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Items: 29

1.

Structural Analysis of Hippocampal Kinase Signal Transduction.

McClatchy DB, Yu NK, Martínez-Bartolomé S, Patel R, Pelletier AR, Lavalle-Adam M, Powell SB, Roberto M, Yates JR.

ACS Chem Neurosci. 2018 Aug 13. doi: 10.1021/acschemneuro.8b00284. [Epub ahead of print]

PMID:
30053369
2.

Deducing the presence of proteins and proteoforms in quantitative proteomics.

Bamberger C, Martínez-Bartolomé S, Montgomery M, Pankow S, Hulleman JD, Kelly JW, Yates JR 3rd.

Nat Commun. 2018 Jun 13;9(1):2320. doi: 10.1038/s41467-018-04411-5.

3.

PACOM: A Versatile Tool for Integrating, Filtering, Visualizing, and Comparing Multiple Large Mass Spectrometry Proteomics Data Sets.

Martínez-Bartolomé S, Medina-Aunon JA, López-García MÁ, González-Tejedo C, Prieto G, Navajas R, Salazar-Donate E, Fernández-Costa C, Yates JR 3rd, Albar JP.

J Proteome Res. 2018 Apr 6;17(4):1547-1558. doi: 10.1021/acs.jproteome.7b00858. Epub 2018 Mar 28.

PMID:
29558135
4.

Increased proteomic complexity in Drosophila hybrids during development.

Bamberger C, Martínez-Bartolomé S, Montgomery M, Lavallée-Adam M, Yates JR 3rd.

Sci Adv. 2018 Feb 7;4(2):eaao3424. doi: 10.1126/sciadv.aao3424. eCollection 2018 Feb.

5.

Amyloid Accumulation Drives Proteome-wide Alterations in Mouse Models of Alzheimer's Disease-like Pathology.

Savas JN, Wang YZ, DeNardo LA, Martinez-Bartolome S, McClatchy DB, Hark TJ, Shanks NF, Cozzolino KA, Lavallée-Adam M, Smukowski SN, Park SK, Kelly JW, Koo EH, Nakagawa T, Masliah E, Ghosh A, Yates JR 3rd.

Cell Rep. 2017 Nov 28;21(9):2614-2627. doi: 10.1016/j.celrep.2017.11.009.

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.

∆F508 CFTR interactome remodelling promotes rescue of cystic fibrosis.

Pankow S, Bamberger C, Calzolari D, Martínez-Bartolomé S, Lavallée-Adam M, Balch WE, Yates JR 3rd.

Nature. 2015 Dec 24;528(7583):510-6. doi: 10.1038/nature15729. Epub 2015 Nov 30.

8.

Pulsed Azidohomoalanine Labeling in Mammals (PALM) Detects Changes in Liver-Specific LKB1 Knockout Mice.

McClatchy DB, Ma Y, Liu C, Stein BD, Martínez-Bartolomé S, Vasquez D, Hellberg K, Shaw RJ, Yates JR 3rd.

J Proteome Res. 2015 Nov 6;14(11):4815-22. doi: 10.1021/acs.jproteome.5b00653. Epub 2015 Oct 26.

9.

From raw data to biological discoveries: a computational analysis pipeline for mass spectrometry-based proteomics.

Lavallée-Adam M, Park SK, Martínez-Bartolomé S, He L, Yates JR 3rd.

J Am Soc Mass Spectrom. 2015 Nov;26(11):1820-6. doi: 10.1007/s13361-015-1161-7. Epub 2015 May 22.

10.

Multicenter experiment for quality control of peptide-centric LC-MS/MS analysis - A longitudinal performance assessment with nLC coupled to orbitrap MS analyzers.

Campos A, Díaz R, Martínez-Bartolomé S, Sierra J, Gallardo O, Sabidó E, López-Lucendo M, Ignacio Casal J, Pasquarello C, Scherl A, Chiva C, Borras E, Odena A, Elortza F, Azkargorta M, Ibarrola N, Canals F, Albar JP, Oliveira E.

J Proteomics. 2015 Sep 8;127(Pt B):264-74. doi: 10.1016/j.jprot.2015.05.012. Epub 2015 May 14.

PMID:
25982386
11.

Quantitative Proteomics of Human Fibroblasts with I1061T Mutation in Niemann-Pick C1 (NPC1) Protein Provides Insights into the Disease Pathogenesis.

Rauniyar N, Subramanian K, Lavallée-Adam M, Martínez-Bartolomé S, Balch WE, Yates JR 3rd.

Mol Cell Proteomics. 2015 Jul;14(7):1734-49. doi: 10.1074/mcp.M114.045609. Epub 2015 Apr 14.

12.

Global quantitative analysis of phosphorylation underlying phencyclidine signaling and sensorimotor gating in the prefrontal cortex.

McClatchy DB, Savas JN, Martínez-Bartolomé S, Park SK, Maher P, Powell SB, Yates JR 3rd.

Mol Psychiatry. 2016 Feb;21(2):205-15. doi: 10.1038/mp.2015.41. Epub 2015 Apr 14.

13.

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.

14.

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.

15.

Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome.

Segura V, Medina-Aunon JA, Mora MI, Martínez-Bartolomé S, Abian J, Aloria K, Antúnez O, Arizmendi JM, Azkargorta M, Barceló-Batllori S, Beaskoetxea J, Bech-Serra JJ, Blanco F, Monteiro MB, Cáceres D, Canals F, Carrascal M, Casal JI, Clemente F, Colomé N, Dasilva N, Díaz P, Elortza F, Fernández-Puente P, Fuentes M, Gallardo O, Gharbi SI, Gil C, González-Tejedo C, Hernáez ML, Lombardía M, Lopez-Lucendo M, Marcilla M, Mato JM, Mendes M, Oliveira E, Orera I, Pascual-Montano A, Prieto G, Ruiz-Romero C, Sánchez del Pino MM, Tabas-Madrid D, Valero ML, Vialas V, Villanueva J, Albar JP, Corrales FJ.

J Proteome Res. 2014 Jan 3;13(1):158-72. doi: 10.1021/pr400721r. Epub 2013 Nov 5.

PMID:
24138474
16.

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
17.

Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML.

Ghali F, Krishna R, Lukasse P, Martínez-Bartolomé S, Reisinger F, Hermjakob H, Vizcaíno JA, Jones AR.

Mol Cell Proteomics. 2013 Nov;12(11):3026-35. doi: 10.1074/mcp.O113.029777. Epub 2013 Jun 28.

18.

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
19.

Spanish human proteome project: dissection of chromosome 16.

Segura V, Medina-Aunon JA, Guruceaga E, Gharbi SI, González-Tejedo C, Sánchez del Pino MM, Canals F, Fuentes M, Casal JI, Martínez-Bartolomé S, Elortza F, Mato JM, Arizmendi JM, Abian J, Oliveira E, Gil C, Vivanco F, Blanco F, Albar JP, Corrales FJ.

J Proteome Res. 2013 Jan 4;12(1):112-22. doi: 10.1021/pr300898u. Epub 2012 Dec 12.

PMID:
23234512
20.

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
21.

The ProteoRed MIAPE web toolkit: a user-friendly framework to connect and share proteomics standards.

Medina-Aunon JA, Martínez-Bartolomé S, López-García MA, Salazar E, Navajas R, Jones AR, Paradela A, Albar JP.

Mol Cell Proteomics. 2011 Oct;10(10):M111.008334. doi: 10.1074/mcp.M111.008334.

22.

A DIGE study on the effects of salbutamol on the rat muscle proteome - an exemplar of best practice for data sharing in proteomics.

Kenyani J, Medina-Aunon JA, Martinez-Bartolomé S, Albar JP, Wastling JM, Jones AR.

BMC Res Notes. 2011 Mar 28;4:86. doi: 10.1186/1756-0500-4-86.

23.

The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative.

Gibson F, Hoogland C, Martinez-Bartolomé S, Medina-Aunon JA, Albar JP, Babnigg G, Wipat A, Hermjakob H, Almeida JS, Stanislaus R, Paton NW, Jones AR.

Proteomics. 2010 Sep;10(17):3073-81. doi: 10.1002/pmic.201000120.

24.

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
25.

Relevance of proteomics standards for the ProteoRed Spanish organization.

Martinez-Bartolome S, Blanco F, Albar JP.

J Proteomics. 2010 Apr 18;73(6):1061-6. doi: 10.1016/j.jprot.2010.01.006. Epub 2010 Jan 25. Review.

PMID:
20097317
26.

Semi-automatic tool to describe, store and compare proteomics experiments based on MIAPE compliant reports.

Martínez-Bartolomé S, Medina-Aunon JA, Jones AR, Albar JP.

Proteomics. 2010 Mar;10(6):1256-60. doi: 10.1002/pmic.200900367.

PMID:
20077409
27.

Properties of average score distributions of SEQUEST: the probability ratio method.

Martínez-Bartolomé S, Navarro P, Martín-Maroto F, López-Ferrer D, Ramos-Fernández A, Villar M, García-Ruiz JP, Vázquez J.

Mol Cell Proteomics. 2008 Jun;7(6):1135-45. doi: 10.1074/mcp.M700239-MCP200. Epub 2008 Feb 25.

28.

Quantitative proteomics using 16O/18O labeling and linear ion trap mass spectrometry.

López-Ferrer D, Ramos-Fernández A, Martínez-Bartolomé S, García-Ruiz P, Vázquez J.

Proteomics. 2006 Apr;6 Suppl 1:S4-11.

PMID:
16534745
29.

Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST.

López-Ferrer D, Martínez-Bartolomé S, Villar M, Campillos M, Martín-Maroto F, Vázquez J.

Anal Chem. 2004 Dec 1;76(23):6853-60.

PMID:
15571333

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