[HTML][HTML] Acquisition and analysis of DIA-based proteomic data: A comprehensive survey in 2023

R Lou, W Shui - Molecular & Cellular Proteomics, 2024‏ - Elsevier
Data-independent acquisition (DIA) mass spectrometry (MS) has emerged as a powerful
technology for high-throughput, accurate, and reproducible quantitative proteomics. This …

Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP

A Leduc, L Khoury, J Cantlon, S Khan, N Slavov - Nature protocols, 2024‏ - nature.com
Single-cell proteomics by mass spectrometry (MS) allows the quantification of proteins with
high specificity and sensitivity. To increase its throughput, we developed nano-proteomic …

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

F Yu, GC Teo, AT Kong, K Fröhlich, GX Li… - Nature …, 2023‏ - nature.com
Liquid chromatography (LC) coupled with data-independent acquisition (DIA) mass
spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we …

Immunopeptidomics-based identification of naturally presented non-canonical circRNA-derived peptides

HJ Ferreira, BJ Stevenson, HS Pak, F Yu… - Nature …, 2024‏ - nature.com
Circular RNAs (circRNAs) are covalently closed non-coding RNAs lacking the 5'cap and the
poly-A tail. Nevertheless, it has been demonstrated that certain circRNAs can undergo active …

Sage: an open-source tool for fast proteomics searching and quantification at scale

MR Lazear - Journal of Proteome Research, 2023‏ - ACS Publications
The growing complexity and volume of proteomics data necessitate the development of
efficient software tools for peptide identification and quantification from mass spectra. Given …

Prediction of glycopeptide fragment mass spectra by deep learning

Y Yang, Q Fang - Nature Communications, 2024‏ - nature.com
Deep learning has achieved a notable success in mass spectrometry-based proteomics and
is now emerging in glycoproteomics. While various deep learning models can predict …

Analysis and visualization of quantitative proteomics data using FragPipe-Analyst

Y Hsiao, H Zhang, GX Li, Y Deng, F Yu… - Journal of Proteome …, 2024‏ - ACS Publications
The FragPipe computational proteomics platform is gaining widespread popularity among
the proteomics research community because of its fast processing speed and user-friendly …

Oktoberfest: Open‐source spectral library generation and rescoring pipeline based on Prosit

M Picciani, W Gabriel, VG Giurcoiu, O Shouman… - …, 2024‏ - Wiley Online Library
Abstract Machine learning (ML) and deep learning (DL) models for peptide property
prediction such as Prosit have enabled the creation of high quality in silico reference …

Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF

C Adams, W Gabriel, K Laukens, M Picciani… - Nature …, 2024‏ - nature.com
Immunopeptidomics is crucial for immunotherapy and vaccine development. Because the
generation of immunopeptides from their parent proteins does not adhere to clear-cut rules …

Optimizing differential expression analysis for proteomics data via high-performing rules and ensemble inference

H Peng, H Wang, W Kong, J Li, WWB Goh - Nature Communications, 2024‏ - nature.com
Identification of differentially expressed proteins in a proteomics workflow typically
encompasses five key steps: raw data quantification, expression matrix construction, matrix …