: A Comprehensive View of the Proteome.

We describe a new release of the PeptideAtlas proteomics spectral resource (build 2024-03), providing a sequence coverage of 79.5% at the canonical protein level, matched mass spectrometry spectra, and experimental evidence identifying 3382 and 536 phosphorylated serine and threonine sites with false localization rates of 1% and 5.3%, respectively.

Limelight: An Open, Web-Based Tool for Visualizing, Sharing, and Analyzing Mass Spectrometry Data from DDA Pipelines.

Liquid chromatography-tandem mass spectrometry employing data-dependent acquisition (DDA) is a mature, widely used proteomics technique routinely applied to proteome profiling, protein-protein interaction studies, biomarker discovery, and protein modification analysis. Numerous tools exist for searching DDA data and myriad file formats are output as results. While some search and post processing tools include data visualization features to aid biological interpretation, they are often limited or tied to specific software pipelines.

Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment.

Thousands of short open reading frames (sORFs) are translated outside of annotated coding sequences. Recent studies have pioneered searching for sORF-encoded microproteins in mass spectrometry (MS)-based proteomics and peptidomics datasets. Here, we assessed literature-reported MS-based identifications of unannotated human proteins.

[Differential diagnosis of epidermotropic neoplasia].

Many benign and malignant neoplasms may involve the epidermis, a phenomenon which is commonly referred to as epidermotropism. Intraepidermal localization is an important diagnostic clue. However, differentiation of neoplastic cells can be challenging, especially when the cells are completely confined to the epidermis.

Is Kaposi sarcoma a novel comorbidity of cutaneous lymphoma? A systematic review of the literature.

Background And Objectives: Patients with cutaneous lymphomas (CL) are at an increased risk of developing secondary malignancies. This study aimed to assess the frequency of association between CL and Kaposi sarcoma (KS) and to identify factors that may promote the co-occurrence of these two diseases.

Patients And Methods: On January 25, 2024, we conducted a systematic search of four electronic medical databases to identify all published cases of KS associated with CL.