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Items: 1 to 50 of 76

1.

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
2.

Expanding the Use of Spectral Libraries in Proteomics.

Deutsch EW, Perez-Riverol Y, Chalkley RJ, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski EL, Wilmes P, Dorfer V, Kuster B, Volders PJ, Jehmlich N, Vissers JPC, Wolan DW, Wang AY, Mendoza L, Shofstahl J, Dowsey AW, Griss J, Salek RM, Neumann S, Binz PA, Lam H, Vizcaíno JA, Bandeira N, Röst H.

J Proteome Res. 2018 Dec 7;17(12):4051-4060. doi: 10.1021/acs.jproteome.8b00485. Epub 2018 Oct 11.

3.

Semisynthetic sensor proteins enable metabolic assays at the point of care.

Yu Q, Xue L, Hiblot J, Griss R, Fabritz S, Roux C, Binz PA, Haas D, Okun JG, Johnsson K.

Science. 2018 Sep 14;361(6407):1122-1126. doi: 10.1126/science.aat7992.

PMID:
30213915
4.

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

Deutsch EW, Orchard S, Binz PA, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, Walzer M, Jones AR.

J Proteome Res. 2017 Dec 1;16(12):4288-4298. doi: 10.1021/acs.jproteome.7b00370. Epub 2017 Sep 15.

5.

Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.

Deutsch EW, Sun Z, Campbell DS, Binz PA, Farrah T, Shteynberg D, Mendoza L, Omenn GS, Moritz RL.

J Proteome Res. 2016 Nov 4;15(11):4091-4100. Epub 2016 Sep 12.

6.

Development of data representation standards by the human proteome organization proteomics standards initiative.

Deutsch EW, Albar JP, Binz PA, Eisenacher M, Jones AR, Mayer G, Omenn GS, Orchard S, Vizcaíno JA, Hermjakob H.

J Am Med Inform Assoc. 2015 May;22(3):495-506. doi: 10.1093/jamia/ocv001. Epub 2015 Feb 28. Review.

7.

Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany.

Orchard S, Albar JP, Binz PA, Kettner C, Jones AR, Salek RM, Vizcaino JA, Deutsch EW, Hermjakob H.

Proteomics. 2014 Nov;14(21-22):2363-8. doi: 10.1002/pmic.201470164. Epub 2014 Oct 9.

PMID:
25297050
8.

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.

9.

ProteomeXchange provides globally coordinated proteomics data submission and dissemination.

Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H.

Nat Biotechnol. 2014 Mar;32(3):223-6. doi: 10.1038/nbt.2839. No abstract available.

10.

The Minimal Information about a Proteomics Experiment (MIAPE) from the Proteomics Standards Initiative.

Martínez-Bartolomé S, Binz PA, Albar JP.

Methods Mol Biol. 2014;1072:765-80. doi: 10.1007/978-1-62703-631-3_53.

PMID:
24136562
11.

Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK.

Orchard S, Binz PA, Jones AR, Vizcaino JA, Deutsch EW, Hermjakob H.

Proteomics. 2013 Oct;13(20):2931-7. doi: 10.1002/pmic.201370166.

PMID:
24108681
12.

Guidelines for reporting quantitative mass spectrometry based experiments in proteomics.

Martínez-Bartolomé S, Deutsch EW, Binz PA, Jones AR, Eisenacher M, Mayer G, Campos A, Canals F, Bech-Serra JJ, Carrascal M, Gay M, Paradela A, Navajas R, Marcilla M, Hernáez ML, Gutiérrez-Blázquez MD, Velarde LF, Aloria K, Beaskoetxea J, Medina-Aunon JA, Albar JP.

J Proteomics. 2013 Dec 16;95:84-8. doi: 10.1016/j.jprot.2013.02.026. Epub 2013 Mar 14.

PMID:
23500130
13.

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.

Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Vizcaíno JA, Hermjakob H, Stephan C, Meyer HE, Eisenacher M; HUPO-PSI Group.

Database (Oxford). 2013 Mar 12;2013:bat009. doi: 10.1093/database/bat009. Print 2013.

14.

Controlled vocabularies and ontologies in proteomics: overview, principles and practice.

Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, Vizcaíno JA, Hermjakob H, Oveillero D, Julian R, Stephan C, Meyer HE, Eisenacher M.

Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):98-107. doi: 10.1016/j.bbapap.2013.02.017. Epub 2013 Feb 19. Review.

15.

Different fever definitions and the rate of fever and neutropenia diagnosed in children with cancer: a retrospective two-center cohort study.

Binz P, Bodmer N, Leibundgut K, Teuffel O, Niggli FK, Ammann RA.

Pediatr Blood Cancer. 2013 May;60(5):799-805. doi: 10.1002/pbc.24380. Epub 2012 Nov 28.

16.

Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA.

Orchard S, Binz PA, Borchers C, Gilson MK, Jones AR, Nicola G, Vizcaino JA, Deutsch EW, Hermjakob H.

Proteomics. 2012 Sep;12(18):2767-72. doi: 10.1002/pmic.201270126.

17.

Standard guidelines for the chromosome-centric human proteome project.

Paik YK, Omenn GS, Uhlen M, Hanash S, Marko-Varga G, Aebersold R, Bairoch A, Yamamoto T, Legrain P, Lee HJ, Na K, Jeong SK, He F, Binz PA, Nishimura T, Keown P, Baker MS, Yoo JS, Garin J, Archakov A, Bergeron J, Salekdeh GH, Hancock WS.

J Proteome Res. 2012 Apr 6;11(4):2005-13. doi: 10.1021/pr200824a. Epub 2012 Mar 26.

PMID:
22443261
18.

The mzIdentML data standard for mass spectrometry-based proteomics results.

Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, Griss J, Vizcaíno JA, Chambers M, Pizarro A, Creasy D.

Mol Cell Proteomics. 2012 Jul;11(7):M111.014381. doi: 10.1074/mcp.M111.014381. Epub 2012 Feb 27.

19.

From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland.

Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Martinez-Bartolomé S, Vizcaíno JA, Hermjakob H.

Proteomics. 2012 Feb;12(3):351-5. doi: 10.1002/pmic.201290016.

PMID:
22290802
20.

TraML--a standard format for exchange of selected reaction monitoring transition lists.

Deutsch EW, Chambers M, Neumann S, Levander F, Binz PA, Shofstahl J, Campbell DS, Mendoza L, Ovelleiro D, Helsens K, Martens L, Aebersold R, Moritz RL, Brusniak MY.

Mol Cell Proteomics. 2012 Apr;11(4):R111.015040. doi: 10.1074/mcp.R111.015040. Epub 2011 Dec 12.

21.

mzML--a community standard for mass spectrometry data.

Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Römpp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, Hermjakob H, Binz PA, Deutsch EW.

Mol Cell Proteomics. 2011 Jan;10(1):R110.000133. doi: 10.1074/mcp.R110.000133. Epub 2010 Aug 17.

22.

implementing data standards: a report on the HUPOPSI workshop September 2009, Toronto, Canada.

Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Hermjakob H.

Proteomics. 2010 May;10(10):1895-8. doi: 10.1002/pmic.201090034.

PMID:
20623474
23.

Guidelines for reporting the use of gel image informatics in proteomics.

Hoogland C, O'Gorman M, Bogard P, Gibson F, Berth M, Cockell SJ, Ekefjärd A, Forsstrom-Olsson O, Kapferer A, Nilsson M, Martínez-Bartolomé S, Albar JP, Echevarría-Zomeño S, Martínez-Gomariz M, Joets J, Binz PA, Taylor CF, Dowsey A, Jones AR; Minimum Information About a Proteomics Experiment (MIAPE).

Nat Biotechnol. 2010 Jul;28(7):655-6. doi: 10.1038/nbt0710-655. No abstract available.

PMID:
20622830
24.

X-Rank: a robust algorithm for small molecule identification using tandem mass spectrometry.

Mylonas R, Mauron Y, Masselot A, Binz PA, Budin N, Fathi M, Viette V, Hochstrasser DF, Lisacek F.

Anal Chem. 2009 Sep 15;81(18):7604-10. doi: 10.1021/ac900954d.

PMID:
19702277
25.

Annual spring meeting of the Proteomics Standards Initiative.

Orchard S, Deutsch EW, Binz PA, Jones AR, Creasy D, Montechi-Palazzi L, Corthals G, Hermjakob H.

Proteomics. 2009 Oct;9(19):4429-32. doi: 10.1002/pmic.200900407.

PMID:
19670378
26.

Second Joint HUPO publication and Proteomics Standards Initiative workshop.

Orchard S, Binz PA, Hermjakob H.

Proteomics. 2009 Oct;9(19):4426-8. doi: 10.1002/pmic.200900406.

PMID:
19670377
27.

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

Eisenacher M, Martens L, Hardt T, Kohl M, Barsnes H, Helsens K, Häkkinen J, Levander F, Aebersold R, Vandekerckhove J, Dunn MJ, Lisacek F, Siepen JA, Hubbard SJ, Binz PA, Blüggel M, Thiele H, Cottrell J, Meyer HE, Apweiler R, Stephan C.

Proteomics. 2009 Aug;9(15):3928-33. doi: 10.1002/pmic.200900247.

PMID:
19637238
28.

A simple workflow to increase MS2 identification rate by subsequent spectral library search.

Ahrné E, Masselot A, Binz PA, Müller M, Lisacek F.

Proteomics. 2009 Mar;9(6):1731-6. doi: 10.1002/pmic.200800410.

PMID:
19235171
29.

Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands.

Orchard S, Hoogland C, Bairoch A, Eisenacher M, Kraus HJ, Binz PA.

Proteomics. 2009 Feb;9(3):499-501. doi: 10.1002/pmic.200800838.

PMID:
19132688
30.

Annual spring meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain.

Orchard S, Albar JP, Deutsch EW, Binz PA, Jones AR, Creasy D, Hermjakob H.

Proteomics. 2008 Oct;8(20):4168-72. doi: 10.1002/pmic.200800555.

PMID:
18814335
31.

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.

Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK Jr, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ Jr, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S.

Nat Biotechnol. 2008 Aug;26(8):889-96. doi: 10.1038/nbt.1411. No abstract available.

32.

The PSI-MOD community standard for representation of protein modification data.

Montecchi-Palazzi L, Beavis R, Binz PA, Chalkley RJ, Cottrell J, Creasy D, Shofstahl J, Seymour SL, Garavelli JS.

Nat Biotechnol. 2008 Aug;26(8):864-6. doi: 10.1038/nbt0808-864. No abstract available.

PMID:
18688235
33.

Guidelines for reporting the use of gel electrophoresis in proteomics.

Gibson F, Anderson L, Babnigg G, Baker M, Berth M, Binz PA, Borthwick A, Cash P, Day BW, Friedman DB, Garland D, Gutstein HB, Hoogland C, Jones NA, Khan A, Klose J, Lamond AI, Lemkin PF, Lilley KS, Minden J, Morris NJ, Paton NW, Pisano MR, Prime JE, Rabilloud T, Stead DA, Taylor CF, Voshol H, Wipat A, Jones AR.

Nat Biotechnol. 2008 Aug;26(8):863-4. doi: 10.1038/nbt0808-863. No abstract available.

34.

Guidelines for reporting the use of mass spectrometry informatics in proteomics.

Binz PA, Barkovich R, Beavis RC, Creasy D, Horn DM, Julian RK Jr, Seymour SL, Taylor CF, Vandenbrouck Y.

Nat Biotechnol. 2008 Aug;26(8):862. doi: 10.1038/nbt0808-862. No abstract available.

PMID:
18688233
35.

Guidelines for reporting the use of mass spectrometry in proteomics.

Taylor CF, Binz PA, Aebersold R, Affolter M, Barkovich R, Deutsch EW, Horn DM, Hühmer A, Kussmann M, Lilley K, Macht M, Mann M, Müller D, Neubert TA, Nickson J, Patterson SD, Raso R, Resing K, Seymour SL, Tsugita A, Xenarios I, Zeng R, Julian RK Jr.

Nat Biotechnol. 2008 Aug;26(8):860-1. doi: 10.1038/nbt0808-860. No abstract available.

PMID:
18688232
36.

ESF workshop on 'Sustainability and Governance of Web and GRID Resources in Functional Genomics'.

van der Vet P, Huibers T, Binz PA, Hofmann M.

Comp Funct Genomics. 2005;6(5-6):307-10. doi: 10.1002/cfg.488. No abstract available.

37.

The ESF Programme on Functional Genomics Workshop on 'Data Integration in Functional Genomics: Application to Biological Pathways'.

Binz PA, Hermjakob H, van der Vet P.

Comp Funct Genomics. 2004;5(2):148-55. doi: 10.1002/cfg.389.

38.

Conference Report: The ESF Programme on Integrated Approaches for Functional Genomics. Workshop on 'Data Integration in Functional Genomics and Proteomics'.

Binz PA, Martin A, Taussig M, de Daruvar A.

Comp Funct Genomics. 2002;3(1):16-21. doi: 10.1002/cfg.134. No abstract available.

39.

On the benefits of acquiring peptide fragment ions at high measured mass accuracy.

Scherl A, Shaffer SA, Taylor GK, Hernandez P, Appel RD, Binz PA, Goodlett DR.

J Am Soc Mass Spectrom. 2008 Jun;19(6):891-901. doi: 10.1016/j.jasms.2008.02.005. Epub 2008 Mar 4.

40.

6th HUPO Annual World Congress - Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea.

Orchard S, Martens L, Tasman J, Binz PA, Albar JP, Hermjakob H.

Proteomics. 2008 Apr;8(7):1331-3. doi: 10.1002/pmic.200701086.

PMID:
18318010
41.

Functional specifications of an integrated proteomics information management and analysis platform.

Tsiknakis M, Grangeat P, Binz PA, Potamias G, Lisacek F, Gerfault L, Paulus C, Manakanatas D, Kritsotakis V, Kondylakis H, Perez M, Plexousakis D, Kaforou S, Kafetzopoulos D.

Conf Proc IEEE Eng Med Biol Soc. 2007;2007:6065-9.

PMID:
18003398
42.

Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France.

Orchard S, Montechi-Palazzi L, Deutsch EW, Binz PA, Jones AR, Paton N, Pizarro A, Creasy DM, Wojcik J, Hermjakob H.

Proteomics. 2007 Oct;7(19):3436-40.

PMID:
17907277
43.

The minimum information about a proteomics experiment (MIAPE).

Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK Jr, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR 3rd, Hermjakob H.

Nat Biotechnol. 2007 Aug;25(8):887-93. Review.

PMID:
17687369
44.
45.

Entering the implementation era: a report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA.

Orchard S, Taylor CF, Jones P, Montechi-Palazzo L, Binz PA, Jones AR, Pizarro A, Julian RK Jr, Hermjakob H.

Proteomics. 2007 Feb;7(3):337-9.

PMID:
17274075
46.

Exploring glycopeptide-resistance in Staphylococcus aureus: a combined proteomics and transcriptomics approach for the identification of resistance-related markers.

Scherl A, François P, Charbonnier Y, Deshusses JM, Koessler T, Huyghe A, Bento M, Stahl-Zeng J, Fischer A, Masselot A, Vaezzadeh A, Gallé F, Renzoni A, Vaudaux P, Lew D, Zimmermann-Ivol CG, Binz PA, Sanchez JC, Hochstrasser DF, Schrenzel J.

BMC Genomics. 2006 Nov 22;7:296.

47.

Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase.

Stephan C, Reidegeld KA, Hamacher M, van Hall A, Marcus K, Taylor C, Jones P, Müller M, Apweiler R, Martens L, Körting G, Chamrad DC, Thiele H, Blüggel M, Parkinson D, Binz PA, Lyall A, Meyer HE.

Proteomics. 2006 Sep;6(18):5015-29.

PMID:
16927432
48.

Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005.

Orchard S, Hermjakob H, Taylor C, Binz PA, Hoogland C, Julian R, Garavelli JS, Aebersold R, Apweiler R.

Proteomics. 2006 Feb;6(3):738-41.

PMID:
16411267
49.

5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame.

Stephan C, Hamacher M, Blüggel M, Körting G, Chamrad D, Scheer C, Marcus K, Reidegeld KA, Lohaus C, Schäfer H, Martens L, Jones P, Müller M, Auyeung K, Taylor C, Binz PA, Thiele H, Parkinson D, Meyer HE, Apweiler R.

Proteomics. 2005 Sep;5(14):3560-2.

PMID:
16167371
50.

MSight: an image analysis software for liquid chromatography-mass spectrometry.

Palagi PM, Walther D, Quadroni M, Catherinet S, Burgess J, Zimmermann-Ivol CG, Sanchez JC, Binz PA, Hochstrasser DF, Appel RD.

Proteomics. 2005 Jun;5(9):2381-4.

PMID:
15880814

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