Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins

W Shao, T Guo, NC Toussaint, P Xue, U Wagner… - Nature …, 2019 - nature.com
Deterioration of biomolecules in clinical tissues is an inevitable pre-analytical process, which
affects molecular measurements and thus potentially confounds conclusions from cohort …

Tandem mass spectral libraries of peptides and their roles in proteomics research

W Shao, H Lam - Mass spectrometry reviews, 2017 - Wiley Online Library
Proteomics is a rapidly maturing field aimed at the high‐throughput identification and
quantification of all proteins in a biological system. The cornerstone of proteomic technology is …

The SysteMHC atlas project

W Shao, PGA Pedrioli, W Wolski… - Nucleic acids …, 2018 - academic.oup.com
Mass spectrometry (MS)-based immunopeptidomics investigates the repertoire of peptides
presented at the cell surface by major histocompatibility complex (MHC) molecules. The …

Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells

…, M Buljan, T Sajic, PJ Boersema, W Shao… - Nature …, 2017 - nature.com
Down syndrome (DS) is mostly caused by a trisomy of the entire Chromosome 21 (Trisomy
21, T21). Here, we use SWATH mass spectrometry to quantify protein abundance and protein …

Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency

P Forny, X Bonilla, D Lamparter, W Shao, T Plessl… - Nature …, 2023 - nature.com
Methylmalonic aciduria (MMA) is an inborn error of metabolism with multiple monogenic
causes and a poorly understood pathogenesis, leading to the absence of effective causal …

A computational framework for the inference of protein complex remodeling from whole-proteome measurements

…, P Blattmann, F Meier-Abt, W Shao… - Nature …, 2023 - nature.com
Protein complexes are responsible for the enactment of most cellular functions. For the protein
complex to form and function, its subunits often need to be present at defined quantitative …

The SysteMHC Atlas v2. 0, an updated resource for mass spectrometry-based immunopeptidomics

…, H Cui, T Lan, Y Liu, E Caron, W Shao - Nucleic Acids …, 2024 - academic.oup.com
The SysteMHC Atlas v1.0 was the first public repository dedicated to mass spectrometry-based
immunopeptidomics. Here we introduce a newly released version of the SysteMHC Atlas …

DPHL: a DIA pan-human protein mass spectrometry library for robust biomarker discovery

…, T Lu, Z Wu, X Liang, M Wang, Y Shao… - Genomics …, 2020 - academic.oup.com
To address the increasing need for detecting and validating protein biomarkers in clinical
specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the …

Understanding the improved sensitivity of spectral library searching over sequence database searching in proteomics data analysis

X Zhang, Y Li, W Shao, H Lam - Proteomics, 2011 - Wiley Online Library
Spectral library searching has been recently proposed as an alternative to sequence database
searching for peptide identification from MS/MS. We performed a systematic comparison …

A tissue-based draft map of the murine MHC class I immunopeptidome

H Schuster, W Shao, T Weiss, PGA Pedrioli, P Roth… - Scientific data, 2018 - nature.com
The large array of peptides presented to CD8+ T cells by major histocompatibility complex (MHC)
class I molecules is referred to as the MHC class I immunopeptidome. Although the …