Table 1 Characteristics of the datasets (re-)analyzed in this study

From: Metaproteomic portrait of the healthy human gut microbiota

Dataset code

# subjects

Country

Stool PT

Sample prep

LC run (min)

Instrument model

FM

ProteomeXchange accession

Reference

D01

6

Spain

yes

ISD

265

Q-Exactive

HCD

PXD020786

56

D02

16

Australia

yes

ISD

90

Q-Exactive

HCD

PXD008870

57

D03

20

China

no

FASP

150

Fusion

HCD

IPX0002453001

58

D04

17

Germany

no

Gel

165

Elite

CID

PXD010371

59

D05

19

Germany

no

FASP

155

Elite

CID

PXD034175

60

D06

20

Italy

no

FASP

180

Velos

HCD

PXD005780a

14a

D07

8

USA

yes

ISD

265

Fusion

HCD

PXD022433

61

D08

12

Italy

no

FASP

180

Q-Exactive

HCD

PXD046818

unpublished

D09

10

Italy

no

FASP

310

Velos

HCD

PXD046818

unpublished

D10

6

Canada

yes

ISD

120

Q-Exactive

HCD

PXD015482

62

  1. CID Collision-induced dissociation, FASP Filter-aided sample preparation, FM fragmentation mode, HCD Higher energy collisional dissociation, ISD In solution digestion, LC Liquid chromatography, PT Pretreatment. All instruments were Orbitrap mass spectrometers from Thermo Fisher Scientific.
  2. aThe original study (and related dataset) reported data from 15 subjects; further 5 subjects from the same cohort had been analyzed following the same protocol and their data have been included in this study (raw MS files have been deposited in ProteomeXchange along with those of datasets D08 and D09).
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