Project description:In this study we developed metaproteomics based methods for quantifying taxonomic composition of microbiomes (microbial communities). We also compared metaproteomics based quantification to other quantification methods, namely metagenomics and 16S rRNA gene amplicon sequencing. The metagenomic and 16S rRNA data can be found in the European Nucleotide Archive (Study number: PRJEB19901). For the method development and comparison of the methods we analyzed three types of mock communities with all three methods. The communities contain between 28 to 32 species and strains of bacteria, archaea, eukaryotes and bacteriophage. For each community type 4 biological replicate communities were generated. All four replicates were analyzed by 16S rRNA sequencing and metaproteomics. Three replicates of each community type were analyzed with metagenomics. The "C" type communities have same cell/phage particle number for all community members (C1 to C4). The "P" type communities have the same protein content for all community members (P1 to P4). The "U" (UNEVEN) type communities cover a large range of protein amounts and cell numbers (U1 to U4). We also generated proteomic data for four pure cultures to test the specificity of the protein inference method. This data is also included in this submission.
Project description:In this study, we analyzed the microbial communities from a methane-based bio-reactor with selenate as an electron accepter. Four biological replicates were analyzed by metagenomics, of which data can be found in the SRA database (Accession number: SRP136677, SRP136696, SRP136790 and SRP136859). Based on the metagenomic data, we detected the expressed proteins using metaproteomics. This data is also included in this submission.
Project description:Blood from elderly individuals exhibits a reduced "rejuvenating" effect compared to that of young donors, and plasma from older subjects used as a supplement in cell culture media is less effective than plasma from younger individuals. A mass spectrometry-based proteomic analysis of plasma samples from 229 blood donors—including a prepubertal group, a healthy young adult group, and a cohort of individuals over 75 years old—revealed a chronic inflammatory state in the elderly population, along with complement activation and negative regulation of blood coagulation. This inflammatory condition was confirmed by elevated levels of classical pro-inflammatory cytokines in the plasma of older individuals, as measured by microarray and Milliplex Luminex assays. Moreover, the elderly group showed a reduced production of antibody light chains, suggesting concurrent immunosenescence. We identified 25 proteins whose increased abundance, together with acquired immune aging, may constitute a plasma proteomic signature of aging. The degree of upregulation of these proteins varied among elderly subgroups with different lifestyles. An evaluation of the expression patterns of the 25 consistently elevated proteins revealed distinct protein clusters with differential expression across three lifestyle-based subgroups. Notably, a lifestyle aimed at preserving good physical and/or cognitive function appeared to attenuate the intensity of the aging-related proteomic signature. To explore potential gender-related differences in plasma protein expression, we compared samples from male and female donors. Among elderly individuals, no major differences were observed, except for an increased level of Pregnancy Zone Protein (PZP) in females. In contrast, several gender-specific differences were identified in the plasma profiles of young donors.
