Research outputs
2025
An Optimized SP3 Sample Processing Workflow for In-Depth and Reproducible Phosphoproteomics
Daly, L. A., Clarke, C. J., Oswald, S. O., Jankevics, A., Brownridge, P. J., Scheltema, R. A., & Eyers, C. E. (2025). An Optimized SP3 Sample Processing Workflow for In-Depth and Reproducible Phosphoproteomics. JOURNAL OF PROTEOME RESEARCH, 24(8), 4300-4308. doi:10.1021/acs.jproteome.5c00220
2024
Inceptor binds to and directs insulin towards lysosomal degradation in βcells
Siehler, J., Bilekova, S., Chapouton, P., Dema, A., Albanese, P., Tamara, S., . . . Lickert, H. (2024). Inceptor binds to and directs insulin towards lysosomal degradation in βcells. NATURE METABOLISM, 6(12), 2374-+. doi:10.1038/s42255-024-01164-y
Life history shapes variation in egg composition in the blue tit Cyanistes caeruleus
Fast and Accurate Disulfide Bridge Detection
Heissel, S., He, Y., Jankevics, A., Shi, Y., Molina, H., Viner, R., & Scheltema, R. A. (2024). Fast and Accurate Disulfide Bridge Detection. MOLECULAR & CELLULAR PROTEOMICS, 23(5). doi:10.1016/j.mcpro.2024.100759
Thrombin activation of the factor XI dimer is a multistaged process for each subunit
Barroeta, A. B., Albanese, P., Kadava, T., Jankevics, A., Marquart, J. A., Meijers, J. C. M., & Scheltema, R. A. (2024). Thrombin activation of the factor XI dimer is a multistaged process for each subunit. JOURNAL OF THROMBOSIS AND HAEMOSTASIS, 22(5), 1336-1346. doi:10.1016/j.jtha.2023.12.038
Type III-B CRISPR-Cas cascade of proteolytic cleavages
Steens, J. A., Bravo, J. P. K., Salazar, C. R. P., Yildiz, C., Amieiro, A. M., Kostlbacher, S., . . . Staals, R. H. J. (2024). Type III-B CRISPR-Cas cascade of proteolytic cleavages. SCIENCE, 383(6682), 512-519. doi:10.1126/science.adk0378
2023
Combination of deep XLMS with deep learning reveals an ordered rearrangement and assembly of a major protein component of the vaccinia virion
Mirzakhanyan, Y., Jankevics, A., Scheltema, R. A., & Gershon, P. D. (2023). Combination of deep XLMS with deep learning reveals an ordered rearrangement and assembly of a major protein component of the vaccinia virion. MBIO, 14(5). doi:10.1128/mbio.01135-23
Late Breaking Abstract - Evolution of epithelial-mesenchymal cell circuits in the progression of pulmonary fibrosis
De Sadeleer, L., Chen, Y., Jentzsch, C., Wang, Z., Qazi, N., Lang, N., . . . Schiller, H. (2023). Late Breaking Abstract - Evolution of epithelial-mesenchymal cell circuits in the progression of pulmonary fibrosis. In Airway cell biology and immunopathology (pp. OA772). European Respiratory Society. doi:10.1183/13993003.congress-2023.oa772
CAF-1 deposits newly synthesized histones during DNA replication using distinct mechanisms on the leading and lagging strands
Rouillon, C., Eckhardt, B. V., Kollenstart, L., Gruss, F., Verkennis, A. E. E., Rondeel, I., . . . Mattiroli, F. (2023). CAF-1 deposits newly synthesized histones during DNA replication using distinct mechanisms on the leading and lagging strands. NUCLEIC ACIDS RESEARCH, 51(8), 3770-3792. doi:10.1093/nar/gkad171
Revealing determinants of translation efficiency via whole-gene codon randomization and machine learning
Nieuwkoop, T., Terlouw, B. R., Stevens, K. G., Scheltema, R. A., de Ridder, D., van der Oost, J., & Claassens, N. J. (2023). Revealing determinants of translation efficiency via whole-gene codon randomization and machine learning. NUCLEIC ACIDS RESEARCH, 51(5), 2363-2376. doi:10.1093/nar/gkad035
MRPS36 provides a structural link in the eukaryotic 2-oxoglutarate dehydrogenase complex
Hevler, J. F., Albanese, P., Cabrera-Orefice, A., Potter, A., Jankevics, A., Misic, J., . . . Heck, A. J. R. (2023). MRPS36 provides a structural link in the eukaryotic 2-oxoglutarate dehydrogenase complex. OPEN BIOLOGY, 13(3). doi:10.1098/rsob.220363
Visualization of translation and protein biogenesis at the ER membrane
Gemmer, M., Chaillet, M. L., van Loenhout, J., Arenas, R. C., Vismpas, D., Grollers-Mulderij, M., . . . Forster, F. (2023). Visualization of translation and protein biogenesis at the ER membrane. NATURE, 614(7946), 160-+. doi:10.1038/s41586-022-05638-5
Towards a structurally resolved human protein interaction network
Burke, D. F., Bryant, P., Barrio-Hernandez, I., Memon, D., Pozzati, G., Shenoy, A., . . . Elofsson, A. (2023). Towards a structurally resolved human protein interaction network. NATURE STRUCTURAL & MOLECULAR BIOLOGY, 30(2), 216-+. doi:10.1038/s41594-022-00910-8
Oxonium Ion-Guided Optimization of Ion Mobility-Assisted Glycoproteomics on the timsTOF Pro
Mukherjee, S., Jankevics, A., Busch, F., Lubeck, M., Zou, Y., Kruppa, G., . . . Reiding, K. R. (2023). Oxonium Ion-Guided Optimization of Ion Mobility-Assisted Glycoproteomics on the timsTOF Pro. MOLECULAR & CELLULAR PROTEOMICS, 22(2). doi:10.1016/j.mcpro.2022.100486
2022
Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology
Klykov, O., Kopylov, M., Carragher, B., Heck, A. J. R., Noble, A. J., & Scheltema, R. A. (2022). Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology. MOLECULAR CELL, 82(2), 285-303. doi:10.1016/j.molcel.2021.12.027
2021
Towards a structurally resolved human protein interaction network
The assessment of <i>Pseudomonas aeruginosa</i> lectin LecA binding characteristics of divalent galactosides using multiple techniques
Zaree, P., Torano, J. S., de Haan, C. A. M., Scheltema, R. A., Barendregt, A., Thijssen, V., . . . Pieters, R. J. (2021). The assessment of <i>Pseudomonas aeruginosa</i> lectin LecA binding characteristics of divalent galactosides using multiple techniques. GLYCOBIOLOGY, 31(11), 1490-1499. doi:10.1093/glycob/cwab074
Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage
Liaci, A. M., Steigenberger, B., de Souza, P. C. T., Tamara, S., Grollers-Mulderij, M., Ogrissek, P., . . . Forster, F. (2021). Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage. MOLECULAR CELL, 81(19), 3934-+. doi:10.1016/j.molcel.2021.07.031
Nse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding
Taschner, M., Basquin, J., Steigenberger, B., Schaefer, I. B., Soh, Y. -M., Basquin, C., . . . Gruber, S. (2021). Nse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding. EMBO JOURNAL, 40(15). doi:10.15252/embj.2021107807
Notch-Jagged signaling complex defined by an interaction mosaic
Zeronian, M. R., Klykov, O., Portell i de Montserrat, J., Konijnenberg, M. J., Gaur, A., Scheltema, R. A., & Janssen, B. J. C. (2021). Notch-Jagged signaling complex defined by an interaction mosaic. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 118(30). doi:10.1073/pnas.2102502118
Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine.
Rajewsky, N., Almouzni, G., Gorski, S. A., Aerts, S., Amit, I., Bertero, M. G., . . . LifeTime Community Working Groups. (2021). Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine.. Nature, 592(7852), E8. doi:10.1038/s41586-021-03287-8
Quantifying Positional Isomers (QPI) by Top-Down Mass Spectrometry
Brunner, A. M., Lossl, P., Geurink, P. P., Ovaa, H., Albanese, P., Altelaar, A. F. M., . . . Scheltema, R. A. (2021). Quantifying Positional Isomers (QPI) by Top-Down Mass Spectrometry. MOLECULAR & CELLULAR PROTEOMICS, 20. doi:10.1016/j.mcpro.2021.100070
2020
How paired PSII-LHCII supercomplexes mediate the stacking of plant thylakoid membranes unveiled by structural mass-spectrometry
Albanese, P., Tamara, S., Saracco, G., Scheltema, R. A., & Pagliano, C. (2020). How paired PSII-LHCII supercomplexes mediate the stacking of plant thylakoid membranes unveiled by structural mass-spectrometry. NATURE COMMUNICATIONS, 11(1). doi:10.1038/s41467-020-15184-1
LifeTime and improving European healthcare through cell-based interceptive medicine.
Rajewsky, N., Almouzni, G., Gorski, S. A., Aerts, S., Amit, I., Bertero, M. G., . . . LifeTime Community Working Groups. (2020). LifeTime and improving European healthcare through cell-based interceptive medicine.. Nature, 587(7834), 377-386. doi:10.1038/s41586-020-2715-9
Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry
Leitner, A., Bonvin, A. M. J. J., Borchers, C. H., Chalkley, R. J., Chamot-Rooke, J., Combe, C. W., . . . Rappsilber, J. (2020). Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry. STRUCTURE, 28(11), 1259-1268. doi:10.1016/j.str.2020.09.011
Benefits of Collisional Cross Section Assisted Precursor Selection (caps-PASEF) for Crosslinking Mass Spectrometry
Steigenberger, B., van den Toorn, H. W. P., Bijl, E., Greisch, J. -F., Rather, O., Lubeck, M., . . . Scheltema, R. A. (2020). Benefits of Collisional Cross Section Assisted Precursor Selection (caps-PASEF) for Crosslinking Mass Spectrometry. MOLECULAR & CELLULAR PROTEOMICS, 19(10), 1677-1687. doi:10.1074/mcp.RA120.002094
Structural Proteomics Applied to Plant Membrane Protein Complexes
Albanese, P., Tamara, S., Scheltema, R. A., & Pagliano, C. (2020). Structural Proteomics Applied to Plant Membrane Protein Complexes. TRENDS IN PLANT SCIENCE, 25(9), 945-946. doi:10.1016/j.tplants.2020.04.002
To Cleave or Not To Cleave in XL-MS?
Steigenberger, B., Albanese, P., Heck, A. J. R., & Scheltema, R. A. (2020). To Cleave or Not To Cleave in XL-MS?. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 31(2), 196-206. doi:10.1021/jasms.9b00085
Missing regions within the molecular architecture of human fibrin clots structurally resolved by XL-MS and integrative structural modeling
Klykov, O., van der Zwaan, C., Heck, A. J. R., Meijer, A. B., & Scheltema, R. A. (2020). Missing regions within the molecular architecture of human fibrin clots structurally resolved by XL-MS and integrative structural modeling. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 117(4), 1976-1987. doi:10.1073/pnas.1911785117
2019
Life history shapes variation in egg composition in the blue tit <i>Cyanistes caeruleus</i>
Valcu, C. -M., Scheltema, R. A., Schweiggert, R. M., Valcu, M., Teltscher, K., Walther, D. M., . . . Kempenaers, B. (2019). Life history shapes variation in egg composition in the blue tit <i>Cyanistes caeruleus</i>. COMMUNICATIONS BIOLOGY, 2. doi:10.1038/s42003-018-0247-8
Finding and using diagnostic ions in collision induced crosslinked peptide fragmentation spectra
Steigenberger, B., Schiller, H. B., Pieters, R. J., & Scheltema, R. A. (2019). Finding and using diagnostic ions in collision induced crosslinked peptide fragmentation spectra. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, 444. doi:10.1016/j.ijms.2019.116184
PhoX: An IMAC-Enrichable Cross-Linking Reagent
Steigenberger, B., Pieters, R. J., Heck, A. J. R., & Scheltema, R. A. (2019). PhoX: An IMAC-Enrichable Cross-Linking Reagent. ACS CENTRAL SCIENCE, 5(9), 1514-1522. doi:10.1021/acscentsci.9b00416
First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study
Iacobucci, C., Piotrowski, C., Aebersold, R., Amaral, B. C., Andrews, P., Bernfur, K., . . . Sinz, A. (2019). First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study. ANALYTICAL CHEMISTRY, 91(11), 6953-6961. doi:10.1021/acs.analchem.9b00658
A Colorful Pallet of B-Phycoerythrin Proteoforms Exposed by a Multimodal Mass Spectrometry Approach
Tamara, S., Hoek, M., Scheltema, R. A., Leney, A. C., & Heck, A. J. R. (2019). A Colorful Pallet of B-Phycoerythrin Proteoforms Exposed by a Multimodal Mass Spectrometry Approach. CHEM, 5(5), 1302-1317. doi:10.1016/j.chempr.2019.03.006
Cross-ID: Analysis and Visualization of Complex XL-MS-Driven Protein Interaction Networks
de Graaf, S. C., Klykov, O., van den Toorn, H., & Scheltema, R. A. (2019). Cross-ID: Analysis and Visualization of Complex XL-MS-Driven Protein Interaction Networks. JOURNAL OF PROTEOME RESEARCH, 18(2), 642-651. doi:10.1021/acs.jproteome.8b00725
Expanding the mass range for UVPD-based native top-down mass spectrometry
Greisch, J. -F., Tamara, S., Scheltema, R. A., Maxwell, H. W. R., Fagerlund, R. D., Fineran, P. C., . . . Heck, A. J. R. (2019). Expanding the mass range for UVPD-based native top-down mass spectrometry. CHEMICAL SCIENCE, 10(30), 7163-7171. doi:10.1039/c9sc01857c
2018
Efficient and robust proteome-wide approaches for cross-linking mass spectrometry
Klykov, O., Steigenberger, B., Pektas, S., Fasci, D., Heck, A. J. R., & Scheltema, R. A. (2018). Efficient and robust proteome-wide approaches for cross-linking mass spectrometry. NATURE PROTOCOLS, 13(12), 2964-2990. doi:10.1038/s41596-018-0074-x
Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei
Fasci, D., van Ingen, H., Scheltema, R. A., & Heck, A. J. R. (2018). Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. MOLECULAR & CELLULAR PROTEOMICS, 17(10), 2018-2033. doi:10.1074/mcp.RA118.000924
Regulation of KIF1A-Driven Dense Core Vesicle Transport: Ca<SUP>2+</SUP>/CaM Controls DCV Binding and Liprin-α/TANC2 Recruits DCVs to Postsynaptic Sites
Stucchi, R., Plucinska, G., Hummel, J. J. A., Zahavi, E. E., San Juan, I. G., Klykov, O., . . . Hoogenraad, C. C. (2018). Regulation of KIF1A-Driven Dense Core Vesicle Transport: Ca<SUP>2+</SUP>/CaM Controls DCV Binding and Liprin-α/TANC2 Recruits DCVs to Postsynaptic Sites. CELL REPORTS, 24(3), 685-700. doi:10.1016/j.celrep.2018.06.071
2017
Phosphate Transfer in Activated Protein Complexes Reveals Interaction Sites
Tamara, S., Scheltema, R. A., Heck, A. J. R., & Leney, A. C. (2017). Phosphate Transfer in Activated Protein Complexes Reveals Interaction Sites. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 56(44), 13641-13644. doi:10.1002/anie.201706749
Spacer capture and integration by a type I-F Cas1-Cas2-3 CRISPR adaptation complex
Fagerlund, R. D., Wilkinson, M. E., Klykov, O., Barendregt, A., Pearce, F. G., Kieper, S. N., . . . Fineran, P. C. (2017). Spacer capture and integration by a type I-F Cas1-Cas2-3 CRISPR adaptation complex. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(26), E5122-E5128. doi:10.1073/pnas.1618421114
Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification
Liu, F., Lossl, P., Scheltema, R., Viner, R., & Heck, A. J. R. (2017). Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification. NATURE COMMUNICATIONS, 8. doi:10.1038/ncomms15473
Combining Deep Sequencing, Proteomics, Phosphoproteomics, and Functional Screens To Discover Novel Regulators of Sphingolipid Homeostasis
Lebesgue, N., Megyeri, M., Cristobal, A., Scholten, A., Chuartzman, S. G., Voichek, Y., . . . Lemeer, S. (2017). Combining Deep Sequencing, Proteomics, Phosphoproteomics, and Functional Screens To Discover Novel Regulators of Sphingolipid Homeostasis. JOURNAL OF PROTEOME RESEARCH, 16(2), 571-582. doi:10.1021/acs.jproteome.6b00691
Opposite Electron-Transfer Dissociation and Higher-Energy Collisional Dissociation Fragmentation Characteristics of Proteolytic K/R(X)<i><sub>n</sub></i> and (X)<i><sub>n</sub></i>K/R Peptides Provide Benefits for Peptide Sequencing in Proteomics and Phosphoproteomics
Tsiatsiani, L., Giansanti, P., Scheltema, R. A., van den Toorn, H., Overall, C. M., Altelaar, A. F. M., & Heck, A. J. R. (2017). Opposite Electron-Transfer Dissociation and Higher-Energy Collisional Dissociation Fragmentation Characteristics of Proteolytic K/R(X)<i><sub>n</sub></i> and (X)<i><sub>n</sub></i>K/R Peptides Provide Benefits for Peptide Sequencing in Proteomics and Phosphoproteomics. JOURNAL OF PROTEOME RESEARCH, 16(2), 852-861. doi:10.1021/acs.jproteome.6b00825
Arginine (Di)methylated Human Leukocyte Antigen Class I Peptides Are Favorably Presented by HLA-B*07
Marino, F., Mommen, G. P. M., Jeko, A., Meiring, H. D., van Gaans-van den Brink, J. A. M., Scheltema, R. A., . . . Heck, A. J. R. (2017). Arginine (Di)methylated Human Leukocyte Antigen Class I Peptides Are Favorably Presented by HLA-B*07. JOURNAL OF PROTEOME RESEARCH, 16(1), 34-44. doi:10.1021/acs.jproteome.6b00528
2016
Symmetry of Charge Partitioning in Collisional and UV Photon Induced Dissociation of Protein Assemblies
Tamara, S., Dyachenko, A., Fort, K. L., Makarov, A. A., Scheltema, R. A., & Heck, A. J. R. (2016). Symmetry of Charge Partitioning in Collisional and UV Photon Induced Dissociation of Protein Assemblies. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 138(34), 10860-10868. doi:10.1021/jacs.6b05147
Deciphering the Interplay among Multisite Phosphorylation, Interaction Dynamics, and Conformational Transitions in a Tripartite Protein System
Loessl, P., Brunner, A. M., Liu, F., Leney, A. C., Yamashita, M., Scheltema, R. A., & Heck, A. J. R. (2016). Deciphering the Interplay among Multisite Phosphorylation, Interaction Dynamics, and Conformational Transitions in a Tripartite Protein System. ACS CENTRAL SCIENCE, 2(7), 445-455. doi:10.1021/acscentsci.6b00053
Implementation of Ultraviolet Photodissociation on a Benchtop Q Exactive Mass Spectrometer and Its Application to Phosphoproteomics
Fort, K. L., Dyachenko, A., Potel, C. M., Corradini, E., Marino, F., Barendregt, A., . . . Heck, A. J. R. (2016). Implementation of Ultraviolet Photodissociation on a Benchtop Q Exactive Mass Spectrometer and Its Application to Phosphoproteomics. ANALYTICAL CHEMISTRY, 88(4), 2303-2310. doi:10.1021/acs.analchem.5b04162
2015
A Double-Barrel Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) System to Quantify 96 Interactomes per Day
Hosp, F., Scheltema, R. A., Eberl, H. C., Kulak, N. A., Keilhauer, E. C., Mayr, K., & Mann, M. (2015). A Double-Barrel Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) System to Quantify 96 Interactomes per Day. MOLECULAR & CELLULAR PROTEOMICS, 14(7), 2030-2041. doi:10.1074/mcp.O115.049460
Time- and compartment-resolved proteome profiling of the extracellular niche in lung injury and repair
Schiller, H. B., Fernandez, I. E., Burgstaller, G., Schaab, C., Scheltema, R. A., Schwarzmayr, T., . . . Mann, M. (2015). Time- and compartment-resolved proteome profiling of the extracellular niche in lung injury and repair. MOLECULAR SYSTEMS BIOLOGY, 11(7). doi:10.15252/msb.20156123
2014
The Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High-performance Quadrupole and an Ultra-high-field Orbitrap Analyzer
Scheltema, R. A., Hauschild, J. -P., Lange, O., Hornburg, D., Denisov, E., Damoc, E., . . . Mann, M. (2014). The Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High-performance Quadrupole and an Ultra-high-field Orbitrap Analyzer. MOLECULAR & CELLULAR PROTEOMICS, 13(12), 3698-3708. doi:10.1074/mcp.M114.043489
Structural Model of a CRISPR RNA-Silencing Complex Reveals the RNA-Target Cleavage Activity in Cmr4
Benda, C., Ebert, J., Scheltema, R. A., Schiller, H. B., Baumgaertner, M., Bonneau, F., . . . Conti, E. (2014). Structural Model of a CRISPR RNA-Silencing Complex Reveals the RNA-Target Cleavage Activity in Cmr4. MOLECULAR CELL, 56(1), 43-54. doi:10.1016/j.molcel.2014.09.002
qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments
Walzer, M., Pernas, L. E., Nasso, S., Bittremieux, W., Nahnsen, S., Kelchtermans, P., . . . Martens, L. (2014). qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments. MOLECULAR & CELLULAR PROTEOMICS, 13(8), 1905-1913. doi:10.1074/mcp.M113.035907
2013
High Performance Computational Analysis of Large-scale Proteome Data Sets to Assess Incremental Contribution to Coverage of the Human Genome
Neuhauser, N., Nagaraj, N., McHardy, P., Zanivan, S., Scheltema, R., Cox, J., & Mann, M. (2013). High Performance Computational Analysis of Large-scale Proteome Data Sets to Assess Incremental Contribution to Coverage of the Human Genome. JOURNAL OF PROTEOME RESEARCH, 12(6), 2858-2868. doi:10.1021/pr400181q
Direct Proteomic Quantification of the Secretome of Activated Immune Cells
Meissner, F., Scheltema, R. A., Mollenkopf, H. -J., & Mann, M. (2013). Direct Proteomic Quantification of the Secretome of Activated Immune Cells. SCIENCE, 340(6131), 475-478. doi:10.1126/science.1232578
2012
SprayQc: A Real-Time LC-MS/MS Quality Monitoring System To Maximize Uptime Using Off the Shelf Components
Scheltema, R. A., & Mann, M. (2012). SprayQc: A Real-Time LC-MS/MS Quality Monitoring System To Maximize Uptime Using Off the Shelf Components. JOURNAL OF PROTEOME RESEARCH, 11(6), 3458-3466. doi:10.1021/pr201219e
A Framework for Intelligent Data Acquisition and Real-Time Database Searching for Shotgun Proteomics
Graumann, J., Scheltema, R. A., Zhang, Y., Cox, J., & Mann, M. (2012). A Framework for Intelligent Data Acquisition and Real-Time Database Searching for Shotgun Proteomics. MOLECULAR & CELLULAR PROTEOMICS, 11(3). doi:10.1074/mcp.M111.013185
2011
Bayesian Approaches for Mass Spectrometry‐Based Metabolomics
Rogers, S., Scheltema, R. A., Barrett, M., & Breitling, R. (2011). Bayesian Approaches for Mass Spectrometry‐Based Metabolomics. In Unknown Book (pp. 467-476). Wiley. doi:10.1002/9781119970606.ch24
Richard A Scheltema.
Scheltema, R. A. (2011). Richard A Scheltema.. Bioanalysis, 3(11), 1197-1199. doi:10.4155/bio.11.96
Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment
Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., & Mann, M. (2011). Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment. JOURNAL OF PROTEOME RESEARCH, 10(4), 1794-1805. doi:10.1021/pr101065j
PeakML/mzMatch: A File Format, Java Library, R Library, and Tool-Chain for Mass Spectrometry Data Analysis
Scheltema, R. A., Jankevics, A., Jansen, R. C., Swertz, M. A., & Breitling, R. (2011). PeakML/mzMatch: A File Format, Java Library, R Library, and Tool-Chain for Mass Spectrometry Data Analysis. ANALYTICAL CHEMISTRY, 83(7), 2786-2793. doi:10.1021/ac2000994
Towards an unbiased metabolic profiling of protozoan parasites: optimisation of a Leishmania sampling protocol for HILIC-orbitrap analysis (vol 398, pg 2059, 2010)
t'Kindt, R., Jankevics, A., Scheltema, R. A., Zheng, L., Watson, D. G., Dujardin, J. -C., . . . Decuypere, S. (2011). Towards an unbiased metabolic profiling of protozoan parasites: optimisation of a Leishmania sampling protocol for HILIC-orbitrap analysis (vol 398, pg 2059, 2010). ANALYTICAL AND BIOANALYTICAL CHEMISTRY, 400(2), 635. doi:10.1007/s00216-011-4796-7
2010
Metabolomics to Unveil and Understand Phenotypic Diversity between Pathogen Populations
t'Kindt, R., Scheltema, R. A., Jankevics, A., Brunker, K., Rijal, S., Dujardin, J. -C., . . . Decuypere, S. (2010). Metabolomics to Unveil and Understand Phenotypic Diversity between Pathogen Populations. PLOS NEGLECTED TROPICAL DISEASES, 4(11). doi:10.1371/journal.pntd.0000904
Two time-point assessment of bile acid kinetics in humans using stable isotopes
Stellaard, F., Bloks, V. W., Burgerhof, H. G. M., Scheltema, R. A., Murphy, E. J., Romijn, H. A., . . . Kuipers, F. (2010). Two time-point assessment of bile acid kinetics in humans using stable isotopes. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES, 46(3), 325-336. doi:10.1080/10256016.2010.503894
The potential of metabolomics for <i>Leishmania</i> research in the post-genomics era
Scheltema, R. A., Decuypere, S., T'Kindt, R., Dujardin, J. -C., Coombs, G. H., & Breitling, R. (2010). The potential of metabolomics for <i>Leishmania</i> research in the post-genomics era. PARASITOLOGY, 137(9), 1291-1302. doi:10.1017/S0031182009992022
Use of reconstituted metabolic networks to assist in metabolomic data visualization and mining
Jourdan, F., Cottret, L., Huc, L., Wildridge, D., Scheltema, R., Hillenweck, A., . . . Debrauwer, L. (2010). Use of reconstituted metabolic networks to assist in metabolomic data visualization and mining. METABOLOMICS, 6(2), 312-321. doi:10.1007/s11306-009-0196-9
Metabolomic Characterization of the Salt Stress Response in <i>Streptomyces coelicolor</i>
Kol, S., Merlo, M. E., Scheltema, R. A., de Vries, M., Vonk, R. J., Kikkert, N. A., . . . Takano, E. (2010). Metabolomic Characterization of the Salt Stress Response in <i>Streptomyces coelicolor</i>. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 76(8), 2574-2581. doi:10.1128/AEM.01992-09
XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments
Swertz, M. A., van der Velde, K. J., Tesson, B. M., Scheltema, R. A., Arends, D., Vera, G., . . . Jansen, R. C. (2010). XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments. GENOME BIOLOGY, 11(3). doi:10.1186/gb-2010-11-3-r27
Towards an unbiased metabolic profiling of protozoan parasites: optimisation of a Leishmania sampling protocol for HILIC-orbitrap analysis
t'Kindt, R., Jankevics, A., Scheltema, R. A., Zheng, L., Watson, D. G., Dujardin, J. -C., . . . Decuypere, S. (2010). Towards an unbiased metabolic profiling of protozoan parasites: optimisation of a Leishmania sampling protocol for HILIC-orbitrap analysis. ANALYTICAL AND BIOANALYTICAL CHEMISTRY, 398(5), 2059-2069. doi:10.1007/s00216-010-4139-0
2009
Probabilistic assignment of formulas to mass peaks in metabolomics experiments
Rogers, S., Scheltema, R. A., Girolami, M., & Breitling, R. (2009). Probabilistic assignment of formulas to mass peaks in metabolomics experiments. BIOINFORMATICS, 25(4), 512-518. doi:10.1093/bioinformatics/btn642
System-wide molecular evidence for phenotypic buffering in <i>Arabidopsis</i>
Fu, J., Keurentjes, J. J. B., Bouwmeester, H., America, T., Verstappen, F. W. A., Ward, J. L., . . . Jansen, R. C. (2009). System-wide molecular evidence for phenotypic buffering in <i>Arabidopsis</i>. NATURE GENETICS, 41(2), 166-167. doi:10.1038/ng.308
Simple data-reduction method for high-resolution LC-MS data in metabolomics
Scheltema, R. A., Decuypere, S., Dujardin, J. C., Watson, D. G., Jansen, R. C., & Breitling, R. (2009). Simple data-reduction method for high-resolution LC-MS data in metabolomics. BIOANALYSIS, 1(9), 1551-1557. doi:10.4155/BIO.09.146
2008
Increasing the mass accuracy of high-resolution LC-MS data using background ions - a case study on the LTQ-Orbitrap
Scheltema, R. A., Kamleh, A., Wildridge, D., Ebikeme, C., Watson, D. G., Barrett, M. R., . . . Breitling, R. (2008). Increasing the mass accuracy of high-resolution LC-MS data using background ions - a case study on the LTQ-Orbitrap. PROTEOMICS, 8(22), 4647-4656. doi:10.1002/pmic.200800314
Metabolomic profiling using Orbitrap Fourier transform mass spectrometry with hydrophilic interaction chromatography: a method with wide applicability to analysis of biomolecules
Kamleh, A., Barrett, M. P., Wildridge, D., Burchmore, R. J. S., Scheltema, R. A., & Watson, D. G. (2008). Metabolomic profiling using Orbitrap Fourier transform mass spectrometry with hydrophilic interaction chromatography: a method with wide applicability to analysis of biomolecules. RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 22(12), 1912-1918. doi:10.1002/rcm.3564