Evidence map›Paper›PMID 31057293›Full record

ArticleJournal of proteomics & bioinformatics2019

A Method for Isolation and Proteomic Analysis of Outer Membrane Vesicles from Fecal Samples by LC-MS/MS.

Jing Wu, Mingrui An, Jianhui Zhu, Zhijing Tan, Grace Y Chen, Ryan W Stidham, David M Lubman

Abstract read
In one paragraph

Article in Journal of proteomics & bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed.

  1. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Jing WuDepartment of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA.
Mingrui AnDepartment of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA.
Jianhui ZhuDepartment of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA.
Zhijing TanDepartment of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA.
Grace Y ChenDepartment of Internal Medicine, Division of Hematology/Oncology University of Michigan, Ann Arbor, MI 48109, USA.
Ryan W StidhamDepartment of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI, 48109, USA.
David M LubmanDepartment of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA.

Funding

Tumor Biology and Microenvironment (Program 1)P30CA022453 · NCI · WAYNE STATE UNIVERSITY · PI Julie Lynn Boerner · 1985 to 2026
$68.4M
University of Michigan Center for Gastrointestinal ResearchP30DK034933 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI OMARY, BISHR · 1986 to 2021
$22.5M
Pilot Project ProgramP30ES020957 · NIEHS · WAYNE STATE UNIVERSITY · PI RUDEN, DOUGLAS M · 2014 to 2021
$10.1M
Microsequencing in an Ion Trap/reTOF DeviceR01GM049500 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI LUBMAN, DAVID M. · 1994 to 2016
$3.0M
Orbitrap Velos with ETD for Wayne State ProteomicsS10OD010700 · OD · WAYNE STATE UNIVERSITY · PI STEMMER, PAUL M · 2012 to 2012
$575k
Identifying bacterial regulators of tumorigenesisR21CA191744 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI CHEN, GRACE Y., LUBMAN, DAVID M. · 2015 to 2016
$371k
Therapeutic Monitoring in Pancreatic Cancer Using an Exosome Based Mass Spec AssayR21CA189775 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI LUBMAN, DAVID M. · 2015 to 2016
$371k
NCI NIH HHS P30 CA022453NCI NIH HHS R21 CA189775NCI NIH HHS R21 CA191744NIDDK NIH HHS P30 DK034933NIEHS NIH HHS P30 ES020957NIGMS NIH HHS R01 GM049500NIH HHS S10 OD010700
6 · The paper itself

Abstract

Outer membrane vesicles (OMVs) are nanosized spheres secreted by bacteria that are similar to the vesicles known as exosomes, which are secreted by most mammalian cell types. In contrast to many studies focusing on optimizing methods for enriching exosomes from biological fluid, few studies have been conducted to investigate outer membrane vesicles from fecal samples. Herein, we have developed a pipeline comprised of membrane filtration and multiple cycles of ultracentrifugation (UC) to isolate OMVs from fecal samples for proteomics analysis, where multiple cycles of UC are required for removal of contaminants. By iTRAQ labeling quantitative proteomics analysis, different filter sizes (0.22 μm and 0.45 μm) were compared in terms of their performance in enriching OMVs and eliminating background fecal material. Using the 0.45 μm filter, a slightly higher protein yield was obtained but no additional contaminating proteins from bacteria were identified compared to those from the 0.22 μm filter. The 0.45 μm filter together with the multiple cycles of UC were thus used to isolate OMVs for proteomics analysis. To our knowledge, this is the first study profiling a large number of OMV proteins from fecal samples. Such capabilities may help provide valuable information in understanding the communication between the host and microbiota, which is critical in preventing cancer and disease development.

Indexed as

BacteriaFecal samplesFilterOuter membrane vesiclesUltracentrifugation

Identifiers

PMID31057293
PMCPMC6497448

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.