A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides

Zhen-Lin Chen, Jia‐Ming Meng, Yong Cao, +13

Nature Communications

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

Hao Chi, Chao Liu, Hao Yang, +16

Nature Biotechnology

Comprehensive IdentificationBiochemistryMedicineNatural SciencesPeptide Library +11

pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification

Mingqi Liu, Wen‐Feng Zeng, Fang Pan, +18

Nature Communications

pNovo: <i>De novo</i> Peptide Sequencing and Identification Using HCD Spectra

Hao Chi, Rui-Xiang Sun, Bing Yang, +8

Journal of Proteome Research

Peptide SequencingMolecular BiologyPeptide ScienceIon Trap InstrumentsMolecular Characterization +14

Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states

Dan Tan, Qiang Li, Meijun Zhang, +18

eLife

Protein AssemblyMolecular BiologyProtein Conformational StatesProtein-protein Interaction NetworksProtein Folding +19

pGlyco: a pipeline for the identification of intact N-glycopeptides by using HCD- and CID-MS/MS and MS3

Wen‐Feng Zeng, Mingqi Liu, Yang Zhang, +12

Scientific Reports

GlycoproteomicsProtein GlycosylationBiochemistryIntact GlycopeptidesNatural Sciences +13

Pulsed Azidohomoalanine Labeling in Mammals (PALM) Detects Changes in Liver-Specific LKB1 Knockout Mice

Daniel B. McClatchy, Yuanhui Ma, Chao Liu, +6

Journal of Proteome Research

Proteomic TechnologyProtein ExpressionSignaling PathwayHepatotoxicityBiomarker Discovery +16

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

Zuo‐Fei Yuan, Chao Liu, Hai‐Peng Wang, +9

PROTEOMICS

pTop 1.0: A High-Accuracy and High-Efficiency Search Engine for Intact Protein Identification

Rui-Xiang Sun, Lan Luo, Long Wu, +5

Analytical Chemistry

Structural BioinformaticsMolecular BiologyProteomic TechnologyIntact Protein IdentificationProteomics +23

Modeling Protein Excited-state Structures from “Over-length” Chemical Cross-links

Yue‐He Ding, Zhou Gong, Dong Xu, +6

Journal of Biological Chemistry