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Items: 26

1.

Deep learning adds an extra dimension to peptide fragmentation.

Röst HL.

Nat Methods. 2019 Jun;16(6):469-470. doi: 10.1038/s41592-019-0428-5. No abstract available.

PMID:
31147636
2.

Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic Analysis.

Chalkley RJ, MacCoss MJ, Jaffe JD, Röst HL.

Mol Cell Proteomics. 2019 Jan;18(1):1-2. doi: 10.1074/mcp.E118.001286. No abstract available.

3.

High-frequency actionable pathogenic exome variants in an average-risk cohort.

Rego S, Dagan-Rosenfeld O, Zhou W, Sailani MR, Limcaoco P, Colbert E, Avina M, Wheeler J, Craig C, Salins D, Röst HL, Dunn J, McLaughlin T, Steinmetz LM, Bernstein JA, Snyder MP.

Cold Spring Harb Mol Case Stud. 2018 Dec 17;4(6). pii: a003178. doi: 10.1101/mcs.a003178. Print 2018 Dec.

4.

Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses.

Rosenberger G, Bludau I, Schmitt U, Heusel M, Hunter CL, Liu Y, MacCoss MJ, MacLean BX, Nesvizhskii AI, Pedrioli PGA, Reiter L, Röst HL, Tate S, Ting YS, Collins BC, Aebersold R.

Nat Methods. 2017 Sep;14(9):921-927. doi: 10.1038/nmeth.4398. Epub 2017 Aug 21.

5.

Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide.

Shi Z, Fujii K, Kovary KM, Genuth NR, Röst HL, Teruel MN, Barna M.

Mol Cell. 2017 Jul 6;67(1):71-83.e7. doi: 10.1016/j.molcel.2017.05.021. Epub 2017 Jun 15.

6.

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS.

Rosenberger G, Liu Y, Röst HL, Ludwig C, Buil A, Bensimon A, Soste M, Spector TD, Dermitzakis ET, Collins BC, Malmström L, Aebersold R.

Nat Biotechnol. 2017 Aug;35(8):781-788. doi: 10.1038/nbt.3908. Epub 2017 Jun 12.

7.

Quantitative proteomics: challenges and opportunities in basic and applied research.

Schubert OT, Röst HL, Collins BC, Rosenberger G, Aebersold R.

Nat Protoc. 2017 Jul;12(7):1289-1294. doi: 10.1038/nprot.2017.040. Epub 2017 Jun 1.

PMID:
28569762
8.

BioContainers: an open-source and community-driven framework for software standardization.

da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y.

Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192.

9.

Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms.

Röst HL, Aebersold R, Schubert OT.

Methods Mol Biol. 2017;1550:289-307. doi: 10.1007/978-1-4939-6747-6_20.

PMID:
28188537
10.

A multicenter study benchmarks software tools for label-free proteome quantification.

Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, Tenzer S.

Nat Biotechnol. 2016 Nov;34(11):1130-1136. doi: 10.1038/nbt.3685. Epub 2016 Oct 3.

11.

OpenMS: a flexible open-source software platform for mass spectrometry data analysis.

Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O.

Nat Methods. 2016 Aug 30;13(9):741-8. doi: 10.1038/nmeth.3959.

PMID:
27575624
12.

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics.

Röst HL, Liu Y, D'Agostino G, Zanella M, Navarro P, Rosenberger G, Collins BC, Gillet L, Testa G, Malmström L, Aebersold R.

Nat Methods. 2016 Sep;13(9):777-83. doi: 10.1038/nmeth.3954. Epub 2016 Aug 1.

13.

Reproducible quantitative proteotype data matrices for systems biology.

Röst HL, Malmström L, Aebersold R.

Mol Biol Cell. 2015 Nov 5;26(22):3926-31. doi: 10.1091/mbc.E15-07-0507.

14.

xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry.

Walzthoeni T, Joachimiak LA, Rosenberger G, Röst HL, Malmström L, Leitner A, Frydman J, Aebersold R.

Nat Methods. 2015 Dec;12(12):1185-90. doi: 10.1038/nmeth.3631. Epub 2015 Oct 26.

15.

Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis.

Schubert OT, Ludwig C, Kogadeeva M, Zimmermann M, Rosenberger G, Gengenbacher M, Gillet LC, Collins BC, Röst HL, Kaufmann SH, Sauer U, Aebersold R.

Cell Host Microbe. 2015 Jul 8;18(1):96-108. doi: 10.1016/j.chom.2015.06.001. Epub 2015 Jun 18.

16.

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry.

Röst HL, Schmitt U, Aebersold R, Malmström L.

PLoS One. 2015 Apr 30;10(4):e0125108. doi: 10.1371/journal.pone.0125108. eCollection 2015.

17.

Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.

Röst HL, Rosenberger G, Aebersold R, Malmström L.

Bioinformatics. 2015 Jul 15;31(14):2415-7. doi: 10.1093/bioinformatics/btv152. Epub 2015 Mar 18.

18.

Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps.

Guo T, Kouvonen P, Koh CC, Gillet LC, Wolski WE, Röst HL, Rosenberger G, Collins BC, Blum LC, Gillessen S, Joerger M, Jochum W, Aebersold R.

Nat Med. 2015 Apr;21(4):407-13. doi: 10.1038/nm.3807. Epub 2015 Mar 2.

19.

DIANA--algorithmic improvements for analysis of data-independent acquisition MS data.

Teleman J, Röst HL, Rosenberger G, Schmitt U, Malmström L, Malmström J, Levander F.

Bioinformatics. 2015 Feb 15;31(4):555-62. doi: 10.1093/bioinformatics/btu686. Epub 2014 Oct 27.

20.

aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data.

Rosenberger G, Ludwig C, Röst HL, Aebersold R, Malmström L.

Bioinformatics. 2014 Sep 1;30(17):2511-3. doi: 10.1093/bioinformatics/btu200. Epub 2014 Apr 20.

21.

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data.

Röst HL, Rosenberger G, Navarro P, Gillet L, Miladinović SM, Schubert OT, Wolski W, Collins BC, Malmström J, Malmström L, Aebersold R.

Nat Biotechnol. 2014 Mar;32(3):219-23. doi: 10.1038/nbt.2841. No abstract available.

PMID:
24727770
22.

Numerical compression schemes for proteomics mass spectrometry data.

Teleman J, Dowsey AW, Gonzalez-Galarza FF, Perkins S, Pratt B, Röst HL, Malmström L, Malmström J, Jones AR, Deutsch EW, Levander F.

Mol Cell Proteomics. 2014 Jun;13(6):1537-42. doi: 10.1074/mcp.O114.037879. Epub 2014 Mar 27.

23.

pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library.

Röst HL, Schmitt U, Aebersold R, Malmström L.

Proteomics. 2014 Jan;14(1):74-7. doi: 10.1002/pmic.201300246.

PMID:
24420968
24.

A repository of assays to quantify 10,000 human proteins by SWATH-MS.

Rosenberger G, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, Lam H, Bader SL, Campbell DS, Deutsch EW, Moritz RL, Tate S, Aebersold R.

Sci Data. 2014 Sep 16;1:140031. doi: 10.1038/sdata.2014.31. eCollection 2014.

25.

Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system.

Collins BC, Gillet LC, Rosenberger G, Röst HL, Vichalkovski A, Gstaiger M, Aebersold R.

Nat Methods. 2013 Dec;10(12):1246-53. doi: 10.1038/nmeth.2703. Epub 2013 Oct 27.

PMID:
24162925
26.

The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis.

Schubert OT, Mouritsen J, Ludwig C, Röst HL, Rosenberger G, Arthur PK, Claassen M, Campbell DS, Sun Z, Farrah T, Gengenbacher M, Maiolica A, Kaufmann SHE, Moritz RL, Aebersold R.

Cell Host Microbe. 2013 May 15;13(5):602-612. doi: 10.1016/j.chom.2013.04.008.

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