Article
Biochemical Research Methods
Runmin Yang, Jingjing Ma, Shu Zhang, Yu Zheng, Lusheng Wang, Daming Zhu
Summary: This study introduces a new storage format called mzMD for MS datasets and presents an algorithm to query this format for summarizing a given data window. Experimental results demonstrate the high speed and stability of mzMD in retrieving high-quality data window summaries.
Article
Biochemical Research Methods
Soroosh Gholamizoj, Bin Ma
Summary: SPEQ is a spectrum quality assessment tool that classifies spectra into high-quality and low-quality using a deep neural network, which has demonstrated improved prediction accuracy compared to other models.
Article
Biochemistry & Molecular Biology
Gabor Kecskemeti, Edit Toth-Molnar, Tamas Janaky, Zoltan Szabo
Summary: Tear samples are valuable sources of information for precision medicine, and this study evaluates a novel sample collection technique for human tear samples. The results show that this new technique is equally or even more suitable for proteomic sample collection compared to traditional methods.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Neil A. McCracken, Sarah A. Peck Justice, Aruna B. Wijeratne, Amber L. Mosley
Summary: The study introduces a user-friendly analysis of the melt shift calculation workflow and quantitatively assesses the impact of key steps in the analysis workflow on the final output list of stabilized and destabilized proteins. It also presents a more optimized analysis workflow, illustrating the importance of selected calculation steps on the final list of reported proteins of interest in a study. The development of the R based program Inflect offers a valuable resource for the research community to analyze data from TPP and CETSA experiments.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Environmental Sciences
Tsuyoshi Kawakami, Shinobu Sakai, Tomoko Obama, Reiji Kubota, Kaoru Inoue, Yoshiaki Ikarashi
Summary: This study investigates the concentrations of rubber additives and related chemicals in rubber infills used in synthetic turf fields in Japan. The analysis found variations in the types and concentrations of compounds detected between different products and within the same product. Elution tests showed that compound elution rates varied and were affected by coatings, with most compounds having low elution rates.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Agriculture, Multidisciplinary
Christopher J. Silva, Bruce C. Onisko, Irina C. Dynin, Melissa Erickson-Beltran, Jesus R. Requena
Summary: The study found that mass spectrometry detection of PrP 27-30 in hamsters infected with prions was consistent with the timing of prion detection by bioassay, indicating the potential of mass spectrometry technology in early prion disease detection.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Food Science & Technology
Ana G. Abril, Monica Carrera, Karola Boehme, Jorge Barros-Velazquez, Benito Canas, Jose-Luis R. Rama, Tomas G. Villa, Pilar Calo-Mata
Summary: This study utilized LC-ESI-MS/MS MS to analyze peptides from bacteriophages infecting mastitis-causing Staphylococcus aureus, identifying a large number of specific peptides that could be useful for identifying and characterizing the bacteria causing mastitis. Additionally, a study of bacteriophage phylogeny and its relationship with the respective Staphylococcus spp. infected was conducted, revealing specific peptides present in closely related phages and highlighting the connection between bacteriophage phylogeny and the infected Staphylococcus spp.
Article
Biochemical Research Methods
Jinjun Gao, Yuan Liu, Fan Yang, Xuemin Chen, Benjamin F. Cravatt, Chu Wang
Summary: ABPP is a powerful chemical proteomic method for studying protein activity, modifications, and interactions, where accurate quantification is crucial. CIMAGE is a specialized quantification software for ABPP data analysis, providing efficient and accurate quantification with the ability to visualize results conveniently.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Mohd Afiq Hazlami Habib, Mohd Nazri Ismail
Summary: The fruit and leaf of God's crown plant have been traditionally used for treating various diseases. However, the proteins of this tropical plant are still not well studied. Three protein extraction methods were compared for their efficiency in recovering proteins from the plant, with the phenol extraction method showing the highest percentage of protein recovery. Liquid chromatography-tandem mass spectrometry analysis revealed that proteins identified through the phenol extraction method included a significant percentage of enzymatic proteins with various biological functions.
JOURNAL OF FOOD BIOCHEMISTRY
(2021)
Review
Pharmacology & Pharmacy
Theo Tasoulis, Tara L. Pukala, Geoffrey K. Isbister
Summary: Understanding snake venom proteomes is crucial for comprehending snake venom biology, evolution, as well as the clinical effects of venoms and approaches to antivenom development. This study reviewed a range of research on snake venom proteomes and found that different methodological strategies can enhance protein identification, while combining methods can maximize proteome coverage. Variation in protein diversity and abundance was observed among different snake species, with viper venoms being compositionally more complex than elapid venoms. To ensure equivalent comparisons between studies, it is necessary to clarify methodological differences and establish standardized protein classification, nomenclature, and reporting procedures.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemical Research Methods
Antony McCabe, Andrew R. Jones
Summary: Complex biological samples are often analyzed using mass spectrometry paired with liquid chromatography or gas chromatography in proteomics and metabolomics research. lcmsWorld is a new software that utilizes graphics hardware to quickly examine and compare LC-MS data, providing a more intuitive way to visualize the data.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Olga Shevchuk, Antonija Jurak Begonja, Stepan Gambaryan, Matthias Totzeck, Tienush Rassaf, Tobias B. Huber, Andreas Greinacher, Thomas Renne, Albert Sickmann
Summary: This review discusses the role of proteomics in understanding the molecular basics of traditional and emerging functions of platelets, as well as the application of proteomic technologies in platelet biogenesis, signaling, and storage. Additionally, the potential of newly appeared trapped ion mobility spectrometry (TIMS) in platelet research is highlighted, along with discussions on the implementation of proteomic methods in platelet transfusion medicine, diagnostics, and prognostics.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Analytical
Xuefei Zhong, Shruti Nayak, Lili Guo, Shivkumar Raidas, Yunlong Zhao, Rachel Weiss, Matthew Andisik, Chinnasamy Elango, Giane Sumner, Susan C. Irvin, Michael A. Partridge, Hong Yan, Sook E. Yen, Haibo Qiu, Yuan Mao, Albert Torri, Ning Li
Summary: REGEN-COV, a cocktail of two human monoclonal antibodies, has shown promising results in reducing SARS-CoV-2 viral load in COVID-19 patients. A liquid chromatography-mass spectrometry method was developed for the determination of REGEN-COV concentrations in serum samples from patients participating in clinical trials. The concentrations measured by this method were comparable to those measured by a validated immunoassay.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Rafael Fogaca de Almeida, Aline Castro Rodrigues Lucena, Michel Batista, Fabricio Klerynton Marchini, Lyris Martins Franco de Godoy
Summary: Non-histone methylation plays a significant role in Trypanosoma cruzi, impacting important biological processes such as translation, RNA and DNA binding, and metabolism. The study provides insights into the potential impact of methylation on the biology of the parasite.
Review
Chemistry, Analytical
Ligia Lopes-Rocha, Clara Hernandez, Virginia Goncalves, Teresa Pinho, Maria Elizabeth Tiritan
Summary: This systematic review collected the analytical methods for quantifying the release of bisphenol A (BPA) in dental materials and discussed the impacts of BPA on human health and its potential association with dental materials. The findings showed that in in vitro studies, flowable and conventional resins released the highest amounts of BPA, while BPA-free composites and CAD-CAM blocks released the smallest amount. In in vivo studies, saliva had higher concentrations of BPA compared to urine or blood. LC-MS/MS was identified as the best analytical method for trace quantifying BPA.
CRITICAL REVIEWS IN ANALYTICAL CHEMISTRY
(2022)