Spectral prediction features as a solution for the search space size problem in proteogenomics

The hunt for sORFs: A multidisciplinary strategy

(2020) Marlies Peeters et al.   EXPERIMENTAL CELL RESEARCH

PROTEOFORMER 2.0: further developments in the ribosome profiling-assisted proteogenomic hunt for new proteoforms

(2019) Steven Verbruggen et al.   MOLECULAR & CELLULAR PROTEOMICS

Increasing the accuracy of nanopore DNA sequencing using a time-varying cross membrane voltage

(2019) Matthew T. Noakes et al.   NATURE BIOTECHNOLOGY

Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning

(2019) Siegfried Gessulat et al.   NATURE METHODS

High-quality MS/MS spectrum prediction for data-dependent and data-independent acquisition data analysis

(2019) Shivani Tiwary et al.   NATURE METHODS

Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques

(2019) Ralf Gabriels et al.   NUCLEIC ACIDS RESEARCH

CharmeRT: Boosting Peptide Identifications by Chimeric Spectra Identification and Retention Time Prediction

(2018) Viktoria Dorfer et al.   JOURNAL OF PROTEOME RESEARCH

ProteomeTools: Systematic characterization of 21 post-translational protein modifications by LC-MS/MS using synthetic peptides

(2018) Daniel Paul Zolg et al.   MOLECULAR & CELLULAR PROTEOMICS

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

mQC: A post-mapping data exploration tool for ribosome profiling

(2018) Steven Verbruggen et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes

(2018) Marie A Brunet et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-wide measurement of translation by ribosome profiling

(2017) Nicholas J. McGlincy et al.   METHODS

Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify

(2017) Malgorzata A. Komor et al.   MOLECULAR & CELLULAR PROTEOMICS

Building ProteomeTools based on a complete synthetic human proteome

(2017) Daniel P Zolg et al.   NATURE METHODS

An update on sORFs.org: a repository of small ORFs identified by ribosome profiling

(2017) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

Nanopore DNA Sequencing and Genome Assembly on the International Space Station

(2017) Sarah L. Castro-Wallace et al.   Scientific Reports

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0

(2016) Matthew The et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments

(2014) Bo Wen et al.   BIOINFORMATICS

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations

(2014) Gloria M Sheynkman et al.   BMC GENOMICS

Nanopore Sequencing: From Imagination to Reality

(2014) H. Bayley   CLINICAL CHEMISTRY

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

(2014) Jeroen Crappé et al.   NUCLEIC ACIDS RESEARCH

A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites

(2014) Alexander Koch et al.   PROTEOMICS

Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data

(2014) Sunghee Woo et al.   PROTEOMICS

Leveraging the complementary nature of RNA-Seq and shotgun proteomics data

(2014) Xiaojing Wang et al.   PROTEOMICS

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

MS2PIP: a tool for MS/MS peak intensity prediction

(2013) Sven Degroeve et al.   BIOINFORMATICS

Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions

(2013) Jainab Khatun et al.   BMC GENOMICS

Proteogenomic Database Construction Driven from Large Scale RNA-seq Data

(2013) Sunghee Woo et al.   JOURNAL OF PROTEOME RESEARCH

Up-regulation of SUMO1 pseudogene 3 (SUMO1P3) in gastric cancer and its clinical association

(2013) Danyi Mei et al.   MEDICAL ONCOLOGY

Deep Proteome Coverage Based on Ribosome Profiling Aids Mass Spectrometry-based Protein and Peptide Discovery and Provides Evidence of Alternative Translation Products and Near-cognate Translation Initiation Events*

(2013) Gerben Menschaert et al.   MOLECULAR & CELLULAR PROTEOMICS

A glimpse into past, present, and future DNA sequencing

(2013) Marcos Morey et al.   MOLECULAR GENETICS AND METABOLISM

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics

(2013) Rui M M Branca et al.   NATURE METHODS

Proteoform: a single term describing protein complexity

(2013) Lloyd M Smith et al.   NATURE METHODS

Direct Detection of Alternative Open Reading Frames Translation Products in Human Significantly Expands the Proteome

(2013) Benoît Vanderperre et al.   PLoS One

Addressing Statistical Biases in Nucleotide-Derived Protein Databases for Proteogenomic Search Strategies

(2012) Paul Blakeley et al.   JOURNAL OF PROTEOME RESEARCH

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

(2012) Nicholas T Ingolia et al.   Nature Protocols

Analysis of the Resolution Limitations of Peptide Identification Algorithms

(2011) Niklaas Colaert et al.   JOURNAL OF PROTEOME RESEARCH

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Efficient Marginalization to Compute Protein Posterior Probabilities from Shotgun Mass Spectrometry Data

(2010) Oliver Serang et al.   JOURNAL OF PROTEOME RESEARCH

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE