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Items: 27

1.

Protein Inference Using PIA Workflows and PSI Standard File Formats.

Uszkoreit J, Perez-Riverol Y, Eggers B, Marcus K, Eisenacher M.

J Proteome Res. 2019 Feb 1;18(2):741-747. doi: 10.1021/acs.jproteome.8b00723. Epub 2018 Dec 5.

PMID:
30474983
2.

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

Perez-Riverol Y, Csordas A, Bai J, Bernal-Llinares M, Hewapathirana S, Kundu DJ, Inuganti A, Griss J, Mayer G, Eisenacher M, Pérez E, Uszkoreit J, Pfeuffer J, Sachsenberg T, Yilmaz S, Tiwary S, Cox J, Audain E, Walzer M, Jarnuczak AF, Ternent T, Brazma A, Vizcaíno JA.

Nucleic Acids Res. 2019 Jan 8;47(D1):D442-D450. doi: 10.1093/nar/gky1106.

3.

Characterization of Cerebrospinal Fluid via Data-Independent Acquisition Mass Spectrometry.

Barkovits K, Linden A, Galozzi S, Schilde L, Pacharra S, Mollenhauer B, Stoepel N, Steinbach S, May C, Uszkoreit J, Eisenacher M, Marcus K.

J Proteome Res. 2018 Oct 5;17(10):3418-3430. doi: 10.1021/acs.jproteome.8b00308. Epub 2018 Sep 12.

PMID:
30207155
4.

Proceedings of the EuBIC developer's meeting 2018.

Willems S, Bouyssié D, Deforce D, Dorfer V, Gorshkov V, Kopczynski D, Laukens K, Locard-Paulet M, Schwämmle V, Uszkoreit J, Valkenborg D, Vaudel M, Bittremieux W.

J Proteomics. 2018 Sep 15;187:25-27. doi: 10.1016/j.jprot.2018.05.015. Epub 2018 Jun 2.

PMID:
29864591
5.

BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication.

Turewicz M, Kohl M, Ahrens M, Mayer G, Uszkoreit J, Naboulsi W, Bracht T, Megger DA, Sitek B, Marcus K, Eisenacher M.

J Biotechnol. 2017 Nov 10;261:116-125. doi: 10.1016/j.jbiotec.2017.06.005. Epub 2017 Jun 9. Review.

6.

The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics.

Vizcaíno JA, Mayer G, Perkins S, Barsnes H, Vaudel M, Perez-Riverol Y, Ternent T, Uszkoreit J, Eisenacher M, Fischer L, Rappsilber J, Netz E, Walzer M, Kohlbacher O, Leitner A, Chalkley RJ, Ghali F, Martínez-Bartolomé S, Deutsch EW, Jones AR.

Mol Cell Proteomics. 2017 Jul;16(7):1275-1285. doi: 10.1074/mcp.M117.068429. Epub 2017 May 17.

7.

Proceedings of the EuBIC Winter School 2017.

Willems S, Bouyssié D, David M, Locard-Paulet M, Mechtler K, Schwämmle V, Uszkoreit J, Vaudel M, Dorfer V.

J Proteomics. 2017 May 24;161:78-80. doi: 10.1016/j.jprot.2017.04.001. Epub 2017 Apr 4.

PMID:
28385664
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.

Proteomics of rimmed vacuoles define new risk allele in inclusion body myositis.

Güttsches AK, Brady S, Krause K, Maerkens A, Uszkoreit J, Eisenacher M, Schreiner A, Galozzi S, Mertens-Rill J, Tegenthoff M, Holton JL, Harms MB, Lloyd TE, Vorgerd M, Weihl CC, Marcus K, Kley RA.

Ann Neurol. 2017 Feb;81(2):227-239. doi: 10.1002/ana.24847. Epub 2017 Jan 27.

10.

One Sample, One Shot - Evaluation of sample preparation protocols for the mass spectrometric proteome analysis of human bile fluid without extensive fractionation.

Megger DA, Padden J, Rosowski K, Uszkoreit J, Bracht T, Eisenacher M, Gerges C, Neuhaus H, Schumacher B, Schlaak JF, Sitek B.

J Proteomics. 2017 Feb 10;154:13-21. doi: 10.1016/j.jprot.2016.11.021. Epub 2016 Dec 5.

PMID:
27932303
11.

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.

Audain E, Uszkoreit J, Sachsenberg T, Pfeuffer J, Liang X, Hermjakob H, Sanchez A, Eisenacher M, Reinert K, Tabb DL, Kohlbacher O, Perez-Riverol Y.

J Proteomics. 2017 Jan 6;150:170-182. doi: 10.1016/j.jprot.2016.08.002. Epub 2016 Aug 4.

PMID:
27498275
12.

Ten Simple Rules for Taking Advantage of Git and GitHub.

Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, Leprevost Fda V, Fufezan C, Ternent T, Eglen SJ, Katz DS, Pollard TJ, Konovalov A, Flight RM, Blin K, Vizcaíno JA.

PLoS Comput Biol. 2016 Jul 14;12(7):e1004947. doi: 10.1371/journal.pcbi.1004947. eCollection 2016 Jul. No abstract available. Erratum in: PLoS Comput Biol. 2019 Jun 14;15(6):e1007142.

13.

New insights into the protein aggregation pathology in myotilinopathy by combined proteomic and immunolocalization analyses.

Maerkens A, Olivé M, Schreiner A, Feldkirchner S, Schessl J, Uszkoreit J, Barkovits K, Güttsches AK, Theis V, Eisenacher M, Tegenthoff M, Goldfarb LG, Schröder R, Schoser B, van der Ven PF, Fürst DO, Vorgerd M, Marcus K, Kley RA.

Acta Neuropathol Commun. 2016 Feb 3;4:8. doi: 10.1186/s40478-016-0280-0.

14.

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.

Perez-Riverol Y, Xu QW, Wang R, Uszkoreit J, Griss J, Sanchez A, Reisinger F, Csordas A, Ternent T, Del-Toro N, Dianes JA, Eisenacher M, Hermjakob H, Vizcaíno JA.

Mol Cell Proteomics. 2016 Jan;15(1):305-17. doi: 10.1074/mcp.O115.050229. Epub 2015 Nov 6.

15.

PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface.

Uszkoreit J, Maerkens A, Perez-Riverol Y, Meyer HE, Marcus K, Stephan C, Kohlbacher O, Eisenacher M.

J Proteome Res. 2015 Jul 2;14(7):2988-97. doi: 10.1021/acs.jproteome.5b00121. Epub 2015 Jun 10.

PMID:
25938255
16.

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.

Perez-Riverol Y, Uszkoreit J, Sanchez A, Ternent T, Del Toro N, Hermjakob H, Vizcaíno JA, Wang R.

Bioinformatics. 2015 Sep 1;31(17):2903-5. doi: 10.1093/bioinformatics/btv250. Epub 2015 Apr 24.

17.

The bacterial proteogenomic pipeline.

Uszkoreit J, Plohnke N, Rexroth S, Marcus K, Eisenacher M.

BMC Genomics. 2014;15 Suppl 9:S19. doi: 10.1186/1471-2164-15-S9-S19. Epub 2014 Dec 8.

18.

A standardized framing for reporting protein identifications in mzIdentML 1.2.

Seymour SL, Farrah T, Binz PA, Chalkley RJ, Cottrell JS, Searle BC, Tabb DL, Vizcaíno JA, Prieto G, Uszkoreit J, Eisenacher M, Martínez-Bartolomé S, Ghali F, Jones AR.

Proteomics. 2014 Nov;14(21-22):2389-99. doi: 10.1002/pmic.201400080. Epub 2014 Sep 23.

19.

Amyloid beta a4 precursor protein-binding family B member 1 (FE65) interactomics revealed synaptic vesicle glycoprotein 2A (SV2A) and sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (SERCA2) as new binding proteins in the human brain.

Nensa FM, Neumann MH, Schrötter A, Przyborski A, Mastalski T, Susdalzew S, Looβe C, Helling S, El Magraoui F, Erdmann R, Meyer HE, Uszkoreit J, Eisenacher M, Suh J, Guénette SY, Röhner N, Kögel D, Theiss C, Marcus K, Müller T.

Mol Cell Proteomics. 2014 Feb;13(2):475-88. doi: 10.1074/mcp.M113.029280. Epub 2013 Nov 27.

20.

A combination of two electrophoretical approaches for detailed proteome-based characterization of SCLC subtypes.

Poschmann G, Lendzian A, Uszkoreit J, Eisenacher M, Borght AV, Ramaekers FC, Meyer HE, Stühler K.

Arch Physiol Biochem. 2013 Jul;119(3):114-25. doi: 10.3109/13813455.2013.789529. Epub 2013 May 8.

PMID:
23651173
21.

Differential proteomic analysis of abnormal intramyoplasmic aggregates in desminopathy.

Maerkens A, Kley RA, Olivé M, Theis V, van der Ven PF, Reimann J, Milting H, Schreiner A, Uszkoreit J, Eisenacher M, Barkovits K, Güttsches AK, Tonillo J, Kuhlmann K, Meyer HE, Schröder R, Tegenthoff M, Fürst DO, Müller T, Goldfarb LG, Vorgerd M, Marcus K.

J Proteomics. 2013 Sep 2;90:14-27. doi: 10.1016/j.jprot.2013.04.026. Epub 2013 Apr 30.

22.

The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics.

Walzer M, Qi D, Mayer G, Uszkoreit J, Eisenacher M, Sachsenberg T, Gonzalez-Galarza FF, Fan J, Bessant C, Deutsch EW, Reisinger F, Vizcaíno JA, Medina-Aunon JA, Albar JP, Kohlbacher O, Jones AR.

Mol Cell Proteomics. 2013 Aug;12(8):2332-40. doi: 10.1074/mcp.O113.028506. Epub 2013 Apr 18.

23.

FE65 regulates and interacts with the Bloom syndrome protein in dynamic nuclear spheres - potential relevance to Alzheimer's disease.

Schrötter A, Mastalski T, Nensa FM, Neumann M, Loosse C, Pfeiffer K, Magraoui FE, Platta HW, Erdmann R, Theiss C, Uszkoreit J, Eisenacher M, Meyer HE, Marcus K, Müller T.

J Cell Sci. 2013 Jun 1;126(Pt 11):2480-92. doi: 10.1242/jcs.121004. Epub 2013 Apr 9.

24.

A combined laser microdissection and mass spectrometry approach reveals new disease relevant proteins accumulating in aggregates of filaminopathy patients.

Kley RA, Maerkens A, Leber Y, Theis V, Schreiner A, van der Ven PF, Uszkoreit J, Stephan C, Eulitz S, Euler N, Kirschner J, Müller K, Meyer HE, Tegenthoff M, Fürst DO, Vorgerd M, Müller T, Marcus K.

Mol Cell Proteomics. 2013 Jan;12(1):215-27. doi: 10.1074/mcp.M112.023176. Epub 2012 Oct 31.

25.

Search and decoy: the automatic identification of mass spectra.

Eisenacher M, Kohl M, Turewicz M, Koch MH, Uszkoreit J, Stephan C.

Methods Mol Biol. 2012;893:445-88. doi: 10.1007/978-1-61779-885-6_28.

PMID:
22665317
26.

Sense and nonsense of pathway analysis software in proteomics.

Müller T, Schrötter A, Loosse C, Helling S, Stephan C, Ahrens M, Uszkoreit J, Eisenacher M, Meyer HE, Marcus K.

J Proteome Res. 2011 Dec 2;10(12):5398-408. doi: 10.1021/pr200654k. Epub 2011 Nov 14.

PMID:
21978018
27.

Automated nuclear segmentation in the determination of the Ki-67 labeling index in meningiomas.

Kim YJ, Romeike BF, Uszkoreit J, Feiden W.

Clin Neuropathol. 2006 Mar-Apr;25(2):67-73.

PMID:
16550739

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