Supplemental Materials
This article contains the following supporting material:
- Supplemental Materials
- Table S1 - Table S1. SDS-insoluble proteins identified in aged S. cerevisiae. Insoluble proteins were extracted from two biological replicates of both young and aged cells and analyzed using iTRAQ mass spectrometry (see Materials & Methods). Of the 480 proteins confidently identified from aged cells using this method, only six proteins were found at significantly different levels (p-value < 0.05) between aged biological replicates (denoted A and B). Those six cases where protein levels were significantly different between the A and B replicate are highlighted in yellow. In cases where the iTRAQ signal was too low to calculate ratio, none is reported. No labeled peptides that met confidence requirements were detected from either young biological replicate.
- Table S2 - Table S2. Summary of Gene Ontology analysis and homology analysis of SDS-insoluble proteins identified in S. cerevisiae. Proteins identified as becoming insoluble with age in S. cerevisiae were analyzed using DAVID Gene Ontology (Huang da et al., 2009) to determine if certain cellular components were enriched (see Materials & Methods). This analysis revealed only three significantly enriched GO categories (false discovery rate < 0.05): Mitochondrion, Ribonucleoprotein and Chaperonin-containing T complex. Genes that are a part of one or more of these three enriched GO categories are noted (Column D). C. elegans homologs were determined using the HomoloGene database. Insol in aged C. elegans (Column G) refers to those proteins also identified as becoming insoluble with age in a related C. elegans study (David et al., 2010).
- Table S3 - Table S3. iTRAQ comparison of SDS-insoluble proteins extracted from nitrogen-starved and aged cells. Insoluble proteins were extracted and compared using iTRAQ mass spectrometry from aged cells (AGD) and nitrogen-starved cells from a logarithmically-growing culture (STV). As this analysis was done using biological replicates (labeled a and b) of both samples, the levels of the identified proteins were evaluated between these conditions in four distinct comparisons. Individual proteins were judged to be at different levels in Aged and Starved samples based on the following criteria: 1) iTRAQ ratios exceeded biological-variance for the protein (identified in Supplemental Table 1), 2) iTRAQ ratio was accompanied with a statistically significant p-value (< 0.05) in at least two of the four comparisons, and 3) were on average 1.5 fold different between nitrogen-starved and aged samples. Proteins that met these criteria are highlighted in Column W.