Data-independent acquisition mass spectrometry (DIA-MS) for proteomic applications in oncology

L Krasny, PH Huang - Molecular omics, 2021 - pubs.rsc.org
Data-independent acquisition mass spectrometry (DIA-MS) is a next generation proteomic
methodology that generates permanent digital proteome maps offering highly reproducible …

Advances in data‐independent acquisition mass spectrometry towards comprehensive digital proteome landscape

RB Kitata, JC Yang, YJ Chen - Mass spectrometry reviews, 2023 - Wiley Online Library
The data‐independent acquisition mass spectrometry (DIA‐MS) has rapidly evolved as a
powerful alternative for highly reproducible proteome profiling with a unique strength of …

Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis

B Wen, K Li, Y Zhang, B Zhang - Nature communications, 2020 - nature.com
Genomics-based neoantigen discovery can be enhanced by proteomic evidence, but there
remains a lack of consensus on the performance of different quality control methods for …

A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS

MK Midha, U Kusebauch, D Shteynberg, C Kapil… - Scientific data, 2020 - nature.com
Abstract Data-Independent Acquisition (DIA) is a method to improve consistent identification
and precise quantitation of peptides and proteins by mass spectrometry (MS). The targeted …

Technical advancement and practical considerations of LC-MS/MS-based methods for host cell protein identification and quantitation to support process development

J Guo, R Kufer, D Li, S Wohlrab… - MAbs, 2023 - Taylor & Francis
Host cell proteins (HCPs) are process-related impurities derived from the manufacturing of
recombinant biotherapeutics. Residual HCP in drug products, ranging from 1 to 100 ppm (ng …

Surfaceome dynamics reveal proteostasis-independent reorganization of neuronal surface proteins during development and synaptic plasticity

M van Oostrum, B Campbell, C Seng, M Müller… - Nature …, 2020 - nature.com
Neurons are highly compartmentalized cells with tightly controlled subcellular protein
organization. While brain transcriptome, connectome and global proteome maps are being …

Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes

I Bludau, M Heusel, M Frank, G Rosenberger… - Nature protocols, 2020 - nature.com
Most catalytic, structural and regulatory functions of the cell are carried out by functional
modules, typically complexes containing or consisting of proteins. The composition and …

A new mass spectral library for high-coverage and reproducible analysis of the Plasmodium falciparum–infected red blood cell proteome

G Siddiqui, A De Paoli, CA MacRaild, AE Sexton… - …, 2022 - academic.oup.com
Background Plasmodium falciparum causes the majority of malaria mortality worldwide, and
the disease occurs during the asexual red blood cell (RBC) stage of infection. In the …

Stratification of follicular thyroid tumours using data‐independent acquisition proteomics and a comprehensive thyroid tissue spectral library

Y Sun, L Li, Y Zhou, W Ge, H Wang, R Wu… - Molecular …, 2022 - Wiley Online Library
Thyroid nodules occur in about 60% of the population. A major challenge in thyroid nodule
diagnosis is to distinguish between follicular adenoma (FA) and carcinoma (FTC). Here, we …

Computational optimization of spectral library size improves DIA-MS proteome coverage and applications to 15 tumors

W Ge, X Liang, F Zhang, Y Hu, L Xu… - Journal of Proteome …, 2021 - ACS Publications
Efficient peptide and protein identifications from data-independent acquisition mass
spectrometric (DIA-MS) data typically rely on a project-specific spectral library with a suitable …