List of works by Nuno Bandeira

A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria

scientific article published on 06 January 2021

A high-stringency blueprint of the human proteome

scientific article published on 16 October 2020

A proteomics sample metadata representation for multiomics integration and big data analysis

scientific article published in 2021

A turn-key approach for large-scale identification of complex posttranslational modifications

scientific article published on 29 January 2014

Accurate mass spectrometry based protein quantification via shared peptides

scientific article published on 13 March 2012

Advancing next-generation proteomics through computational research.

scientific article published on 31 May 2011

Assembling the Community-Scale Discoverable Human Proteome

scientific article published on 29 August 2018

Automated de novo protein sequencing of monoclonal antibodies

scientific article published on December 2008

Automated genome mining of ribosomal peptide natural products

scientific article

Clostridiolysin S, a post-translationally modified biotoxin from Clostridium botulinum

scientific article

Clustering millions of tandem mass spectra

scientific article published on 8 December 2007

Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra

scientific article published on 03 February 2014

Connecting Chemotypes and Phenotypes of Cultured Marine Microbial Assemblages by Imaging Mass Spectrometry

scientific article published on 05 May 2011

Connecting chemotypes and phenotypes of cultured marine microbial assemblages by imaging mass spectrometry.

scientific article published on 13 May 2011

Cover Picture: Connecting Chemotypes and Phenotypes of Cultured Marine Microbial Assemblages by Imaging Mass Spectrometry (Angew. Chem. Int. Ed. 26/2011)

scientific article published on 11 May 2011

Data Independent Acquisition analysis in ProHits 4.0.

scientific article

Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future

scientific article published on 10 March 2021

De Novo MS/MS Sequencing of Native Human Antibodies

scientific article

Dereplication and de novo sequencing of nonribosomal peptides

scientific article published on 13 July 2009

Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae

scientific article

Discovering and linking public omics data sets using the Omics Discovery Index.

scientific article

Expanding proteome coverage with orthogonal-specificity α-lytic proteases

scientific article published on 14 January 2014

Expanding the use of spectral libraries in proteomics

False discovery rates in spectral identification

scientific article

Feature-based molecular networking in the GNPS analysis environment

scientific article published on 24 August 2020

GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser

scientific article published on 03 December 2021

Gapped spectral dictionaries and their applications for database searches of tandem mass spectra

scientific article

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0.

scientific article published on 21 October 2019

Identifying Urinary and Serum Exosome Biomarkers for Radiation Exposure Using a Data Dependent Acquisition and SWATH-MS Combined Workflow

scientific article

Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project

scientific article published on 09 November 2020

Interactome Rewiring Following Pharmacological Targeting of BET Bromodomains

scientific article published on 13 December 2018

Interkingdom metabolic transformations captured by microbial imaging mass spectrometry

scientific article

Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides

scientific article published on June 2009

Lifestyle chemistries from phones for individual profiling

scientific article (publication date: 29 November 2016)

MS/MS networking guided analysis of molecule and gene cluster families.

scientific article published on 24 June 2013

MSPLIT-DIA: sensitive peptide identification for data-independent acquisition

scientific article

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats.

scientific article published on 12 October 2016

Mass spectral molecular networking of living microbial colonies

scientific article

Mass spectrometry searches using MASST

scientific article published on 01 January 2020

MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets

scientific article published on 14 September 2020

MixGF: spectral probabilities for mixture spectra from more than one peptide

scientific article

Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis

scientific article published on 24 September 2019

Molecular cartography of the human skin surface in 3D

scientific article published on 30 March 2015

Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species ⬇️

scientific article published on 9 April 2015

Multi-spectra peptide sequencing and its applications to multistage mass spectrometry

scientific article

NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters

NPOmix: a machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters

scientific article published on 6 October 2021

NeuroPedia: neuropeptide database and spectral library

scientific article

Neuropeptidomic components generated by proteomic functions in secretory vesicles for cell-cell communication

scientific article

Neuropeptidomics Mass Spectrometry Reveals Signaling Networks Generated by Distinct Protease Pathways in Human Systems

scientific article published on 19 October 2015

Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome

article

Omics Discovery Index - Discovering and Linking Public Omics Datasets

Open Science Resources for the Mass Spectrometry-Based Analysis of SARS-CoV-2

scientific article published in 2021

Peptide identification by database search of mixture tandem mass spectra

scientific article published on 23 August 2011

Peptide identification by tandem mass spectrometry with alternate fragmentation modes

scientific article

Peptide identification from mixture tandem mass spectra

scientific article

Protein identification by spectral networks analysis

scholarly article

ProteinExplorer: A Repository-Scale Resource for Exploration of Protein Detection in Public Mass Spectrometry Data Sets

scientific article published on 15 October 2018

Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture.

scientific article published on 31 October 2013

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

scientific article (publication date: March 2014)

Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms

scientific article published on 15 March 2022

Quantitative proteomics reveal ATM kinase-dependent exchange in DNA damage response complexes

scientific article

Quick-start infrastructure for untargeted metabolomics analysis in GNPS

scientific article published in 2021

ReDU: a framework to find and reanalyze public mass spectrometry data

scientific article published on 17 August 2020

Reproducible Molecular Networking Of Untargeted Mass Spectrometry Data Using GNPS

scholarly article published 8 August 2019

Reproducible molecular networking of untargeted mass spectrometry data using GNPS

scientific article published on 13 May 2020

Research on The Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, according to the HUPO Human Proteome Project

scientific article published on 15 September 2020

SPLASH, a hashed identifier for mass spectra ⬇️

scientific article

Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/ETD) from overlapping peptides

scientific article

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

scientific article (publication date: 9 August 2016)

Shotgun protein sequencing by tandem mass spectra assembly

scientific article published in December 2004

Shotgun protein sequencing with meta-contig assembly

scientific article

Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins.

scientific article published on 19 April 2007

Significance estimation for large scale metabolomics annotations by spectral matching

scientific article published on 14 November 2017

Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra

scientific article

Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra

scientific article published on 14 August 2008

Spectral library generating function for assessing spectrum-spectrum match significance

scientific article

Spectral profiles, a novel representation of tandem mass spectra and their applications for de novo peptide sequencing and identification

scientific article published on 02 March 2009

SweetNET: A Bioinformatics Workflow for Glycopeptide MS/MS Spectral Analysis

scientific article published on 11 July 2016

Target-decoy approach and false discovery rate: when things may go wrong

scientific article published on 5 May 2011

The ProteomeXchange consortium at 10 years: 2023 update

scientific article published on 12 November 2022

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition

scientific article

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics

scientific article published on 01 January 2020

The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search

scientific article

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience

scientific article

The spectral networks paradigm in high throughput mass spectrometry

scientific article published on October 2012

Three Dimensional Cartography of Microbiome and Metabolome Data onto Radiological Images of the Human Lung

scientific article published in 2018

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung

scientific article published on 17 October 2017

Titelbild: Connecting Chemotypes and Phenotypes of Cultured Marine Microbial Assemblages by Imaging Mass Spectrometry (Angew. Chem. 26/2011)

scientific article published on 11 May 2011

Universal Spectrum Identifier for mass spectra

scientific article published on 28 June 2021

Untargeted Mass Spectrometry-Based Metabolomics Tracks Molecular Changes in Raw and Processed Foods and Beverages

scientific article published on 15 June 2018

Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages

scientific article published on 30 July 2019

microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data ⬇️

scientific article published in 2024

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