuman Proteins in Human Milk

Author(s): Jing Zhu, Luc Garrigues, Henk Van den Toorn, Bernd Stahl, Albert J. R. Heck
Published in: Journal of Proteome Research, Issue 18/1, 2018, Page(s) 225-238, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.8b00550

Distinct Stabilities of the Structurally Homologous Heptameric Co-Chaperonins GroES and gp31

Author(s): Andrey Dyachenko, Sem Tamara, Albert J. R. Heck
Published in: Journal of The American Society for Mass Spectrometry, Issue 30/1, 2019, Page(s) 7-15, ISSN 1044-0305
Publisher: Elsevier BV
DOI: 10.1007/s13361-018-1910-5

Targeted Analysis of Lysosomal Directed Proteins and Their Sites of Mannose-6-phosphate Modification

Author(s): Tomislav Čaval, Jing Zhu, Weihua Tian, Sanne Remmelzwaal, Zhang Yang, Henrik Clausen, Albert J.R. Heck
Published in: Molecular & Cellular Proteomics, Issue 18/1, 2019, Page(s) 16-27, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.ra118.000967

Cross-ID: Analysis and Visualization of Complex XL–MS-Driven Protein Interaction Networks

Author(s): Sebastiaan C. de Graaf, Oleg Klykov, Henk van den Toorn, Richard A. Scheltema
Published in: Journal of Proteome Research, Issue 18/2, 2018, Page(s) 642-651, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.8b00725

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

Author(s): Christoph Wichmann, Florian Meier, Sebastian Virreira Winter, Andreas-David Brunner, Jürgen Cox, Matthias Mann
Published in: Molecular & Cellular Proteomics, Issue 18/5, 2019, Page(s) 982-994, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.tir118.001131

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

Author(s): Philipp E Geyer, Eugenia Voytik, Peter V Treit, Sophia Doll, Alisa Kleinhempel, Lili Niu, Johannes B Müller, Marie‐Luise Buchholtz, Jakob M Bader, Daniel Teupser, Lesca M Holdt, Matthias Mann
Published in: EMBO Molecular Medicine, Issue 11/11, 2019, Page(s) e10427, ISSN 1757-4676
Publisher: John Wiley & Sons Ltd.
DOI: 10.15252/emmm.201910427

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

Author(s): Lili Niu, Philipp E Geyer, Nicolai J Wewer Albrechtsen, Lise L Gluud, Alberto Santos, Sophia Doll, Peter V Treit, Jens J Holst, Filip K Knop, Tina Vilsbøll, Anders Junker, Stephan Sachs, Kerstin Stemmer, Timo D Müller, Matthias H Tschöp, Susanna M Hofmann, Matthias Mann
Published in: Molecular Systems Biology, Issue 15/3, 2019, Page(s) e8793, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.20188793

Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites

Author(s): Alicia Lundby, Giulia Franciosa, Kristina B. Emdal, Jan C. Refsgaard, Sebastian P. Gnosa, Dorte B. Bekker-Jensen, Anna Secher, Svetlana R. Maurya, Indranil Paul, Blanca L. Mendez, Christian D. Kelstrup, Chiara Francavilla, Marie Kveiborg, Guillermo Montoya, Lars J. Jensen, Jesper V. Olsen
Published in: Cell, Issue 179/2, 2019, Page(s) 543-560.e26, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2019.09.008

Protein Aggregation Capture on Microparticles Enables Multipurpose Proteomics Sample Preparation

Author(s): Tanveer S. Batth, Maxim A. X. Tollenaere, Patrick Rüther, Alba Gonzalez-Franquesa, Bhargav S. Prabhakar, Simon Bekker-Jensen, Atul S. Deshmukh, Jesper V. Olsen
Published in: Molecular & Cellular Proteomics, Issue 18/5, 2019, Page(s) 1027-1035, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.tir118.001270

Integrated proximal proteomics reveals IRS2 as a determinant of cell survival in ALK-driven neuroblastoma

Author(s): Kristina B. Emdal, Anna-Kathrine Pedersen, Dorte B. Bekker-Jensen, Alicia Lundby, Shana Claeys, Katleen De Preter, Frank Speleman, Chiara Francavilla, Jesper V. Olsen
Published in: Science Signaling, Issue 11/557, 2018, Page(s) eaap9752, ISSN 1937-9145
Publisher: American Association for the Advancement of Science
DOI: 10.1126/scisignal.aap9752

Limits for Resolving Isobaric Tandem Mass Tag Reporter Ions Using Phase-Constrained Spectrum Deconvolution

Author(s): Christian D. Kelstrup, Konstantin Aizikov, Tanveer S. Batth, Arne Kreutzman, Dmitry Grinfeld, Oliver Lange, Daniel Mourad, Alexander A. Makarov, Jesper V. Olsen
Published in: Journal of Proteome Research, Issue 17/11, 2018, Page(s) 4008-4016, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.8b00381

UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites

Author(s): Vyacheslav Akimov, Inigo Barrio-Hernandez, Sten V. F. Hansen, Philip Hallenborg, Anna-Kathrine Pedersen, Dorte B. Bekker-Jensen, Michele Puglia, Stine D. K. Christensen, Jens T. Vanselow, Mogens M. Nielsen, Irina Kratchmarova, Christian D. Kelstrup, Jesper V. Olsen, Blagoy Blagoev
Published in: Nature Structural & Molecular Biology, Issue 25/7, 2018, Page(s) 631-640, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/s41594-018-0084-y

Cultivation of Podospora anserina on soybean hulls results in an efficient enzyme cocktail for plant biomass hydrolysis

Author(s): Miia R. Mäkelä, Ourdia Bouzid, Diogo Robl, Harm Post, Mao Peng, Albert Heck, Maarten Altelaar, Ronald P. de Vries
Published in: New Biotechnology, Issue 37, 2017, Page(s) 162-171, ISSN 1871-6784
Publisher: Elsevier BV
DOI: 10.1016/j.nbt.2017.02.002

Fundamentals and Advances of Orbitrap Mass Spectrometry

Author(s): Hecht, E.S., Scigelova, M., Eliuk, S. and Makarov, A.
Published in: Encyclopedia of Analytical Chemistry, 2019
Publisher: Wiley Online Library

A streamlined mass spectrometry-based proteomics workflow for large scale FFPE tissue analysis

Author(s): Fabian Coscia, Sophia Doll, Jacob Mathias Bech, Andreas Mund, Ernst Lengyel, Jan Lindebjerg, Gunvor Iben Madsen, José M. A. Moreira, Matthias Mann
Published in: bioRxiv, 2019
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/779009

A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients

Author(s): Dorte B. Bekker-Jensen, Ana Martínez del Val, Sophia Steigerwald, Patrick Rüther, Kyle Fort, Tabiwang N. Arrey, Alexander Harder, Alexander Makarov, Jesper V. Olsen
Published in: bioRxiv, 2019
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/860643

Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition (DIA) without the need for spectral libraries

Author(s): Dorte B. Bekker-Jensen, Oliver M. Bernhardt, Alexander Hogrebe, Ana Martinez del Val, Lynn Verbeke, Tejas Gandhi, Christian D. Kelstrup, Lukas Reiter, Jesper V. Olsen
Published in: bioRxiv, 2019
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/657858

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Wave transmission networks

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A METHOD OF PRODUCING A MASS SPECTRUM

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MULTI-REFLECTION MASS SPECTROMETER WITH DECELERATION STAGE

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METHOD FOR IDENTIFICATION OF THE MONOISOTOPIC MASS OF SPECIES OF MOLECULES

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METHOD FOR IDENTIFICATION OF THE MONOISOTOPIC MASS OF SPECIES OF MOLECULES

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