LC-MS/MS-based proteomics studies rely on stable analytical system performance that can be evaluated by objective criteria. The National Institute of Standards and Technology (NIST) introduced the MSQC software to compute diverse metrics from experimental LC-MS/MS data, enabling quality analysis and quality control (QA/QC) of proteomics instrumentation. In practice, however, several attributes of the MSQC software prevent its use for routine instrument monitoring. Here, we present QuaMeter, an open-source tool that improves MSQC in several aspects. QuaMeter can directly read raw data from instruments manufactured by different vendors. The software can work with a wide variety of peptide identification software for improved reliability and flexibility. Finally, QC metrics implemented in QuaMeter are rigorously defined and tested. The source code and binary versions of QuaMeter are available under Apache 2.0 License at http://fenchurch.mc.vanderbilt.edu.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3730131 | PMC |
| http://dx.doi.org/10.1021/ac300629p | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Noncanonical roles of ATG5 and membrane atg8ylation in retromer assembly and function.
Elife
January 2025
Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of Medicine, Albuquerque, United States.
ATG5 is one of the core autophagy proteins with additional functions such as noncanonical membrane atg8ylation, which among a growing number of biological outputs includes control of tuberculosis in animal models. Here, we show that ATG5 associates with retromer's core components VPS26, VPS29, and VPS35 and modulates retromer function. Knockout of ATG5 blocked trafficking of a key glucose transporter sorted by the retromer, GLUT1, to the plasma membrane.
View Article and Find Full Text PDFComprehensive Optimization of Packing Parameters for Hydraulic-Packed Capillary Columns.
Rapid Commun Mass Spectrom
April 2025
Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, and Cancer Center, School of Medicine, Tongji University, Shanghai, China.
Rationale: The performance of the capillary column directly impacts the separation efficiency of complex sample in liquid chromatography-mass spectrometry-based proteomics studies. The hydraulic packing system offers an effective solution by reducing packing time and expediting the preparation process of column preparation. However, its operational complexity and strict parameter regulation requirements hinder efficient application.
View Article and Find Full Text PDFSelf-Assembly of Human Fibrinogen into Microclot-Mimicking Antifibrinolytic Amyloid Fibrinogen Particles.
ACS Appl Bio Mater
December 2024
MOE Key Laboratory of Bio-Intelligent Manufacturing, Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116024, China.
Recent clinical studies have highlighted the presence of microclots in the form of amyloid fibrinogen particles (AFPs) in plasma samples from Long COVID patients. However, the clinical significance of these abnormal, nonfibrillar self-assembly aggregates of human fibrinogen remains debated due to the limited understanding of their structural and biological characteristics. In this study, we present a method for generating mimetic microclots in vitro.
View Article and Find Full Text PDFSpatial Proteomics towards cellular Resolution.
Expert Rev Proteomics
December 2024
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA.
Introduction: Spatial biology is an emerging interdisciplinary field facilitating biological discoveries through the use of spatial omics technologies. Recent advancements in spatial transcriptomics, spatial genomics (e.g.
View Article and Find Full Text PDFMS -Pushing the Limits for Biomolecular Mass Spectrometry.
J Am Soc Mass Spectrom
January 2025
Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany.
Electrospray mass spectrometry has become indispensable in many disciplines including the classic "omics" techniques such as proteomics or lipidomics, as well as other life science applications in molecular, cellular, and structural biology. However, a limiting factor that often arises for the detection of biomolecular analytes is their poor ionization efficiency in the ion source. Here, we present an add-on device for the electrospray source, termed MS (MS Spectral Impurity Eliminator & Value Enhancer), which is placed between the electrospray needle and the cone of the mass spectrometer.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!