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Items: 38

1.

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

Greisch JF, Tamara S, Scheltema RA, Maxwell HWR, Fagerlund RD, Fineran PC, Tetter S, Hilvert D, Heck AJR.

Chem Sci. 2019 Jul 1;10(30):7163-7171. doi: 10.1039/c9sc01857c. eCollection 2019 Aug 14.

2.

PhoX: An IMAC-Enrichable Cross-Linking Reagent.

Steigenberger B, Pieters RJ, Heck AJR, Scheltema RA.

ACS Cent Sci. 2019 Sep 25;5(9):1514-1522. doi: 10.1021/acscentsci.9b00416. Epub 2019 Aug 19.

3.

First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study.

Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews P, Bernfur K, Borchers C, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis T, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez C, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kukačka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Ferreira AGC, Ninnis R, Novák P, O'Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A.

Anal Chem. 2019 Jun 4;91(11):6953-6961. doi: 10.1021/acs.analchem.9b00658. Epub 2019 May 22.

4.

Life history shapes variation in egg composition in the blue tit Cyanistes caeruleus.

Valcu CM, Scheltema RA, Schweiggert RM, Valcu M, Teltscher K, Walther DM, Carle R, Kempenaers B.

Commun Biol. 2019 Jan 4;2:6. doi: 10.1038/s42003-018-0247-8. eCollection 2019.

5.

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

de Graaf SC, Klykov O, van den Toorn H, Scheltema RA.

J Proteome Res. 2019 Feb 1;18(2):642-651. doi: 10.1021/acs.jproteome.8b00725. Epub 2019 Jan 17.

6.

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

Klykov O, Steigenberger B, Pektaş S, Fasci D, Heck AJR, Scheltema RA.

Nat Protoc. 2018 Dec;13(12):2964-2990. doi: 10.1038/s41596-018-0074-x.

PMID:
30446747
7.

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

Fasci D, van Ingen H, Scheltema RA, Heck AJR.

Mol Cell Proteomics. 2018 Oct;17(10):2018-2033. doi: 10.1074/mcp.RA118.000924. Epub 2018 Jul 18.

8.

Regulation of KIF1A-Driven Dense Core Vesicle Transport: Ca2+/CaM Controls DCV Binding and Liprin-α/TANC2 Recruits DCVs to Postsynaptic Sites.

Stucchi R, Plucińska G, Hummel JJA, Zahavi EE, Guerra San Juan I, Klykov O, Scheltema RA, Altelaar AFM, Hoogenraad CC.

Cell Rep. 2018 Jul 17;24(3):685-700. doi: 10.1016/j.celrep.2018.06.071.

9.

Phosphate Transfer in Activated Protein Complexes Reveals Interaction Sites.

Tamara S, Scheltema RA, Heck AJR, Leney AC.

Angew Chem Int Ed Engl. 2017 Oct 23;56(44):13641-13644. doi: 10.1002/anie.201706749. Epub 2017 Sep 27.

PMID:
28869719
10.

Spacer capture and integration by a type I-F Cas1-Cas2-3 CRISPR adaptation complex.

Fagerlund RD, Wilkinson ME, Klykov O, Barendregt A, Pearce FG, Kieper SN, Maxwell HWR, Capolupo A, Heck AJR, Krause KL, Bostina M, Scheltema RA, Staals RHJ, Fineran PC.

Proc Natl Acad Sci U S A. 2017 Jun 27;114(26):E5122-E5128. doi: 10.1073/pnas.1618421114. Epub 2017 Jun 13.

11.

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

Lebesgue N, Megyeri M, Cristobal A, Scholten A, Chuartzman SG, Voichek Y, Scheltema RA, Mohammed S, Futerman AH, Schuldiner M, Heck AJ, Lemeer S.

J Proteome Res. 2017 Feb 3;16(2):571-582. doi: 10.1021/acs.jproteome.6b00691. Epub 2016 Nov 29.

PMID:
28152593
12.

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

Tsiatsiani L, Giansanti P, Scheltema RA, van den Toorn H, Overall CM, Altelaar AF, Heck AJ.

J Proteome Res. 2017 Feb 3;16(2):852-861. doi: 10.1021/acs.jproteome.6b00825. Epub 2016 Dec 2.

PMID:
28111955
13.

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

Lössl P, Brunner AM, Liu F, Leney AC, Yamashita M, Scheltema RA, Heck AJ.

ACS Cent Sci. 2016 Jul 27;2(7):445-55. doi: 10.1021/acscentsci.6b00053. Epub 2016 Jun 10.

14.

Arginine (Di)methylated Human Leukocyte Antigen Class I Peptides Are Favorably Presented by HLA-B*07.

Marino F, Mommen GP, Jeko A, Meiring HD, van Gaans-van den Brink JA, Scheltema RA, van Els CA, Heck AJ.

J Proteome Res. 2017 Jan 6;16(1):34-44. doi: 10.1021/acs.jproteome.6b00528. Epub 2016 Aug 25.

PMID:
27503676
15.

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

Tamara S, Dyachenko A, Fort KL, Makarov AA, Scheltema RA, Heck AJ.

J Am Chem Soc. 2016 Aug 31;138(34):10860-8. doi: 10.1021/jacs.6b05147. Epub 2016 Aug 16.

16.

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

Fort KL, Dyachenko A, Potel CM, Corradini E, Marino F, Barendregt A, Makarov AA, Scheltema RA, Heck AJ.

Anal Chem. 2016 Feb 16;88(4):2303-10. doi: 10.1021/acs.analchem.5b04162. Epub 2016 Jan 29.

PMID:
26760441
17.

Time- and compartment-resolved proteome profiling of the extracellular niche in lung injury and repair.

Schiller HB, Fernandez IE, Burgstaller G, Schaab C, Scheltema RA, Schwarzmayr T, Strom TM, Eickelberg O, Mann M.

Mol Syst Biol. 2015 Jul 14;11(7):819. doi: 10.15252/msb.20156123.

18.

A Double-Barrel Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) System to Quantify 96 Interactomes per Day.

Hosp F, Scheltema RA, Eberl HC, Kulak NA, Keilhauer EC, Mayr K, Mann M.

Mol Cell Proteomics. 2015 Jul;14(7):2030-41. doi: 10.1074/mcp.O115.049460. Epub 2015 Apr 17.

19.

The Q Exactive HF, a Benchtop mass spectrometer with a pre-filter, high-performance quadrupole and an ultra-high-field Orbitrap analyzer.

Scheltema RA, Hauschild JP, Lange O, Hornburg D, Denisov E, Damoc E, Kuehn A, Makarov A, Mann M.

Mol Cell Proteomics. 2014 Dec;13(12):3698-708. doi: 10.1074/mcp.M114.043489. Epub 2014 Oct 30.

20.

Structural model of a CRISPR RNA-silencing complex reveals the RNA-target cleavage activity in Cmr4.

Benda C, Ebert J, Scheltema RA, Schiller HB, Baumgärtner M, Bonneau F, Mann M, Conti E.

Mol Cell. 2014 Oct 2;56(1):43-54. doi: 10.1016/j.molcel.2014.09.002.

21.

qcML: an exchange format for quality control metrics from mass spectrometry experiments.

Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJ, Mechtler K, Aebersold R, Gevaert K, Vizcaíno JA, Hermjakob H, Kohlbacher O, Martens L.

Mol Cell Proteomics. 2014 Aug;13(8):1905-13. doi: 10.1074/mcp.M113.035907. Epub 2014 Apr 23.

22.

Direct proteomic quantification of the secretome of activated immune cells.

Meissner F, Scheltema RA, Mollenkopf HJ, Mann M.

Science. 2013 Apr 26;340(6131):475-8. doi: 10.1126/science.1232578.

23.

SprayQc: a real-time LC-MS/MS quality monitoring system to maximize uptime using off the shelf components.

Scheltema RA, Mann M.

J Proteome Res. 2012 Jun 1;11(6):3458-66. doi: 10.1021/pr201219e. Epub 2012 May 11.

PMID:
22515319
24.

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

Graumann J, Scheltema RA, Zhang Y, Cox J, Mann M.

Mol Cell Proteomics. 2012 Mar;11(3):M111.013185. doi: 10.1074/mcp.M111.013185. Epub 2011 Dec 13.

25.

Richard A Scheltema.

Scheltema RA.

Bioanalysis. 2011 Jun;3(11):1197-9. doi: 10.4155/bio.11.96. No abstract available.

26.

PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis.

Scheltema RA, Jankevics A, Jansen RC, Swertz MA, Breitling R.

Anal Chem. 2011 Apr 1;83(7):2786-93. doi: 10.1021/ac2000994. Epub 2011 Mar 14.

PMID:
21401061
27.

Andromeda: a peptide search engine integrated into the MaxQuant environment.

Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M.

J Proteome Res. 2011 Apr 1;10(4):1794-805. doi: 10.1021/pr101065j. Epub 2011 Feb 22.

PMID:
21254760
28.

Metabolomics to unveil and understand phenotypic diversity between pathogen populations.

t'Kindt R, Scheltema RA, Jankevics A, Brunker K, Rijal S, Dujardin JC, Breitling R, Watson DG, Coombs GH, Decuypere S.

PLoS Negl Trop Dis. 2010 Nov 30;4(11):e904. doi: 10.1371/journal.pntd.0000904.

29.

Simple data-reduction method for high-resolution LC-MS data in metabolomics.

Scheltema R, Decuypere S, Dujardin J, Watson D, Jansen R, Breitling R.

Bioanalysis. 2009 Dec;1(9):1551-7. doi: 10.4155/bio.09.146.

PMID:
21083103
30.

Towards an unbiased metabolic profiling of protozoan parasites: optimisation of a Leishmania sampling protocol for HILIC-orbitrap analysis.

t'Kindt R, Jankevics A, Scheltema RA, Zheng L, Watson DG, Dujardin JC, Breitling R, Coombs GH, Decuypere S.

Anal Bioanal Chem. 2010 Nov;398(5):2059-69. doi: 10.1007/s00216-010-4139-0. Epub 2010 Sep 8. Erratum in: Anal Bioanal Chem. 2011 Apr;400(2):635.

PMID:
20824428
31.

Two time-point assessment of bile acid kinetics in humans using stable isotopes.

Stellaard F, Bloks VW, Burgerhof HG, Scheltema RA, Murphy EJ, Romijn HA, Smelt GH, Brufau G, Kuipers F.

Isotopes Environ Health Stud. 2010 Sep;46(3):325-36. doi: 10.1080/10256016.2010.503894.

PMID:
20645205
32.

XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments.

Swertz MA, Velde KJ, Tesson BM, Scheltema RA, Arends D, Vera G, Alberts R, Dijkstra M, Schofield P, Schughart K, Hancock JM, Smedley D, Wolstencroft K, Goble C, de Brock EO, Jones AR, Parkinson HE; Coordination of Mouse Informatics Resources (CASIMIR); Genotype-To-Phenotype (GEN2PHEN) Consortiums, Jansen RC.

Genome Biol. 2010;11(3):R27. doi: 10.1186/gb-2010-11-3-r27. Epub 2010 Mar 9.

33.

Metabolomic characterization of the salt stress response in Streptomyces coelicolor.

Kol S, Merlo ME, Scheltema RA, de Vries M, Vonk RJ, Kikkert NA, Dijkhuizen L, Breitling R, Takano E.

Appl Environ Microbiol. 2010 Apr;76(8):2574-81. doi: 10.1128/AEM.01992-09. Epub 2010 Feb 26.

34.

The potential of metabolomics for Leishmania research in the post-genomics era.

Scheltema RA, Decuypere S, T'kindt R, Dujardin JC, Coombs GH, Breitling R.

Parasitology. 2010 Aug;137(9):1291-302. doi: 10.1017/S0031182009992022. Epub 2010 Jan 29. Review.

PMID:
20109253
35.

System-wide molecular evidence for phenotypic buffering in Arabidopsis.

Fu J, Keurentjes JJ, Bouwmeester H, America T, Verstappen FW, Ward JL, Beale MH, de Vos RC, Dijkstra M, Scheltema RA, Johannes F, Koornneef M, Vreugdenhil D, Breitling R, Jansen RC.

Nat Genet. 2009 Feb;41(2):166-7. doi: 10.1038/ng.308. Epub 2009 Jan 25.

PMID:
19169256
36.

Probabilistic assignment of formulas to mass peaks in metabolomics experiments.

Rogers S, Scheltema RA, Girolami M, Breitling R.

Bioinformatics. 2009 Feb 15;25(4):512-8. doi: 10.1093/bioinformatics/btn642. Epub 2008 Dec 18.

PMID:
19095699
37.

Increasing the mass accuracy of high-resolution LC-MS data using background ions: a case study on the LTQ-Orbitrap.

Scheltema RA, Kamleh A, Wildridge D, Ebikeme C, Watson DG, Barrett MP, Jansen RC, Breitling R.

Proteomics. 2008 Nov;8(22):4647-56. doi: 10.1002/pmic.200800314.

PMID:
18937253
38.

Metabolomic profiling using Orbitrap Fourier transform mass spectrometry with hydrophilic interaction chromatography: a method with wide applicability to analysis of biomolecules.

Kamleh A, Barrett MP, Wildridge D, Burchmore RJ, Scheltema RA, Watson DG.

Rapid Commun Mass Spectrom. 2008 Jun;22(12):1912-8. doi: 10.1002/rcm.3564.

PMID:
18470888

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