Detection of low-copy proteins in complex biological samples is one of the most important issues of modern proteomics. The main reason for inefficient detection of low protein concentrations is the insufficient sensitivity of mass spectrometric detectors and the high dynamic range of protein concentrations. In this study we have investigated the possibilities and limitations of a targeted mass spectrometric analysis using the reconstructed system of standard proteins UPS1 (Universal Proteomic Standard 1) as an example. The study has shown that the sensitivity of the method is affected by the concentration of target proteins of the UPS1 system, as well as by a high level of biological noise modelled by proteins of whole E. coli cell lysate. The limitations of the method have been overcome by concentrating and pre-fractionating the sample peptides in a reversed phase chromatographic system under alkaline elution conditions. Proteomic analysis of the biological sample (proteins of the human hepatocellular carcinoma cell line HepG2 encoded by genes of human chromosome 18) showed an increase in the sensitivity of the method as compared to the standard targeted mass spectrometric analysis. This culminated in registration of 94 proteins encoded by genes located on human chromosome18.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.18097/PBMC20247005342 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Antimicrobial polyketides from the endophytic fungus Fusarium asiaticum QA-6 derived from medicinal plant Artemisia argyi.
Phytochemistry
January 2025
CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, and Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Nanhai Road 7, Qingdao 266071, PR China; University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, PR China. Electronic address:
Seven previously undescribed polyketide derivatives, fusariumtides A-G (1-7), together with three known analogues (8-10), were isolated from the culture extract of Fusarium asiaticum QA-6, an endophytic fungus obtained from the fresh stem tissue of the medicinal plant Artemisia argyi H. Lev. & Vaniot.
View Article and Find Full Text PDFGlial Biologist's Guide to Mass Spectrometry-Based Lipidomics: A Tutorial From Sample Preparation to Data Analysis.
Glia
January 2025
Department of Chemistry, Purdue University, West Lafayette, Indiana, USA.
Neurological diseases are associated with disruptions in the brain lipidome that are becoming central to disease pathogenesis. Traditionally perceived as static structural support in membranes, lipids are now known to be actively involved in cellular signaling, energy metabolism, and other cellular activities involving membrane curvature, fluidity, fusion or fission. Glia are critical in the development, health, and function of the brain, and glial regulation plays a major role in disease.
View Article and Find Full Text PDFBasic Science and Pathogenesis.
Alzheimers Dement
December 2024
ADBS Lab, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India.
Background: What does neurodevelopment look like when neurodegeneration is the outcome - this is overarching theme of investigations currently ongoing in our lab. The E4 isoform of ApoE protein is the most consistently replicated risk factor in Alzheimer's Disease (AD). And yet, much remains unknown about the biological pathways that connect APOE4 genotype with the development of pathology that eventually leads to AD, nor do we know how early in life these cellular alterations begin.
View Article and Find Full Text PDFNitrite Reduction with HS/Thiol Mediated by Cobalt and Manganese Porphyrins in the Solid State.
Inorg Chem
January 2025
Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States.
The endogenous reduction of nitrite to nitrosyl is drawing increasing attention as a protective mechanism against hypoxic injury in mammalian physiology and as an alternative source of NO, which is involved in a wide variety of biological activities. Thus, chemical mechanisms for this transformation, which are mediated by metallo proteins, are of considerable interest. The study described here examines the reactions of the biomimetic models Co(TTP)(NO) (TTP = meso-tetratolylporphyrinato dianion) and Mn(TPP)(ONO) (TPP = meso-tetraphenyl-porphyrinato dianion) in sublimated solid films with hydrogen sulfide (HS) and with ethanethiol (EtSH) at various temperatures from 77 K to room temperature using in situ infrared and optical spectroscopy.
View Article and Find Full Text PDFMulti-tiered proteome analysis displays the hyper-permeability of the rheumatoid synovial compartment for plasma proteins.
Mol Cell Proteomics
December 2024
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands; Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, the Netherlands. Electronic address:
Rheumatoid arthritis (RA) is characterized by synovial hyperplasia and cartilage/bone destruction. RA affects the synovial joints, the synovial lining and the permeability of the synovium. As the latter is of central relevance for the distribution of systemically delivered therapeutics into synovial fluid (SF), we here assessed the protein composition of paired plasma and SF of patients diagnosed with RA at three distinct levels of depth using mass spectrometric approaches: the "total" proteome, the "total" IgG1 antibody repertoire and the RA-specific ACPA IgG1 autoantibody repertoire.
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!