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1

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Protein Level Quantification

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 70 KB

english, 2013

2

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

Marc Vaudel, Harald Barsnes, Frode S. Berven, Albert Sickmann, Lennart Martens

Journal:

Year:

2011

Language:

english

File:

PDF, 176 KB

english, 2011

3

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Mass Spectrometry and Protein Identification

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 289 KB

english, 2013

4

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Statistical Analysis

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 127 KB

english, 2013

5

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Statistical Normalization

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 173 KB

english, 2013

6

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Experimental Normalization

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 153 KB

english, 2013

7

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Absolute Quantification

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 147 KB

english, 2013

8

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Appendix B: Clustering and Discriminant Analysis

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 156 KB

english, 2013

9

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Introduction

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 120 KB

english, 2013

10

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Protein Quantification by Mass Spectrometry

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 249 KB

english, 2013

11

Viewing the proteome: How to visualize proteomics data?

Oveland, Eystein, Muth, Thilo, Rapp, Erdmann, Martens, Lennart, Berven, Frode S., Barsnes, Harald

Journal:

Year:

2015

Language:

english

File:

PDF, 1.37 MB

english, 2015

12

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

Kelchtermans, Pieter, Bittremieux, Wout, De Grave, Kurt, Degroeve, Sven, Ramon, Jan, Laukens, Kris, Valkenborg, Dirk, Barsnes, Harald, Martens, Lennart

Journal:

Year:

2014

Language:

english

File:

PDF, 658 KB

english, 2014

13

PeptideShaker enables reanalysis of MS-derived proteomics data sets

Vaudel, Marc, Burkhart, Julia M, Zahedi, René P, Oveland, Eystein, Berven, Frode S, Sickmann, Albert, Martens, Lennart, Barsnes, Harald

Journal:

Nature Biotechnology

Year:

2015

Language:

english

File:

PDF, 1.89 MB

english, 2015

14

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

Leprevost, Felipe da Veiga, Grüning, Björn A., Alves Aflitos, Saulo, Röst, Hannes L., Uszkoreit, Julian, Barsnes, Harald, Vaudel, Marc, Moreno, Pablo, Gatto, Laurent, Weber, Jonas, Bai, Mingze, Jimene

Journal:

Year:

2017

Language:

english

File:

PDF, 223 KB

english, 2017

15

PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping

Sánchez, Luis Francisco Hernández, Burger, Bram, Horro, Carlos, Fabregat, Antonio, Johansson, Stefan, Njølstad, Pål Rasmus, Barsnes, Harald, Hermjakob, Henning, Vaudel, Marc

Journal:

Year:

2019

Language:

english

File:

PDF, 4.06 MB

english, 2019

16

ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion

Hulstaert, Niels, Shofstahl, Jim, Sachsenberg, Timo, Walzer, Mathias, Barsnes, Harald, Martens, Lennart, Perez-Riverol, Yasset

Journal:

Journal of Proteome Research

Year:

2019

Language:

english

File:

PDF, 685 KB

english, 2019

17

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

Harald Barsnes, Marc Vaudel, Niklaas Colaert, Kenny Helsens, Albert Sickmann, Frode S Berven, Lennart Martens

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 1.19 MB

english, 2011

18

Proteomics Data Collection – 4th ProDaC Workshop 15 August 2008, Amsterdam, The Netherlands

Martin Eisenacher, Michael Kohl, Lennart Martens, Harald Barsnes, Tanja Hardt, Fredrik Levander, Jari Häkkinen, Rolf Apweiler, Helmut E. Meyer, Christian Stephan

Journal:

Year:

2009

Language:

english

File:

PDF, 261 KB

english, 2009

19

OMSSA Parser: An open-source library to parse and extract data from OMSSA MS/MS search results

Harald Barsnes, Steffen Huber, Albert Sickmann, Ingvar Eidhammer, Lennart Martens

Journal:

Year:

2009

Language:

english

File:

PDF, 144 KB

english, 2009

20

Proteomics Data Collection – 5th ProDaC Workshop 4 March 2009, Kolympari, Crete, Greece

Martin Eisenacher, Lennart Martens, Harald Barsnes, Tanja Hardt, Michael Kohl, Jari Häkkinen, Rolf Apweiler, Helmut E. Meyer, Christian Stephan

Journal:

Year:

2009

Language:

english

File:

PDF, 144 KB

english, 2009

21

Getting a grip on proteomics data – Proteomics Data Collection (ProDaC)

Martin Eisenacher, Lennart Martens, Tanja Hardt, Michael Kohl, Harald Barsnes, Kenny Helsens, Jari Häkkinen, Fredrik Levander, Ruedi Aebersold, Joël Vandekerckhove, Michael J. Dunn, Frederique Lisacek

Journal:

Year:

2009

Language:

english

File:

PDF, 134 KB

english, 2009

22

ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics

Kenny Helsens, Niklaas Colaert, Harald Barsnes, Thilo Muth, Kristian Flikka, An Staes, Evy Timmerman, Steffi Wortelkamp, Albert Sickmann, Joël Vandekerckhove, Kris Gevaert, Lennart Martens

Journal:

Year:

2010

Language:

english

File:

PDF, 153 KB

english, 2010

23

FragmentationAnalyzer: An open-source tool to analyze MS/MS fragmentation data

Harald Barsnes, Ingvar Eidhammer, Lennart Martens

Journal:

Year:

2010

Language:

english

File:

PDF, 209 KB

english, 2010

24

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

Thilo Muth, Marc Vaudel, Harald Barsnes, Lennart Martens, Albert Sickmann

Journal:

Year:

2010

Language:

english

File:

PDF, 135 KB

english, 2010

25

A global analysis of peptide fragmentation variability

Harald Barsnes, Ingvar Eidhammer, Lennart Martens

Journal:

Year:

2011

Language:

english

File:

PDF, 376 KB

english, 2011

26

Erratum: FragmentationAnalyzer: An open-source tool to analyze MS/MS fragmentation data

Harald Barsnes, Ingvar Eidhammer, Lennart Martens

Journal:

Year:

2010

Language:

english

File:

PDF, 43 KB

english, 2010

27

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

Thilo Muth, Marc Vaudel, Harald Barsnes, Lennart Martens, Albert Sickmann

Journal:

Year:

2010

Language:

english

File:

PDF, 43 KB

english, 2010

28

Erratum: ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics

Kenny Helsens, Niklaas Colaert, Harald Barsnes, Thilo Muth, Kristian Flikka, An Staes, Evy Timmerman, Steffi Wortelkamp, Albert Sickmann, Joël Vandekerckhove, Kris Gevaert, Lennart Martens

Journal:

Year:

2010

Language:

english

File:

PDF, 43 KB

english, 2010

29

PRIDE Converter: making proteomics data-sharing easy

Barsnes, Harald, Vizcaíno, Juan Antonio, Eidhammer, Ingvar, Martens, Lennart

Journal:

Nature Biotechnology

Year:

2009

Language:

english

File:

PDF, 291 KB

english, 2009

30

An Evaluation of the Use of Modulated Temperature DSC as a Means of Assessing the Relaxation Behaviour of Amorphous Lactose

Duncan Q. M. Craig, Merete Barsnes, Paul G. Royall, Vicky L. Kett

Journal:

Pharmaceutical Research

Year:

2000

Language:

english

File:

PDF, 165 KB

english, 2000

31

OLS Dialog: An open-source front end to the Ontology Lookup Service

Harald Barsnes, Richard G Côté, Ingvar Eidhammer, Lennart Martens

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 471 KB

english, 2010

32

MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences

Harald Barsnes, Svein-Ole Mikalsen, Ingvar Eidhammer

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 399 KB

english, 2006

33

Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases

Harald Barsnes, Svein-Ole Mikalsen, Ingvar Eidhammer

Journal:

BMC Research Notes

Year:

2008

Language:

english

File:

PDF, 823 KB

english, 2008

34

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Correlations of mRNA and Protein Abundances

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 140 KB

english, 2013

35

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Fragment Based MS/MS Quantification

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 114 KB

english, 2013

36

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Label Based Quantification by MS Spectra

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 241 KB

english, 2013

37

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Label Based Quantification

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 111 KB

english, 2013

38

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Reporter Based MS/MS Quantification

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 202 KB

english, 2013

39

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Targeted Quantification - Selected Reaction Monitoring

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 741 KB

english, 2013

40

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Label free Quantification by MS Spectra

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 164 KB

english, 2013

41

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Appendix A: Statistics

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 226 KB

english, 2013

42

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Label Free Quantification by MS/MS Spectra

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 103 KB

english, 2013

43

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Quantification of Post-Translational Modifications

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 108 KB

english, 2013

44

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Biomarkers

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 63 KB

english, 2013

45

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Standards and Databases

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 63 KB

english, 2013

46

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Front Matter

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 93 KB

english, 2013

47

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || Index

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 68 KB

english, 2013

48

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (Eidhammer/Computational) || References

Eidhammer, Ingvar, Barsnes, Harald, Eide, Geir Egil, Martens, Lennart

Year:

2013

Language:

english

File:

PDF, 111 KB

english, 2013

49

Pride-asap: Automatic fragment ion annotation of identified PRIDE spectra

Hulstaert, Niels, Reisinger, Florian, Rameseder, Jonathan, Barsnes, Harald, Vizcaíno, Juan Antonio, Martens, Lennart

Journal:

Journal of Proteomics

Year:

2013

Language:

english

File:

PDF, 571 KB

english, 2013

50

Crowdsourcing in proteomics: public resources lead to better experiments

Harald Barsnes, Lennart Martens

Journal:

Year:

2013

Language:

english

File:

PDF, 493 KB

english, 2013