Common Contaminants in NGS
Common Contaminants in Proteomic Data
Sample: Drosophila Melanogaster
| Tag | Annotation | From |
|---|---|---|
| Tax_Id=9606 | Human | Human: Duraing experiments |
| Bos taurus | Cattle | Antibody or so |
| Q9U6Y5 Green fluorescent protein (GFP-Cter-HisTag) | GFP protein | Genetic inserted tags |
| P00761 | TRYP_PIG | Trypsin from pig |
| Keratin | Common contamination | from air, skin, nail, or hair |
| P15636 Protease I precursor Lysyl endopeptidase | Achromobacter lyticus | NA |
Common Contaminants from DNA-seq
Microbiome from Ultrapure Water System
| UPW system | Location of sampling ports | Nearest neighbor(s) of main strain in BLAST search of GenBank | No. of isolates (% total) |
|---|---|---|---|
| UPWS-1 | Before UV254 (polishing loop) | Ralstonia pickettii | 8 (13) |
| Bradyrhizobium sp. | 3 (5) | ||
| Flavobacterium sp. | 3 (5) | ||
| Burkholderia sp. | 4 (6.7) | ||
| Stenotrophomonas sp. | 5 (8.3) | ||
| Mycobacterium sp. | 4 (6.7) | ||
| Bacillus sp. | 8 (13.3) | ||
| Other | 25 (41) | ||
| UPWS-1 | DL | Ralstonia pickettii | 8 (24) |
| Bradyrhizobium sp. | 12 (36) | ||
| Pseudomonas saccharophilia | 4 (12) | ||
| Other | 9 (27) | ||
| UPWS-2 | After UV254, UV185, and final filters (0.1 μm) | Bradyrhizobium sp. | 6 (60) |
| Other | 4 (40) | ||
| UPWS-3 | DL | Ralstonia pickettii | 4 (66) |
| Bradyrhizobium sp. | 1 (17) | ||
| Other | 1 (17) | ||
| UPWS-4 | DL and DL (return loop) | Bradyrhizobium sp. | 4 (25) |
| Pseudomonas saccharophilia | 4 (25) | ||
| Sphingomonas sp. | 4 (25) | ||
| Other | 4 (25) | ||
| UPWS-5 | DL | Ralstonia pickettii | 6 (100) |
| UPWS-6 | DL, storage tank, before UV254 and after UV254 | Pseudomonas fluorescens | 6 (28) |
| Ralstonia pickettii | 5 (24) | ||
| Pseudomonas saccharophilia | 1 (5) | ||
| Bradyrhizobium sp. | 2 (10) | ||
| Sphingomonas sp. | 3 (14) | ||
| Other | 4 (19) |
Kulakov LA, McAlister MB, Ogden KL, Larkin MJ, O’Hanlon JF (April 2002). “Analysis of bacteria contaminating ultrapure water in industrial systems”. Applied and Environmental Microbiology. 68 (4): 1548–55. doi:10.1128/AEM.68.4.1548-1555.2002. PMC 123900. PMID 11916667. ↩︎
Common Contaminants in NGS
https://karobben.github.io/2022/09/20/Bioinfor/proteomic-contaminants/
