Table 1.
Summary of metaproteomic studies of human gut microbiota
| Sample type | Subject | Separation method | Mass spectrometer | Database | No. of proteins identified | Reference |
|---|---|---|---|---|---|---|
| Feces | 2 infants | 2-D PAGE | MALDI-TOF | Public database | >200 spots, 1 protein identified | Klaassens et al., 2007 |
| Feces | 1 infant | 2D-LC | LTQ Orbitrap | Databases from metagenomic sequences, microbial species, human and common contaminants | 4,031 proteins | Young et al., 2015 |
| Feces | 1 monozygotic twin pair (adult) | 2D-LC | LTQ Orbitrap | Databases from two human metagenomes, human database and common contaminants | 446 human proteins 1,368 microbial proteins |
Verberkmoes et al., 2009 |
| Feces | 3 healthy adults | 1-DE and LC | LTQ Orbitrap | Databases from intestinal microbes, two metagenomes, human protein and food database | 1,790 proteins | Kolmeder et al., 2012 |
| Mucosal lavage | 38 healthy adults | LC WCX magnetic beads |
LTQ Orbitrap MALDI-TOF |
Swiss-Prot | 300 human proteins | Li et al., 2011 |
| Feces | 1 adult with antibiotic treatment | 1-DE and LC | LTQ Orbitrap | Matched metagenome | 3,011 proteins | Pérez-Cobas et al., 2013 |
| Feces | 6 monozygotic twin pairs (1 set healthy, 3 sets concordant twins with CD, 2 sets discordant twins) | 2D-LC | LTQ Orbitrap | Matched metagenome and human microbial isolate reference genome database | 2,904 proteins | Erickson et al., 2012 |
| Mucosal lavage | First cohort: 3 healthy, 6 UC patients Second cohort: 13 healthy, 14 CD, 15 UC |
WCX Protein Chip arrays | SELDI-TOF | Uniprot | 589 proteins | Presley et al., 2012 |
| Mucosal lavage | Discovery cohort: 51 (17 healthy, 13 UC, 21 CD) Validation cohort: 38 healthy |
WCX magnetic beads LC |
MALDI-TOF LTQ Orbitrap |
Swiss-Prot | 599 protein/peptide peaks | Li et al., 2016 |
| Feces | 1 lean and 1 obese teenager | 1-DE and LC | LTQ Orbitrap | Matched and unmatched metagenomes | 613 proteins | Ferrer et al., 2013 |
| Feces | 9 normal, 4 overweight, 16 obese | 1-DE and LC | Orbitrap | In-house metaproteome database | 893,007 MS/MS spectra | Kolmeder et al., 2015 |
| Feces | 3 liver cirrhosis patients and their corresponding spouse | 1-DE and LC | Quadrupole-Orbitrap | UniProt | 5,020 proteins | Wei et al., 2016 |
| Feces | 15 children with cystic fibrosis and their unaffected siblings | 1-DE and LC | Ion trap-FTICR | NCBI | 1,676 proteins | Debyser et al., 2016 |
| Feces | 16 healthy adults (8 probiotics, 8 placebo) | 1-DE and LC | LTQ Orbitrap | In-house metaproteome database | 4,966 peptides | Kolmeder et al., 2016 |
| Feces | 1 healthy adult | LC | LTQ Orbitrap | UniProtKB Swiss-Prot |
3,911 proteins (not centrifuged) 4,587 proteins (centrifuged) |
Tanca et al., 2015 |
| Feces | 2 premature infants | 2D-LC | LTQ Orbitrap | In-house metaproteome database | 807 and 342 proteins (without filtering) 1264 and 1012 proteins (with double filtering) |
Xiong et al., 2015b |
| Feces | 2 healthy adults | 1-DE and LC | LTQ Orbitrap | Matched metagenomes Synthetic metagenomes (iterative search) |
2,331 and 1,870 peptides 5,010 and 3,542 peptides |
Rooijers et al., 2011 |
| Feces | 4 healthy volunteers | LC | LTQ Orbitrap | Metagenome databases UniProt-based databases All bacterial sequences |
>10,000 peptides | Tanca et al., 2016 |
| Feces Mucosal lavage |
8 mice 8 pediatric volunteers |
LC | Q Exactive | Microbial gene catalog databases Target-decoy database |
30,749 mouse protein groups 19,011 human protein groups |
Zhang et al., 2016b |
| Mucosal lavage | 5 teenagers | LC | LTQ Orbitrap | In-house Human Intestinal Microbial Protein Database Target-decoy database |
4,014 protein groups quantified | Zhang et al., 2016a |
1-DE one-dimensional electrophoresis, 2-D PAGE two-dimensional polyacrylamide gel electrophoresis, 2-D LC two-dimensional liquid chromatography, FTICR Fourier transform ion cyclotron resonance, LC liquid chromatography, LTQ linear trap quadrupole, MALDI-TOF matrix-assisted laser desorption/ionization time-of-flight, NCBI National Center for Biotechnology Information, SELDI-TOF surface-enhanced laser desorption/ionization time-of-flight, WCX weak cation exchange