Fengchao Yu

ChemistryBiochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 48 papers. Top paper: “IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs”.

IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs

Molecular & Cellular Proteomics(2021)10.1016/j.mcpro.2021.100077

N/A

0.949DataRank · unranked

557 citations

Sarah E. Haynes, Alexey I. Nesvizhskii, Fengchao Yu

Comprehensive proteogenomic characterization of rare kidney tumors

Cell Reports Medicine(2024)10.1016/j.xcrm.2024.101547

N/A

0.920DataRank · unranked

46 citations

Lijun Chen, Yi Hsiao, Rahul Mannan, Yuping Zhang, Jie Luo +95 more

Profiling the proteome-wide selectivity of diverse electrophiles

ChemRxiv(2021)10.26434/chemrxiv-2021-w7rss-v2

N/A

0.578DataRank · unranked

46 citations

Fengchao Yu, Patricia Z. Musacchio, Lisa Lewald, Michael Zollo, Kristina Krauskopf +10 more

Profiling the proteome-wide selectivity of diverse electrophiles

(2021)10.33774/chemrxiv-2021-w7rss-v2

N/A

0.510DataRank · unranked

29 citations

Fengchao Yu, Patricia Z. Musacchio, Lisa Lewald, Michael Zollo, Kristina Krauskopf +10 more

Chemoproteogenomic stratification of the missense variant cysteinome

Nature Communications(2024)10.1038/s41467-024-53520-x

N/A

0.460DataRank · unranked

13 citations

Katrina H. Andrews, Kristina V. Bergersen, Samuel Ofori, Fengchao Yu, Flowreen Shikwana +8 more

Proteome-Scale Tissue Mapping Using Mass Spectrometry Based on Label-Free and Multiplexed Workflows

Molecular & Cellular Proteomics(2024)10.1016/j.mcpro.2024.100841

N/A

0.425DataRank · unranked

16 citations

Jongmin Jacob Woo, Fengchao Yu, Sarah Williams, Lye Meng Markillie, Ronald Moore +8 more

PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.08.192583

N/A

0.406DataRank · unranked

14 citations

Andy T. Kong, Dmitry M. Avtonomov, Fengchao Yu, Felipe da Veiga Leprevost, Alexey I. Nesvizhski +1 more

Unraveling the glycosylated immunopeptidome with HLA-Glyco

Nature Communications(2023)10.1038/s41467-023-39270-2

N/A

0.385DataRank · unranked

12 citations

Daniel A. Polasky, Yi Hsiao, Fengchao Yu, Felipe da Veiga Leprevost, Javier A. Alfaro +3 more

Profiling the Proteome-Wide Selectivity of Diverse Electrophiles

ChemRxiv(2021)10.26434/chemrxiv.14186561

N/A

0.345DataRank · unranked

9 citations

Fengchao Yu, Patricia Z. Musacchio, Lisa Lewald, Michael Zollo, Kristina Krauskopf +10 more

diaTracer enables spectrum-centric analysis of diaPASEF proteomics data

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.05.25.595875

N/A

0.292DataRank · unranked

6 citations

Guo Ci Teo, Kevin Yang, Fengchao Yu, Alexey I. Nesvizhskii, Kai Li

Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.27.656447

N/A

0.104DataRank · unranked

1 citations

Yamei Deng, Ruo‐hong Li, Dmitry M. Avtonomov, Bo Wen, Sarah E. Haynes +5 more

Implementing the MSFragger Search Engine as a Node in Proteome Discoverer

(2022)10.1021/acs.jproteome.2c00485

N/A

0DataRank · unranked

1 citations

Sarah E. Haynes, Fengchao Yu, Alexey I. Nesvizhskii, Hui-Yin Chang

MSBooster: Improving Peptide Identification Rates using Deep Learning-Based Features

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.19.512904

N/A

0DataRank · unranked

28 citations

Fengchao Yu, Guo Ci Teo, Vadim Demichev, Markus Ralser, Alexey I. Nesvizhskii +1 more

Mining for ions: diagnostic feature detection in MS/MS spectra of post-translationally modified peptides

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.12.507594

N/A

0DataRank · unranked

8 citations

Daniel A. Polasky, Fengchao Yu, Alexey I. Nesvizhskii, Daniel Geiszler

MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.12.511963

N/A

0DataRank · unranked

4 citations

Daniel Geiszler, Fengchao Yu, Kai Li, Guo Ci Teo, Alexey I. Nesvizhskii +1 more

HLA-Glyco: A large-scale interrogation of the glycosylated immunopeptidome

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.05.519200

N/A

0DataRank · unranked

1 citations

Daniel A. Polasky, Yi Hsiao, Fengchao Yu, Felipe da Veiga Leprevost, Javier A. Alfaro +3 more

Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform

Nature Communications(2023)10.1038/s41467-023-39869-5

N/A

0DataRank · unranked

294 citations

Guo Ci Teo, Andy T. Kong, Klemens Fröhlich, Ginny Xiaohe Li, Vadim Demichev +2 more

MSBooster: improving peptide identification rates using deep learning-based features

Nature Communications(2023)10.1038/s41467-023-40129-9

N/A

0DataRank · unranked

239 citations

Fengchao Yu, Guo Ci Teo, Kai Li, Vadim Demichev, Markus Ralser +2 more

MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics

Molecular & Cellular Proteomics(2023)10.1016/j.mcpro.2023.100538

N/A

0DataRank · unranked

44 citations

Daniel Geiszler, Fengchao Yu, Kai Li, Guo Ci Teo, Alexey I. Nesvizhskii +1 more

Detecting diagnostic features in MS/MS spectra of post-translationally modified peptides

Nature Communications(2023)10.1038/s41467-023-39828-0

N/A

0DataRank · unranked

38 citations

Daniel A. Polasky, Fengchao Yu, Alexey I. Nesvizhskii, Daniel Geiszler

Evaluating Linear Ion Trap for MS3-Based Multiplexed Single-Cell Proteomics

Analytical Chemistry(2023)10.1021/acs.analchem.2c03739

N/A

0DataRank · unranked

25 citations

Fengchao Yu, James Fulcher, Sarah Williams, Kristin Engbrecht, Ronald Moore +5 more

Multi-omic stratification of the missense variant cysteinome

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.12.553095

N/A

0DataRank · unranked

13 citations

Samuel Ofori, Lisa M. Boatner, Fengchao Yu, Miranda Villanueva, Nicholas Ung +3 more

Analysis and Visualization of Quantitative Proteomics Data Using FragPipe-Analyst

Journal of Proteome Research(2024)10.1021/acs.jproteome.4c00294

N/A

0DataRank · unranked

114 citations

Haijian Zhang, Ginny Xiaohe Li, Yamei Deng, Fengchao Yu, Hossein Valipour Kahrood +4 more

An MSstats workflow for detecting differentially abundant proteins in large-scale data-independent acquisition mass spectrometry experiments with FragPipe processing

Nature Protocols(2024)10.1038/s41596-024-01000-3

N/A

0DataRank · unranked

13 citations

Mateusz Staniak, Fengchao Yu, Alexey I. Nesvizhskii, Olga Vitek, Devon Kohler

Quantitative proteome-wide O-glycoproteomics analysis with FragPipe

Analytical and Bioanalytical Chemistry(2024)10.1007/s00216-024-05382-x

N/A

0DataRank · unranked

11 citations

Lei Lü, Fengchao Yu, Kai Li, Michael R. Shortreed, Lloyd M. Smith +2 more

Analysis and visualization of quantitative proteomics data using FragPipe-Analyst

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.05.583643

N/A

0DataRank · unranked

33 citations

Haijian Zhang, Ginny Xiaohe Li, Yamei Deng, Fengchao Yu, Hossein Valipour Kahrood +4 more

MSFragger-DDA+ Enhances Peptide Identification Sensitivity with Full Isolation Window Search

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.10.12.618041

N/A

0DataRank · unranked

4 citations

Yamei Deng, Alexey I. Nesvizhskii, Fengchao Yu

Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.04.583367

N/A

0DataRank · unranked

1 citations

Jongmin Jacob Woo, Fengchao Yu, Sarah Williams, Lye Meng Markillie, Ronald Moore +8 more

diaTracer enables spectrum-centric analysis of diaPASEF proteomics data

Nature Communications(2025)10.1038/s41467-024-55448-8

N/A

0DataRank · unranked

30 citations

Guo Ci Teo, Kevin Yang, Fengchao Yu, Alexey I. Nesvizhskii, Kai Li

Profiling the proteome-wide selectivity of diverse electrophiles

Nature Chemistry(2025)10.1038/s41557-025-01902-z

N/A

0DataRank · unranked

30 citations

Fengchao Yu, Patricia Z. Musacchio, Lisa Lewald, Michael Zollo, Kristina Krauskopf +10 more

MSFragger-DDA+ enhances peptide identification sensitivity with full isolation window search

Nature Communications(2025)10.1038/s41467-025-58728-z

N/A

0DataRank · unranked

25 citations

Yamei Deng, Alexey I. Nesvizhskii, Fengchao Yu

Koina: Democratizing machine learning for proteomics research

Nature Communications(2025)10.1038/s41467-025-64870-5

N/A

0DataRank · unranked

9 citations

Kevin Yang, Tobias Kockmann, Christian Panse, Wassim Gabriel, Del Bold +20 more

Benchmarking SILAC Proteomics Workflows and Data Analysis Platforms

Molecular & Cellular Proteomics(2025)10.1016/j.mcpro.2025.100980

N/A

0DataRank · unranked

6 citations

Kevin Yang, Wan Nur Atiqah binti Mazli, Jamison Shih, Fengchao Yu, Edwin Lo +3 more

Breaking Boundaries in Histone Modification MS-Based Detection: A Tailored Search Strategy for Unrestricted Identification of Novel Epigenetic Marks

Molecular & Cellular Proteomics(2025)10.1016/j.mcpro.2025.101080

N/A

0DataRank · unranked

3 citations

Roberta Noberini, Andrea Graziadei, Daniel A. Polasky, Fengchao Yu, Alexey I. Nesvizhskii +2 more

MHC1-TIP enables single-tube multimodal immunopeptidome profiling and uncovers intratumoral heterogeneity in antigen presentation

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.07.17.664894

N/A

0DataRank · unranked

2 citations

Diana Bocaniciu, Fraser Johnson, Rick C.P. de Jong, Fengchao Yu, Vincenzo Davide Aloi +11 more

A New Detailed Mass Offset Search in MSFragger for Improved Interpretation of Complex PTMs

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.07.28.667198

N/A

0DataRank · unranked

1 citations

Fengchao Yu, Daniel A. Polasky, Alexey I. Nesvizhskii, Carolina Rojas Ramírez

PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results

Molecular & Cellular Proteomics(2020)10.1074/mcp.tir120.002216

N/A

0DataRank · unranked

151 citations

Andy T. Kong, Dmitry M. Avtonomov, Fengchao Yu, Felipe da Veiga Leprevost, Alexey I. Nesvizhskii +1 more

A modular, immunopeptidogenomic (iPepGen) analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.07.647596

N/A

0DataRank · unranked

0 citations

Reid Wagner, Katherine Do, James E. Johnson, Fengchao Yu, Tyler Jubenville +8 more

Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant

Molecular & Cellular Proteomics(2020)10.1074/mcp.tir120.002048

N/A

0DataRank · unranked

400 citations

Sarah E. Haynes, Guo Ci Teo, Dmitry M. Avtonomov, Daniel A. Polasky, Alexey I. Nesvizhskii +1 more

Identification of modified peptides using localization-aware open search

Nature Communications(2020)10.1038/s41467-020-17921-y

N/A

0DataRank · unranked

320 citations

Guo Ci Teo, Andy T. Kong, Sarah E. Haynes, Dmitry M. Avtonomov, Daniel Geiszler +2 more

Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.19.999334

N/A

0DataRank · unranked

28 citations

Sarah E. Haynes, Guo Ci Teo, Dmitry M. Avtonomov, Daniel A. Polasky, Alexey I. Nesvizhskii +1 more

Fast and Comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.18.102665

N/A

0DataRank · unranked

23 citations

Fengchao Yu, Guo Ci Teo, Alexey I. Nesvizhskii, Daniel A. Polasky

IonQuant enables accurate and sensitive label-free quantification with FDR-controlled match-between-runs

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.02.365437

N/A

0DataRank · unranked

4 citations

Sarah E. Haynes, Alexey I. Nesvizhskii, Fengchao Yu

High sensitivity dia-PASEF proteomics with DIA-NN and FragPipe

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.08.434385

N/A

0DataRank · unranked

40 citations

Fengchao Yu, Guo Ci Teo, Łukasz Szyrwiel, George Rosenberger, Jens Decker +6 more

Profiling the Proteome-Wide Selectivity of Diverse Electrophiles

ChemRxiv(2021)10.26434/chemrxiv.14186561.v1

N/A

0DataRank · unranked

36 citations

Fengchao Yu, Patricia Z. Musacchio, Lisa Lewald, Michael Zollo, Kristina Krauskopf +10 more

dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts

Nature Communications(2022)10.1038/s41467-022-31492-0

N/A

0DataRank · unranked

434 citations

Łukasz Szyrwiel, Fengchao Yu, Guo Ci Teo, George Rosenberger, Agathe Niewienda +8 more

Multiattribute Glycan Identification and FDR Control for Glycoproteomics

Molecular & Cellular Proteomics(2022)10.1016/j.mcpro.2022.100205

N/A

0DataRank · unranked

52 citations

Daniel Geiszler, Fengchao Yu, Alexey I. Nesvizhskii, Daniel A. Polasky

SP3-Enabled Rapid and High Coverage Chemoproteomic Identification of Cell-State–Dependent Redox-Sensitive Cysteines

Molecular & Cellular Proteomics(2022)10.1016/j.mcpro.2022.100218

N/A

0DataRank · unranked

44 citations

Tianyang Yan, Fengchao Yu, Alexander W. Sun, Miranda Villanueva, Alexey I. Nesvizhskii +2 more