mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection

Machine Learning Strategy That Leverages Large Data sets to Boost Statistical Power in Small-Scale Experiments

(2020) William E. Fondrie et al.   JOURNAL OF PROTEOME RESEARCH

Transfer posterior error probability estimation for peptide identification

(2020) Xinpei Yi et al.   BMC BIOINFORMATICS

Identification of modified peptides using localization-aware open search

(2020) Fengchao Yu et al.   Nature Communications

ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion

(2019) Niels Hulstaert et al.   JOURNAL OF PROTEOME RESEARCH

Combining high resolution and exact calibration to boost statistical power: A well-calibrated score function for high-resolution MS2 data

(2018) Andy Lin et al.   JOURNAL OF PROTEOME RESEARCH

Assembling the Community-Scale Discoverable Human Proteome

(2018) Mingxun Wang et al.   Cell Systems

Integrated identification and quantification error probabilities for shotgun proteomics

(2018) Matthew The et al.   MOLECULAR & CELLULAR PROTEOMICS

Param-Medic: A Tool for Improving MS/MS Database Search Yield by Optimizing Parameter Settings

(2017) Damon H. May et al.   JOURNAL OF PROTEOME RESEARCH

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

(2017) Andy T Kong et al.   NATURE METHODS

Optimization of Search Engines and Postprocessing Approaches to Maximize Peptide and Protein Identification for High-Resolution Mass Data

(2015) Chengjian Tu et al.   JOURNAL OF PROTEOME RESEARCH

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

(2015) Mikhail M. Savitski et al.   MOLECULAR & CELLULAR PROTEOMICS

A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides

(2015) Joel M Chick et al.   NATURE BIOTECHNOLOGY

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins

(2014) Katharina Kramer et al.   NATURE METHODS

A cross-validation scheme for machine learning algorithms in shotgun proteomics

(2012) Viktor Granholm et al.   BMC BIOINFORMATICS

Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra

(2011) Benjamin J. Diament et al.   JOURNAL OF PROTEOME RESEARCH

qvality: non-parametric estimation of q-values and posterior error probabilities

(2009) Lukas Käll et al.   BIOINFORMATICS

Improvements to the Percolator Algorithm for Peptide Identification from Shotgun Proteomics Data Sets

(2009) Marina Spivak et al.   JOURNAL OF PROTEOME RESEARCH

ProteoWizard: open source software for rapid proteomics tools development

(2008) Darren Kessner et al.   BIOINFORMATICS

Microarrays, Empirical Bayes and the Two-Groups Model

(2008) Bradley Efron   STATISTICAL SCIENCE