Simple, efficient and thorough shotgun proteomic analysis with PatternLab V

Proteogenomic Analysis Reveals Proteins Involved in the First Step of Adipogenesis in Human Adipose-Derived Stem Cells

(2021) Bernardo Bonilauri et al.   Stem Cells International

Repeat-Preserving Decoy Database for False Discovery Rate Estimation in Peptide Identification

(2020) Johra Muhammad Moosa et al.   JOURNAL OF PROTEOME RESEARCH

Extending Comet for Global Amino Acid Variant and Post‐Translational Modification Analysis using the PSI Extended FASTA Format (PEFF)

(2020) Jimmy K. Eng et al.   PROTEOMICS

Methylation of Salmonella Typhimurium flagella promotes bacterial adhesion and host cell invasion

(2020) Julia A. Horstmann et al.   Nature Communications

Essential dynamic interdependence of FtsZ and SepF for Z-ring and septum formation in Corynebacterium glutamicum

(2020) Adrià Sogues et al.   Nature Communications

RawVegetable – A data assessment tool for proteomics and cross-linking mass spectrometry experiments

(2020) Louise U. Kurt et al.   Journal of Proteomics

Mixed-Data Acquisition: Next-Generation Quantitative Proteomics Data Acquisition

(2020) Marlon D.M. Santos et al.   Journal of Proteomics

A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics

(2019) Marlon D.M. Santos et al.   Journal of Proteomics

Comparing intestinal versus diffuse gastric cancer using a PEFF-oriented proteomic pipeline

(2018) Helisa Helena Wippel et al.   Journal of Proteomics

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver

(2018) Arun Prasad Pandurangan et al.   NUCLEIC ACIDS RESEARCH

A non-canonical BRD9-containing BAF chromatin remodeling complex regulates naive pluripotency in mouse embryonic stem cells

(2018) Jovylyn Gatchalian et al.   Nature Communications

The Null-Test for peptide identification algorithm in Shotgun proteomics

(2017) Shu-Rong Zhang et al.   Journal of Proteomics

The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics

(2017) Juan Antonio Vizcaíno et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative, multiplexed workflow for deep analysis of human blood plasma and biomarker discovery by mass spectrometry

(2017) Hasmik Keshishian et al.   Nature Protocols

Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification

(2016) Honglan Li et al.   BMC GENOMICS

MS1-Based Label-Free Proteomics Using a Quadrupole Orbitrap Mass Spectrometer

(2015) Tali Shalit et al.   JOURNAL OF PROTEOME RESEARCH

Reevaluating the Trypanosoma cruzi proteomic map: The shotgun description of bloodstream trypomastigotes

(2015) Giselle Villa Flor Brunoro et al.   Journal of Proteomics

A scoring model for phosphopeptide site localization and its impact on the question of whether to use MSA

(2015) Juliana de S. da G. Fischer et al.   Journal of Proteomics

ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity

(2015) T. Xu et al.   Journal of Proteomics

A Deeper Look into Comet—Implementation and Features

(2015) Jimmy K. Eng et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Novor: Real-Time Peptide de Novo Sequencing Software

(2015) Bin Ma   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

One-hour proteome analysis in yeast

(2015) Alicia L Richards et al.   Nature Protocols

Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0

(2015) Paulo C Carvalho et al.   Nature Protocols

PepExplorer: A Similarity-driven Tool for Analyzingde NovoSequencing Results

(2014) Felipe V. Leprevost et al.   MOLECULAR & CELLULAR PROTEOMICS

On best practices in the development of bioinformatics software

(2014) Felipe da Veiga Leprevost et al.   Frontiers in Genetics

Improving the TFold test for differential shotgun proteomics

(2012) P. C. Carvalho et al.   BIOINFORMATICS

Toward objective evaluation of proteomic algorithms

(2012) John R Yates et al.   NATURE METHODS

Update on activities at the Universal Protein Resource (UniProt) in 2013

(2012)   NUCLEIC ACIDS RESEARCH

Search engine processor: Filtering and organizing peptide spectrum matches

(2012) Paulo C. Carvalho et al.   PROTEOMICS

A Face in the Crowd: Recognizing Peptides Through Database Search

(2011) Jimmy K. Eng et al.   MOLECULAR & CELLULAR PROTEOMICS

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Can the false-discovery rate be misleading?

(2011) Rodrigo Barboza et al.   PROTEOMICS

Analyzing marginal cases in differential shotgun proteomics

(2010) Paulo C. Carvalho et al.   BIOINFORMATICS

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

Chemo-Resistant Protein Expression Pattern of Glioblastoma Cells (A172) to Perillyl Alcohol

(2010) Juliana de Saldanha da Gama Fischer et al.   JOURNAL OF PROTEOME RESEARCH

mzML—a Community Standard for Mass Spectrometry Data

(2010) Lennart Martens et al.   MOLECULAR & CELLULAR PROTEOMICS

Identifying differences in protein expression levels by spectral counting and feature selection

(2009) P.C. Carvalho et al.   GENETICS AND MOLECULAR RESEARCH

PatternLab for proteomics: a tool for differential shotgun proteomics

(2008) Paulo C Carvalho et al.   BMC BIOINFORMATICS