Identification of modified peptides using localization-aware open search

Philosopher: a versatile toolkit for shotgun proteomics data analysis

(2020) Felipe da Veiga Leprevost et al.   NATURE METHODS

TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets

(2019) Arun Devabhaktuni et al.   NATURE BIOTECHNOLOGY

Evaluation of Chemically-Cleavable Linkers for Quantitative Mapping of Small Molecule-Cysteinome Reactivity

(2019) Adam J. Rabalski et al.   ACS Chemical Biology

Bioremediation of a Common Product of Food Processing by a Human Gut Bacterium

(2019) Ashley R. Wolf et al.   Cell Host & Microbe

Open search unveils modification patterns in formalin-fixed, paraffin-embedded thermo HCD and SCIEX TripleTOF shotgun proteomes

(2019) David L. Tabb et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome

(2019) Edward Lau et al.   Cell Reports

Enhanced Global Post-translational Modification Discovery with MetaMorpheus

(2018) Stefan K. Solntsev et al.   JOURNAL OF PROTEOME RESEARCH

Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing

(2018) Wout Bittremieux et al.   JOURNAL OF PROTEOME RESEARCH

The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest

(2018) Jakob Trendel et al.   CELL

Online Parallel Accumulation–Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer

(2018) Florian Meier et al.   MOLECULAR & CELLULAR PROTEOMICS

Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine

(2018) Hao Chi et al.   NATURE BIOTECHNOLOGY

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

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

(2017) Andy T Kong et al.   NATURE METHODS

Evaluation of different peptide fragmentation types and mass analyzers in data-dependent methods using an Orbitrap Fusion Lumos Tribrid mass spectrometer

(2017) Guadalupe Espadas et al.   PROTEOMICS

Region and cell-type resolved quantitative proteomic map of the human heart

(2017) Sophia Doll et al.   Nature Communications

PIPI: PTM-Invariant Peptide Identification Using Coding Method

(2016) Fengchao Yu et al.   JOURNAL OF PROTEOME RESEARCH

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

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

SnapShot: Histone Modifications

(2014) He Huang et al.   CELL

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

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

(2014) Sangtae Kim et al.   Nature Communications

A Proteomics Search Algorithm Specifically Designed for High-Resolution Tandem Mass Spectra

(2013) Craig D. Wenger et al.   JOURNAL OF PROTEOME RESEARCH

Comet: An open-source MS/MS sequence database search tool

(2012) Jimmy K. Eng et al.   PROTEOMICS

Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification

(2011) Minjia Tan et al.   CELL

Fast Multi-blind Modification Search through Tandem Mass Spectrometry

(2011) Seungjin Na et al.   MOLECULAR & CELLULAR PROTEOMICS

pParse: A method for accurate determination of monoisotopic peaks in high-resolution mass spectra

(2011) Zuo-F ei Yuan et al.   PROTEOMICS

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