Project description:Runs used for retention time matching between 5-ASA (combinatorial synthesis and single reaction compound) and biological sample (Rheumatoid arthritis stool). Samples were either run on timsTOF Pro 2 or on Thermo Q Exactive.
Project description:This dataset is created for retention time matching for the conjugated metabolome project, including lactic acid-amino acid conjugates, phenylacetic acid-amino acid conjugates, phenylpropionic acid-amino acid conjugates and others.
Project description:A re-analysis of published data-dependent acquisition glycoproteomics datasets to demonstrate relative retention time prediction on glycopeptide identification and disambiguation of adduct states.
Project description:Runs used for retention time matching bile acids and drugs (combinatorial synthesis and single reaction compound) and biological sample (bacterial cultures and human urine samples). Samples were either run on timsTOF Pro 2, on Thermo Q Exactive, or on Exploris 240
Project description:Runs used for retention time matching between N-acyl lipids (combinatorial synthesis) and biological samples (HNRC - stool; Salmonella infection - cecum; Dead bodies - skin swab; Microbial monocultures - extracts). Two gradients were used (LC1 - total 11 min; LC2 - total 14 min) and a Kinetex 1.6 um polar C18 column (100 x 2.1 mm) was employed . Two spiking levels were used for coinjection (high - 1:3 sample:reaction pool; low - 3:1 sample:reaction pool).
Project description:The change in pH of the mobile phase drastically changes the retention mechanism of peptides, rendering currently available retention time prediction models useless. The aim of this study is to create a dataset of peptide retention times under basic (pH 9) HPLC conditions, allowing for the creation of a retention time prediction model specific for these conditions. Peptides were separated using basic mobile phases and analyzed in positive ion mode, allowing identification with common shotgun proteomics pipeline.
Project description:We describe PROCAL (ProteomeTools Standard), a set of 40 synthetic peptides that span the entire hydrophobicity range of tryptic digests, enabling not only accurate determination of retention time indices but also monitoring of chromatographic separation performance over time. The fragmentation characteristics of the peptides can also be used to calibrate and compare collision energies between mass spectrometers. The sequences of all selected peptides do not occur in any natural protein, thus eliminating the need for stable isotope labeling and allowing straightforward integration into standard peptide identification strategies employing database searching or spectral library matching.