Publications by authors named "Daniel Lopez-Ferrer"

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Precision-Engineered Nano-Electrospray Emitters Enhance Ionization Efficiency for Trap-Assisted Direct Infusion Mass Spectrometry: Application in Plasma Alzheimer's Disease Proteomics.
Ana Montero-Calle, Adolfo Fernández Gómez de Enterría, Daniel López-Ferrer, Rodrigo Barderas

J Proteome Res· July 2025

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INFERYS rescoring: Boosting peptide identifications and scoring confidence of database search results.
Daniel P Zolg, Siegfried Gessulat, Carmen Paschke, Michael Graber, Magnus Rathke-Kuhnert, Daniel Lopez-Ferrer

Rapid Commun Mass Spectrom· May 2025

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SPINDLY mediates O-fucosylation of hundreds of proteins and sugar-dependent growth in Arabidopsis.
Yang Bi, Ruben Shrestha, Zhenzhen Zhang, Chuan-Chih Hsu, Andres V Reyes, Daniel Lopez-Ferrer

Plant Cell· April 2023

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Charge-based interactions through peptide position 4 drive diversity of antigen presentation by human leukocyte antigen class I molecules.
Kyle R Jackson, Dinler A Antunes, Amjad H Talukder, Ariana R Maleki, Kano Amagai, Daniel Lopez-Ferrer

PNAS Nexus· July 2022

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Real-Time Search-Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics.
Benjamin Furtwängler, Nil Üresin, Khatereh Motamedchaboki, Romain Huguet, Daniel Lopez-Ferrer

Mol Cell Proteomics· April 2022

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High-Density, Targeted Monitoring of Tyrosine Phosphorylation Reveals Activated Signaling Networks in Human Tumors.
Lauren E Stopfer, Cameron T Flower, Aaron S Gajadhar, Bhavin Patel, Sebastien Gallien, Daniel Lopez-Ferrer

Cancer Res· May 2021

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Rapid Shotgun Phosphoproteomics Analysis.
Mónica Carrera, Benito Cañas, Daniel Lopez-Ferrer

Methods Mol Biol· April 2021

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Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell.
Yongzheng Cong, Khatereh Motamedchaboki, Santosh A Misal, Yiran Liang, Amanda J Guise, Daniel Lopez-Ferrer

Chem Sci· November 2020

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Dynamic metabolic reprogramming in dendritic cells: An early response to influenza infection that is essential for effector function.
Svetlana Rezinciuc, Lavanya Bezavada, Azadeh Bahadoran, Susu Duan, Ruoning Wang, Daniel Lopez-Ferrer

PLoS Pathog· October 2020

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Transcriptomic and proteomic profiling of glial versus neuronal Dube3a overexpression reveals common molecular changes in gliopathic epilepsies.
Kevin A Hope, Daniel Johnson, P Winston Miller, Daniel Lopez-Ferrer, David Kakhniashvili

Neurobiol Dis· July 2020

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Top-Down Proteomics Applied to Human Cerebrospinal Fluid.
Marina Gay, Ester Sánchez-Jiménez, Laura Villarreal, Mar Vilanova, Romain Huguet

Methods Mol Biol· May 2020

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Improved Single-Cell Proteome Coverage Using Narrow-Bore Packed NanoLC Columns and Ultrasensitive Mass Spectrometry.
Yongzheng Cong, Yiran Liang, Khatereh Motamedchaboki, Romain Huguet, Thy Truong, Daniel Lopez-Ferrer

Anal Chem· February 2020

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Fast Global Phosphoproteome Profiling of Jurkat T Cells by HIFU-TiO-SCX-LC-MS/MS.
Mónica Carrera, Benito Cañas, Daniel Lopez-Ferrer

Anal Chem· September 2017

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Evaluation of selected binding domains for the analysis of ubiquitinated proteomes.
Ernesto S Nakayasu, Charles Ansong, Joseph N Brown, Feng Yang, Daniel Lopez-Ferrer

J Am Soc Mass Spectrom· August 2013

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IMSPeptider: A computational peptide collision cross-section area calculator based on a novel molecular dynamics simulation protocol.
Ranieri V de Carvalho, Daniel Lopez-Ferrer, Katia S Guimarães, Roberto D Lins

J Comput Chem· July 2013

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Aging enhances the production of reactive oxygen species and bactericidal activity in peritoneal macrophages by upregulating classical activation pathways.
Heather S Smallwood, Daniel López-Ferrer, Thomas C Squier

Biochemistry· November 2011

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Fast monitoring of species-specific peptide biomarkers using high-intensity-focused-ultrasound-assisted tryptic digestion and selected MS/MS ion monitoring.
Mónica Carrera, Benito Cañas, Daniel López-Ferrer, Carmen Piñeiro, Jesús Vázquez

Anal Chem· July 2011

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Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells.
Yuexi Wang, Feng Yang, Marina A Gritsenko, Yingchun Wang, Therese Clauss, Daniel Lopez-Ferrer

Proteomics· May 2011

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Pressurized pepsin digestion in proteomics: an automatable alternative to trypsin for integrated top-down bottom-up proteomics.
Daniel López-Ferrer, Konstantinos Petritis, Errol W Robinson, Kim K Hixson, Zhixin Tian

Mol Cell Proteomics· February 2011

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Rapid and efficient protein digestion using trypsin-coated magnetic nanoparticles under pressure cycles.
Byoungsoo Lee, Daniel Lopez-Ferrer, Byoung Chan Kim, Hyon Bin Na, Yong Il Park

Proteomics· January 2011

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Robust trypsin coating on electrospun polymer nanofibers in rigorous conditions and its uses for protein digestion.
Hye-Kyung Ahn, Byoung Chan Kim, Seung-Hyun Jun, Mun Seock Chang, Daniel Lopez-Ferrer

Biotechnol Bioeng· December 2010

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Characterization of macaque pulmonary fluid proteome during monkeypox infection: dynamics of host response.
Joseph N Brown, Ryan D Estep, Daniel Lopez-Ferrer, Heather M Brewer, Theresa R Clauss

Mol Cell Proteomics· December 2010

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Trypsin coatings on electrospun and alcohol-dispersed polymer nanofibers for a trypsin digestion column.
Seung-Hyun Jun, Mun Seock Chang, Byoung Chan Kim, Hyo Jin An, Daniel Lopez-Ferrer

Anal Chem· September 2010

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Proteomic and physiological responses of Kineococcus radiotolerans to copper.
Christopher E Bagwell, Kim K Hixson, Charles E Milliken, Daniel Lopez-Ferrer, Karl K Weitz

PLoS One· August 2010

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Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models.
Nathan E Lewis, Kim K Hixson, Tom M Conrad, Joshua A Lerman, Pep Charusanti, Daniel Lopez-Ferrer

Mol Syst Biol· July 2010

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