PXD027351-1

PXD027351 is an original dataset announced via ProteomeXchange.

Title	Online Nanoflow Two-Dimension Comprehensive Active Modulation Reversed Phase-Reversed Phase Liquid Chromatography High Resolution Mass Spectrometry for Metaproteomics of Environmen-tal and Microbiome Samples
Description	Metaproteomics is a powerful analytical approach that can assess the functional capabilities deployed by microbial communi-ties in both environmental and biomedical microbiome settings. Yet the mass spectra resulting from these mixed biological communities are challenging due to the high number of low intensity peak features. The use of multiple dimensions of chroma-tographic separation prior to mass spectrometry analyses has been applied to proteomics previously but can require increased sampling handling and instrument time. Here we demonstrate an automated online comprehensive active-modulation two-dimensional liquid chromatography method for metaproteome sample analysis. A high pH PLRP-S column was used in the first dimension followed by low pH separation in the second dimension using dual modulating C18 traps and a C18 column. This method increased the number of unique peptides found in ocean metaproteome samples by more than 50% when com-pared to a one dimension separation while using the same amount of sample and instrument time.
HostingRepository	PRIDE
AnnounceDate	2022-05-20
AnnouncementXML	Submission_2022-05-20_03:29:33.426.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD027351
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Matthew McIlvin
SpeciesList	scientific name: marine plankton environmental sample; NCBI TaxID: 632957; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-15 23:42:43	ID requested
⏵ 1	2022-05-20 03:29:34	announced

McIlvin MR, Saito MA, Online Nanoflow Two-Dimension Comprehensive Active Modulation Reversed Phase-Reversed Phase Liquid Chromatography High-Resolution Mass Spectrometry for Metaproteomics of Environmental and Microbiome Samples. J Proteome Res, 20(9):4589-4597(2021) [pubmed]

submitter keyword: metaproteomics, ocean, proteomics, RPRP, 2DLC, automated, LC, LCMS, comprehensive active modulation

Mak Saito
contact affiliation	Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Unites States
contact email	msaito@whoi.edu
lab head
Matthew McIlvin
contact affiliation	Woods Hole Oceanographic Inst.
contact email	mmcilvin@whoi.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/05/PXD027351

PRIDE project URI

• PRIDE
  1. PXD027351
     1. Label: PRIDE project
     2. Name: Online Nanoflow Two-Dimension Comprehensive Active Modulation Reversed Phase-Reversed Phase Liquid Chromatography High Resolution Mass Spectrometry for Metaproteomics of Environmen-tal and Microbiome Samples