Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics

R Lou, Y Cao, S Li, X Lang, Y Li, Y Zhang… - Nature …, 2023 - nature.com
A plethora of software suites and multiple classes of spectral libraries have been developed
to enhance the depth and robustness of data-independent acquisition (DIA) data …

Longitudinal plasma proteomics analysis reveals novel candidate biomarkers in acute COVID-19

Y Mohammed, DR Goodlett, MP Cheng… - Journal of proteome …, 2022 - ACS Publications
The host response to COVID-19 pathophysiology over the first few days of infection remains
largely unclear, especially the mechanisms in the blood compartment. We report on a …

Optimizing single cell proteomics using trapped ion mobility spectrometry for label-free experiments

DG Mun, FA Bhat, H Ding, BJ Madden, S Natesampillai… - Analyst, 2023 - pubs.rsc.org
Although single cell RNA-seq has had a tremendous impact on biological research, a
corresponding technology for unbiased mass spectrometric analysis of single cells has only …

Mass spectrometry measurements of neuropeptides: from identification to quantitation

EA De La Toba, SE Bell, EV Romanova… - Annual Review of …, 2022 - annualreviews.org
Neuropeptides (NPs), a unique class of neuronal signaling molecules, participate in a
variety of physiological processes and diseases. Quantitative measurements of NPs provide …

Proteomics‐based mass spectrometry profiling of SARS‐CoV‐2 infection from human nasopharyngeal samples

S Chatterjee, J Zaia - Mass Spectrometry Reviews, 2024 - Wiley Online Library
Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is the cause of the on‐
going global pandemic of coronavirus disease 2019 (COVID‐19) that continues to pose a …

Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF

DG Mun, R Budhraja, FA Bhat, RM Zenka… - …, 2023 - Wiley Online Library
A quadrupole time‐of‐flight mass spectrometer coupled with a trapped ion mobility
spectrometry (timsTOF) operated in parallel accumulation‐serial fragmentation (PASEF) …

Tryptophan metabolism 'Hub'gene expression associates with increased inflammation and severe disease outcomes in COVID-19 infection and inflammatory bowel …

S Bustamante, Y Yau, V Boys, J Chang… - International Journal of …, 2022 - mdpi.com
The epithelial barrier's primary role is to protect against entry of foreign and pathogenic
elements. Both COVID-19 and Inflammatory Bowel Disease (IBD) show commonalities in …

Noninvasive nasopharyngeal proteomics of COVID-19 patient identify abnormalities related to complement and coagulation cascade and mucosal immune system

MA Ayass, W Cao, J Zhang, J Dai, K Zhu, T Tripathi… - Plos one, 2022 - journals.plos.org
Serum or plasma have been the primary focus of proteomics studies for COVID-19 to identity
biomarkers and potential drug targets. The nasal mucosal environment which consists of …

Serum proteomic analysis identified ITIH4 as a potential novel biomarker for feline infectious peritonitis

Y Jiao, M Yang, L Fang, Y Yan, Z Fu, M Li, L Li, Z Liu… - Journal of …, 2025 - Elsevier
Feline infectious peritonitis (FIP) is a fatal feline disease. At present, the reference standard
for FIP diagnosis is immunohistochemistry (IHC) of organs, but this method involves high …

Identification of endogenous peptides in nasal swab transport media used in MALDI-TOF-MS based COVID-19 screening

H Tsai, BS Phinney, G Grigorean, MR Salemi… - ACS …, 2022 - ACS Publications
Mass spectrometry (MS) based diagnostic detection of 2019 novel coronavirus infectious
disease (COVID-19) has been postulated to be a useful alternative to classical PCR based …