Mass spectrometry-based proteomics empowers deep profiling of proteome and protein
posttranslational modifications (PTMs) in Alzheimer's disease (AD). Here we review the …

Modern genome-scale methods that identify new genes, such as proteogenomics and
ribosome profiling, have revealed, to the surprise of many, that overlap in genes, open …

The dia-PASEF technology uses ion mobility separation to reduce signal interferences and
increase sensitivity in proteomic experiments. Here we present a two-dimensional peak …

Liquid chromatography (LC) coupled with data-independent acquisition (DIA) mass
spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we …

Peptide identification in liquid chromatography-tandem mass spectrometry (LC-MS/MS)
experiments relies on computational algorithms for matching acquired MS/MS spectra …

Missing values weaken the power of label-free quantitative proteomic experiments to
uncover true quantitative differences between biological samples or experimental …

Compound identification in small-molecule research, such as untargeted metabolomics or
exposome research, relies on matching tandem mass spectrometry (MS/MS) spectra against …

We describe pLink 2, a search engine with higher speed and reliability for proteome-scale
identification of cross-linked peptides. With a two-stage open search strategy facilitated by …

There is a need to better understand and handle the'dark matter'of proteomics—the vast
diversity of post-translational and chemical modifications that are unaccounted in a typical …

Combining RNA sequencing, ribosome profiling, and mass spectrometry, we elucidate the
contribution of non-canonical translation to the proteome and major histocompatibility …