QCloud is a cloud-based system to support proteomics laboratories in daily quality assessment using a user-friendly interface, easy setup, and automated data processing. Since its release, QCloud has facilitated automated quality control for proteomics experiments in many laboratories. QCloud provides a quick and effortless evaluation of instrument performance that helps ... More
BoxCar and Library-Free Data-Independent Acquisition Substantially Improve the Depth, Range, and Completeness of Label-Free Quantitative Proteomics.
AuthorsMehta D,Scandola S,Uhrig RG
JournalAnalytical chemistry
PubMed ID34978796
Data-dependent acquisition (DDA) methods are the current standard for quantitative proteomics in many biological systems. However, DDA preferentially measures highly abundant proteins and generates data that is plagued with missing values, requiring extensive imputation. Here, we demonstrate that library-free BoxCarDIA acquisition, combining MS1-level BoxCar acquisition with MS2-level data-independent acquisition (DIA) ... More
Tailoring to Search Engines: Bottom-Up Proteomics with Collision Energies Optimized for Identification Confidence.
AuthorsRévész Á,Milley MG,Nagy K,Szabó D,Kalló G,Csősz É,Vékey K,Drahos L
JournalJournal of proteome research
PubMed ID33284634
Bottom-up proteomics relies on identification of peptides from tandem mass spectra, usually via matching against sequence databases. Confidence in a peptide-spectrum match can be characterized by a score value given by the database search engines, and it depends on the information content and the quality of the spectrum. The latter ... More