Reprocessing of the dataset "Plasma Proteome Profiling Reveals the Effects of Weight Loss on the Apolipoprotein Family and Systemic Inflammation Status"

Reprocessing of the MassIVE repository MSV000080596, originally generated to investigate the dynamic changes in the plasma proteomes of a cohort of individuals with obesity following weight loss and maintenance. The reprocessing included all samples from 52 individuals taken right after the weight-loss process and during the weight maintenance phase of the study (Weeks 0, 4, 13, 26, 39, and 52).

We used the sequence database generated by ProHap (https://github.com/ProGenNo/ProHap) representing all populations from the 1000 Genomes Project (doi.org/10.5281/zenodo.10149277). For the search, SearchGUI version 4.3.1 and PeptideShaker version 3.0.0 were used with the X!Tandem and Tide search engines. The modification settings specified were carbamidomethylation of C as fixed and oxidation of M, deamidation of N and Q, Pyrrolidone of E and Q, and acetylation of protein N-terminus as variable modifications. The maximum peptide length was set to 40 amino acids and the precursor and fragment ion tolerances were set to 7 and 20 ppm, respectively. Resulting PSMs were processed as described in (doi.org/10.1021/acs.jproteome.3c00243) using Percolator version 3.5 provided with features based on peptide retention time (DeepLC version 1.1.2) and fragmentation predictors (MS2PIP version 3.9.0), and filtered at a 1% estimated FDR.

The attached file contains all the peptide-spectrum matches identified at 1% FDR. The peptides have been annotated with transcripts, genes, and alleles using the ProHap Peptide Annotator v1.1 (https://github.com/ProGenNo/ProHap_PeptideAnnotator).