Comparative analysis of anticoagulant influence on PMI estimation based on porcine blood metabolomics profile measured using GC-MS by Patrycja Mojsak, Paulina Samczuk, Paulina Samczuk, Paulina Klimaszewska, Michal Burdukiewicz, Michal Burdukiewicz, Jaroslaw Chilimoniuk, Krystyna Grzesiak, Krystyna Grzesiak, Karolina Pietrowska, Justyna Ciborowska, Anna Niemcunowicz-Janica, Adam Kretowski, Adam Kretowski, Michal Ciborowski, Michal Ciborowski, Michal Szeremeta

Get full text

Characterization of Bozitinib as a potential therapeutic agent for MET-amplified gastric cancer by Hang Lin, Lingzhi Qu, Hudie Wei, Ming Guo, Xiaojuan Chen, Qianmeng Lin, Huajun Zhang, Shuyan Dai, Yongheng Chen

Get full text

A computational tool to infer enzyme activity using post-translational modification profiling data by Dehui Kong, Aijun Zhang, Ling Li, Zuo-Fei Yuan, Yingxue Fu, Long Wu, Ashutosh Mishra, Anthony A. High, Junmin Peng, Xusheng Wang

“…Despite their crucial roles, measuring enzyme activities is typically indirect and performed on a smaller scale, unlike protein abundance measured by high-throughput proteomics. Moreover, it is challenging to derive the activity of enzymes from proteome-wide post-translational modification (PTM) profiling data. …”
Get full text

π-PrimeNovo: an accurate and efficient non-autoregressive deep learning model for de novo peptide sequencing by Xiang Zhang, Tianze Ling, Zhi Jin, Sheng Xu, Zhiqiang Gao, Boyan Sun, Zijie Qiu, Jiaqi Wei, Nanqing Dong, Guangshuai Wang, Guibin Wang, Leyuan Li, Muhammad Abdul-Mageed, Laks V. S. Lakshmanan, Fuchu He, Wanli Ouyang, Cheng Chang, Siqi Sun

“…Abstract Peptide sequencing via tandem mass spectrometry (MS/MS) is essential in proteomics. Unlike traditional database searches, deep learning excels at de novo peptide sequencing, even for peptides missing from existing databases. …”
Get full text

Post-Translational Modifications of Proteins Orchestrate All Hallmarks of Cancer by Pathea Shawnae Bruno, Aneeta Arshad, Maria-Raluca Gogu, Natalie Waterman, Rylie Flack, Kimberly Dunn, Costel C. Darie, Anca-Narcisa Neagu

“…Aberrant PTMs can be considered as enabling characteristics of cancer as long as they orchestrate all malignant modifications and variability in the proteome of cancer cells, cancer-associated cells, and tumor microenvironment (TME). …”
Get full text

Proteogenomic Analysis Reveals Proteins Involved in the First Step of Adipogenesis in Human Adipose-Derived Stem Cells by Bernardo Bonilauri, Amanda C. Camillo-Andrade, Marlon D. M. Santos, Juliana de S. da G. Fischer, Paulo C. Carvalho, Bruno Dallagiovanna

“…Cells were cultured for 24 hours in adipogenic differentiation medium followed by protein extraction. We used shotgun proteomics to compare the proteomic profile of 24 h-adipogenic, differentiated, and undifferentiated hASC. …”
Get full text

Polypeptide Expression in Prostate Hyperplasia and Prostate Adenocarcinoma by Ayodele Alaiya, Uwe Roblick, Lars Egevad, Adelaide Carlsson, Bo Franzén, Daniela Volz, Sören Huwendiek, Stig Linder, Gert Auer

Get full text

Clastogenic Effects of Glyphosate in Bone Marrow Cells of Swiss Albino Mice by Sahdeo Prasad, Smita Srivastava, Madhulika Singh, Yogeshwer Shukla

Get full text

Periodontal Indices as Predictors of Cognitive Decline: Insights from the PerioMind Colombia Cohort by Catalina Arévalo-Caro, Diego López, Jose Antonio Sánchez Milán, Cristina Lorca, María Mulet, Humberto Arboleda, Sergio Losada Amaya, Aida Serra, Xavier Gallart-Palau

Get full text

Gas-phase fractionation DDA promotes in-depth DIA phosphoproteome analysis by Zhiwei Tu, Yabin Li, Shuhui Ji, Shanshan Wang, Rui Zhou, Gertjan Kramer, Yu Cui, Fei Xie

“…Data-independent acquisition (DIA) is a promising method for quantitative proteomics. Library-based DIA database searching against project-specific data-dependent acquisition (DDA) spectral libraries is the gold standard. …”
Get full text

Techniques for Molecular Imaging Probe Design by Fred Reynolds, Kimberly A. Kelly

“…With advances in genomics and proteomics and underlying mechanisms of disease pathology, the number of targets identified has significantly outpaced the number of developed molecular imaging probes. …”
Get full text

Multiplexed Dilute-and-Shoot Liquid Chromatography–Multiple-Reaction Monitoring Mass Spectrometry Clinical Assay for Metanephrines and Catecholamines in Human Urine by Deema O. Qasrawi, Adriano M. C. Pimenta, Evgeniy V. Petrotchenko, Shaun Eintracht, Christoph H. Borchers

Get full text

Association of Inflammatory and Oxidative Stress Markers with Metabolic Syndrome in Asian Indians in India by Veena S. Rao, Radhika K. Nagaraj, Sridhara Hebbagodi, Natesha B. Kadarinarasimhiah, Vijay V. Kakkar

Get full text

Hyperosmotic Stress Induces a Specific Pattern for Stress Granule Formation in Human-Induced Pluripotent Stem Cells by Salam Salloum-Asfar, Rudolf Engelke, Hanaa Mousa, Neha Goswami, I. Richard Thompson, Freshteh Palangi, Kamal Kamal, Muna N. Al-Noubi, Frank Schmidt, Sara A. Abdulla, Mohamed M. Emara

“…In addition, a comprehensive proteomics analysis was performed to identify proteins involved in regulating this specific pattern of hyperosmotic SG formation in hiPSCs/IMR90-1. …”
Get full text

Strategies to Identify Recognition Signals and Targets of SUMOylation by Elisa Da Silva-Ferrada, Fernando Lopitz-Otsoa, Valérie Lang, Manuel S. Rodríguez, Rune Matthiesen

Get full text

Gene Identification and Characterization of Correlations for DEPs_DEGs Same Trend Responding to Salinity Adaptation in Scylla paramamosain by Huan Wang, Hongling Wei, Lei Tang, Junkai Lu, Changkao Mu, Chunlin Wang

“…In our previous study, we had analyzed the mechanism of adapting sudden drop in salinity from the level of transcriptomics and proteomics, respectively. This study performed a correlation analysis of RNA sequencing transcriptomics and iTRAQ proteomics in order to investigate the adaptation mechanisms to sudden salinity drop from 23‰ to 3‰. …”
Get full text

Androgenic Anabolic Steroids Cause Thiol Imbalance in the Vascular Endothelial Cells by Halszka Ponamarczuk, Maria Światkowska, Marcin Popielarski

Get full text

A MALDI-ToF mass spectrometry database for identification and classification of highly pathogenic bacteria by Peter Lasch, Wolfgang Beyer, Alejandra Bosch, Rainer Borriss, Michal Drevinek, Susann Dupke, Monika Ehling-Schulz, Xuewen Gao, Roland Grunow, Daniela Jacob, Silke R. Klee, Armand Paauw, Jörg Rau, Andy Schneider, Holger C. Scholz, Maren Stämmler, Le Thi Thanh Tam, Herbert Tomaso, Guido Werner, Joerg Doellinger

Get full text

Overexpression of Tear Inflammatory Cytokines as Additional Finding in Keratoconus Patients and Their First Degree Family Members by Ioana Catalina Ionescu, Catalina Gabriela Corbu, Cristiana Tanase, Gabriela Ionita, Cristina Nicula, Valeria Coviltir, Vasile Potop, Mihaela Constantin, Elena Codrici, Simona Mihai, Ionela Daniela Popescu, Ana-Maria Enciu, Dana Dascalescu, Miruna Burcel, Radu Ciuluvica, Liliana-Mary Voinea

Get full text

HLA I immunopeptidome of synthetic long peptide pulsed human dendritic cells for therapeutic vaccine design by Amy L. Kessler, Roel F. A. Pieterman, Wouter A. S. Doff, Karel Bezstarosti, Rachid Bouzid, Kim Klarenaar, Diahann T. S. L. Jansen, Robbie J. Luijten, Jeroen A. A. Demmers, Sonja I. Buschow

Get full text