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Items: 1 to 50 of 63

1.

Detecting single amino acids and small peptides by combining isobaric tags and peptidomics.

Burger B, Lereim RR, Berven FS, Barsnes H.

Eur J Mass Spectrom (Chichester). 2019 Jun 12:1469066719857006. doi: 10.1177/1469066719857006. [Epub ahead of print]

PMID:
31189351
2.

Proteomics Standards Initiative Extended FASTA Format.

Binz PA, Shofstahl J, Vizcaíno JA, Barsnes H, Chalkley RJ, Menschaert G, Alpi E, Clauser K, Eng JK, Lane L, Seymour SL, Sánchez LFH, Mayer G, Eisenacher M, Perez-Riverol Y, Kapp EA, Mendoza L, Baker PR, Collins A, Van Den Bossche T, Deutsch EW.

J Proteome Res. 2019 Jun 7;18(6):2686-2692. doi: 10.1021/acs.jproteome.9b00064. Epub 2019 May 23.

PMID:
31081335
3.

Analyzing the Structure of Pathways and Its Influence on the Interpretation of Biomedical Proteomics Data Sets.

Burger B, Hernández Sánchez LF, Lereim RR, Barsnes H, Vaudel M.

J Proteome Res. 2018 Nov 2;17(11):3801-3809. doi: 10.1021/acs.jproteome.8b00464. Epub 2018 Oct 24.

PMID:
30251541
4.

SearchGUI: A Highly Adaptable Common Interface for Proteomics Search and de Novo Engines.

Barsnes H, Vaudel M.

J Proteome Res. 2018 Jul 6;17(7):2552-2555. doi: 10.1021/acs.jproteome.8b00175. Epub 2018 May 25.

PMID:
29774740
5.

An Accessible Proteogenomics Informatics Resource for Cancer Researchers.

Chambers MC, Jagtap PD, Johnson JE, McGowan T, Kumar P, Onsongo G, Guerrero CR, Barsnes H, Vaudel M, Martens L, Grüning B, Cooke IR, Heydarian M, Reddy KL, Griffin TJ.

Cancer Res. 2017 Nov 1;77(21):e43-e46. doi: 10.1158/0008-5472.CAN-17-0331.

6.

Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows.

Verheggen K, Raeder H, Berven FS, Martens L, Barsnes H, Vaudel M.

Mass Spectrom Rev. 2017 Sep 13. doi: 10.1002/mas.21543. [Epub ahead of print] Review.

PMID:
28902424
7.

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets.

Perez-Riverol Y, Ternent T, Koch M, Barsnes H, Vrousgou O, Jupp S, Vizcaíno JA.

Proteomics. 2017 Oct;17(19). doi: 10.1002/pmic.201700244.

8.

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.

9.

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.

10.

PeptideMapper: efficient and versatile amino acid sequence and tag mapping.

Kopczynski D, Barsnes H, Njølstad PR, Sickmann A, Vaudel M, Ahrends R.

Bioinformatics. 2017 Jul 1;33(13):2042-2044. doi: 10.1093/bioinformatics/btx122.

PMID:
28334306
11.

Visualization, Inspection and Interpretation of Shotgun Proteomics Identification Results.

Lereim RR, Oveland E, Berven FS, Vaudel M, Barsnes H.

Adv Exp Med Biol. 2016;919:227-235. Review.

PMID:
27975220
12.

Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics.

Muth T, Rapp E, Berven FS, Barsnes H, Vaudel M.

Adv Exp Med Biol. 2016;919:217-226. Review.

PMID:
27975219
13.

Database Search Engines: Paradigms, Challenges and Solutions.

Verheggen K, Martens L, Berven FS, Barsnes H, Vaudel M.

Adv Exp Med Biol. 2016;919:147-156. Review.

PMID:
27975215
14.

CSF-PR 2.0: An Interactive Literature Guide to Quantitative Cerebrospinal Fluid Mass Spectrometry Data from Neurodegenerative Disorders.

Guldbrandsen A, Farag Y, Kroksveen AC, Oveland E, Lereim RR, Opsahl JA, Myhr KM, Berven FS, Barsnes H.

Mol Cell Proteomics. 2017 Feb;16(2):300-309. doi: 10.1074/mcp.O116.064477. Epub 2016 Nov 27.

15.

In-Depth Cerebrospinal Fluid Quantitative Proteome and Deglycoproteome Analysis: Presenting a Comprehensive Picture of Pathways and Processes Affected by Multiple Sclerosis.

Kroksveen AC, Guldbrandsen A, Vaudel M, Lereim RR, Barsnes H, Myhr KM, Torkildsen Ø, Berven FS.

J Proteome Res. 2017 Jan 6;16(1):179-194. doi: 10.1021/acs.jproteome.6b00659. Epub 2016 Oct 26.

PMID:
27728768
16.

Using Proteomics Bioinformatics Tools and Resources in Proteogenomic Studies.

Vaudel M, Barsnes H, Ræder H, Berven FS.

Adv Exp Med Biol. 2016;926:65-75. Review.

PMID:
27686806
17.

A Pipeline for Differential Proteomics in Unsequenced Species.

Yılmaz Ş, Victor B, Hulstaert N, Vandermarliere E, Barsnes H, Degroeve S, Gupta S, Sticker A, Gabriël S, Dorny P, Palmblad M, Martens L.

J Proteome Res. 2016 Jun 3;15(6):1963-70. doi: 10.1021/acs.jproteome.6b00140. Epub 2016 May 2.

PMID:
27089233
18.

Label-free analysis of human cerebrospinal fluid addressing various normalization strategies and revealing protein groups affected by multiple sclerosis.

Opsahl JA, Vaudel M, Guldbrandsen A, Aasebø E, Van Pesch V, Franciotta D, Myhr KM, Barsnes H, Berle M, Torkildsen Ø, Kroksveen AC, Berven FS.

Proteomics. 2016 Apr;16(7):1154-65. doi: 10.1002/pmic.201500284.

PMID:
26841090
19.

Systemic Analysis of Regulated Functional Networks.

Hernández Sánchez LF, Aasebø E, Selheim F, Berven FS, Ræder H, Barsnes H, Vaudel M.

Methods Mol Biol. 2016;1394:287-310. doi: 10.1007/978-1-4939-3341-9_21.

PMID:
26700057
20.

A Simple Workflow for Large Scale Shotgun Glycoproteomics.

Guldbrandsen A, Barsnes H, Kroksveen AC, Berven FS, Vaudel M.

Methods Mol Biol. 2016;1394:275-286. doi: 10.1007/978-1-4939-3341-9_20.

PMID:
26700056
21.

Interpretation of Quantitative Shotgun Proteomic Data.

Aasebø E, Berven FS, Selheim F, Barsnes H, Vaudel M.

Methods Mol Biol. 2016;1394:261-273. doi: 10.1007/978-1-4939-3341-9_19.

PMID:
26700055
22.

Pladipus Enables Universal Distributed Computing in Proteomics Bioinformatics.

Verheggen K, Maddelein D, Hulstaert N, Martens L, Barsnes H, Vaudel M.

J Proteome Res. 2016 Mar 4;15(3):707-12. doi: 10.1021/acs.jproteome.5b00850. Epub 2015 Nov 6.

PMID:
26510693
23.

Exploring the potential of public proteomics data.

Vaudel M, Verheggen K, Csordas A, Raeder H, Berven FS, Martens L, Vizcaíno JA, Barsnes H.

Proteomics. 2016 Jan;16(2):214-25. doi: 10.1002/pmic.201500295. Epub 2015 Dec 15. Review.

24.

Practical Considerations for Omics Experiments in Biomedical Sciences.

Vaudel M, Barsnes H, Bjerkvig R, Bikfalvi A, Selheim F, Berven FS, Daubon T.

Curr Pharm Biotechnol. 2016;17(1):105-14. Review.

PMID:
26278526
25.

Quantitative proteomics suggests decrease in the secretogranin-1 cerebrospinal fluid levels during the disease course of multiple sclerosis.

Kroksveen AC, Jaffe JD, Aasebø E, Barsnes H, Bjørlykke Y, Franciotta D, Keshishian H, Myhr KM, Opsahl JA, van Pesch V, Teunissen CE, Torkildsen Ø, Ulvik RJ, Vethe H, Carr SA, Berven FS.

Proteomics. 2015 Oct;15(19):3361-9. doi: 10.1002/pmic.201400142. Epub 2015 Sep 8.

PMID:
26152395
26.

Distributed and interactive visual analysis of omics data.

Farag Y, Berven FS, Jonassen I, Petersen K, Barsnes H.

J Proteomics. 2015 Nov 3;129:78-82. doi: 10.1016/j.jprot.2015.05.029. Epub 2015 Jun 3.

PMID:
26047716
27.

Proteomics data visualisation.

Vizcaíno JA, Barsnes H, Hermjakob H.

Proteomics. 2015 Apr;15(8):1339-40. doi: 10.1002/pmic.201570063. No abstract available.

PMID:
25854789
28.

PeptideShaker enables reanalysis of MS-derived proteomics data sets.

Vaudel M, Burkhart JM, Zahedi RP, Oveland E, Berven FS, Sickmann A, Martens L, Barsnes H.

Nat Biotechnol. 2015 Jan;33(1):22-4. doi: 10.1038/nbt.3109. No abstract available.

PMID:
25574629
29.

Viewing the proteome: how to visualize proteomics data?

Oveland E, Muth T, Rapp E, Martens L, Berven FS, Barsnes H.

Proteomics. 2015 Apr;15(8):1341-55. doi: 10.1002/pmic.201400412. Epub 2015 Jan 21. Review.

PMID:
25504833
30.

JSparklines: making tabular proteomics data come alive.

Barsnes H, Vaudel M, Martens L.

Proteomics. 2015 Apr;15(8):1428-31. doi: 10.1002/pmic.201400356. Epub 2015 Jan 19.

PMID:
25422159
31.

Carboxyl-ester lipase maturity-onset diabetes of the young disease protein biomarkers in secretin-stimulated duodenal juice.

Bjorlykke Y, Vethe H, Vaudel M, Barsnes H, Berven FS, Tjora E, Raeder H.

J Proteome Res. 2015 Jan 2;14(1):521-30. doi: 10.1021/pr500750z. Epub 2014 Nov 4.

PMID:
25369532
32.

In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR).

Guldbrandsen A, Vethe H, Farag Y, Oveland E, Garberg H, Berle M, Myhr KM, Opsahl JA, Barsnes H, Berven FS.

Mol Cell Proteomics. 2014 Nov;13(11):3152-63. doi: 10.1074/mcp.M114.038554. Epub 2014 Jul 18.

33.

Bioinformatics for proteomics: opportunities at the interface between the scientists, their experiments, and the community.

Vaudel M, Barsnes H, Martens L, Berven FS.

Methods Mol Biol. 2014;1156:239-48. doi: 10.1007/978-1-4939-0685-7_16.

PMID:
24791993
34.

Shedding light on black boxes in protein identification.

Vaudel M, Venne AS, Berven FS, Zahedi RP, Martens L, Barsnes H.

Proteomics. 2014 May;14(9):1001-5. doi: 10.1002/pmic.201300488. Epub 2014 Mar 20.

PMID:
24678044
35.

Machine learning applications in proteomics research: how the past can boost the future.

Kelchtermans P, Bittremieux W, De Grave K, Degroeve S, Ramon J, Laukens K, Valkenborg D, Barsnes H, Martens L.

Proteomics. 2014 Mar;14(4-5):353-66. doi: 10.1002/pmic.201300289. Epub 2014 Jan 21. Review.

PMID:
24323524
36.

DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra.

Muth T, Weilnböck L, Rapp E, Huber CG, Martens L, Vaudel M, Barsnes H.

J Proteome Res. 2014 Feb 7;13(2):1143-6. doi: 10.1021/pr4008078. Epub 2014 Jan 7.

37.

Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory.

Verheggen K, Barsnes H, Martens L.

Proteomics. 2014 Mar;14(4-5):367-77. doi: 10.1002/pmic.201300288. Epub 2013 Nov 27. Review.

PMID:
24285552
38.

Pride-asap: automatic fragment ion annotation of identified PRIDE spectra.

Hulstaert N, Reisinger F, Rameseder J, Barsnes H, Vizcaíno JA, Martens L.

J Proteomics. 2013 Dec 16;95:89-92. doi: 10.1016/j.jprot.2013.04.011. Epub 2013 Apr 17.

39.

Crowdsourcing in proteomics: public resources lead to better experiments.

Barsnes H, Martens L.

Amino Acids. 2013 Apr;44(4):1129-37. doi: 10.1007/s00726-012-1455-z. Epub 2013 Feb 2. Review.

PMID:
23377569
40.

Discovery and initial verification of differentially abundant proteins between multiple sclerosis patients and controls using iTRAQ and SID-SRM.

Kroksveen AC, Aasebø E, Vethe H, Van Pesch V, Franciotta D, Teunissen CE, Ulvik RJ, Vedeler C, Myhr KM, Barsnes H, Berven FS.

J Proteomics. 2013 Jan 14;78:312-25. doi: 10.1016/j.jprot.2012.09.037. Epub 2012 Oct 8.

PMID:
23059536
41.

The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.

Côté RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HW, van Breukelen B, Heck AJ, Hulstaert N, Martens L, Reisinger F, Csordas A, Ovelleiro D, Perez-Rivevol Y, Barsnes H, Hermjakob H, Vizcaíno JA.

Mol Cell Proteomics. 2012 Dec;11(12):1682-9. doi: 10.1074/mcp.O112.021543. Epub 2012 Sep 4.

42.

Use of stable isotope dimethyl labeling coupled to selected reaction monitoring to enhance throughput by multiplexing relative quantitation of targeted proteins.

Aye TT, Low TY, Bjørlykke Y, Barsnes H, Heck AJ, Berven FS.

Anal Chem. 2012 Jun 5;84(11):4999-5006. doi: 10.1021/ac300596r. Epub 2012 May 15.

PMID:
22548487
43.

Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files.

Colaert N, Barsnes H, Vaudel M, Helsens K, Timmerman E, Sickmann A, Gevaert K, Martens L.

J Proteome Res. 2011 Aug 5;10(8):3840-3. doi: 10.1021/pr2005154. Epub 2011 Jul 11.

PMID:
21714566
44.

compomics-utilities: an open-source Java library for computational proteomics.

Barsnes H, Vaudel M, Colaert N, Helsens K, Sickmann A, Berven FS, Martens L.

BMC Bioinformatics. 2011 Mar 8;12:70. doi: 10.1186/1471-2105-12-70.

45.

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.

Vaudel M, Barsnes H, Berven FS, Sickmann A, Martens L.

Proteomics. 2011 Mar;11(5):996-9. doi: 10.1002/pmic.201000595. Epub 2011 Jan 31.

PMID:
21337703
46.

A global analysis of peptide fragmentation variability.

Barsnes H, Eidhammer I, Martens L.

Proteomics. 2011 Mar;11(6):1181-8. doi: 10.1002/pmic.201000640. Epub 2011 Feb 16.

PMID:
21328539
47.

Submitting proteomics data to PRIDE using PRIDE Converter.

Barsnes H, Vizcaíno JA, Reisinger F, Eidhammer I, Martens L.

Methods Mol Biol. 2011;694:237-53. doi: 10.1007/978-1-60761-977-2_16.

PMID:
21082439
48.

IsobariQ: software for isobaric quantitative proteomics using IPTL, iTRAQ, and TMT.

Arntzen MØ, Koehler CJ, Barsnes H, Berven FS, Treumann A, Thiede B.

J Proteome Res. 2011 Feb 4;10(2):913-20. doi: 10.1021/pr1009977. Epub 2010 Nov 29.

PMID:
21067241
49.

The Ontology Lookup Service: bigger and better.

Côté R, Reisinger F, Martens L, Barsnes H, Vizcaino JA, Hermjakob H.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W155-60. doi: 10.1093/nar/gkq331. Epub 2010 May 11.

50.

XTandem Parser: an open-source library to parse and analyse X!Tandem MS/MS search results.

Muth T, Vaudel M, Barsnes H, Martens L, Sickmann A.

Proteomics. 2010 Apr;10(7):1522-4. doi: 10.1002/pmic.200900759. Erratum in: Proteomics. 2010 Jul;10(13):2560.

PMID:
20140905

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