Project : PXD000506

Summary

Title

Host-centric proteomics of stool, part 2 of 2

Description

Soluble extra-cellular proteins and peptides from human and mouse stool were fractionated on a C-4 solid phase extraction cartidge, trypsin digested, C-18 clean up and identified with MS/MS on a LTQ-Velos Orbitrap. Data processing: The readRAW program was used to generate peak lists from the original data. All protein sequences were reversed and concatenated to the original forward-oriented proteins. Spectra were assigned to peptides using a semi-specific enzyme specificity with the Mascot search algorithm (version 2.3.01) using static carbamidomethylation of cysteines, differential oxidized methionines, 50ppm precursor mass tolerance, 2 miscleavages and 0.8Da fragment ion tolerance. Searched against a mouse or human database. The current dataset contains the human data and PXD000240 contains the mouse data.

Sample Processing Protocol

See details in reference PMID : 23982161

Data Processing Protocol

See details in reference PMID : 23982161

Contact

Joshua Lichtman, Stanford University, School of Medicine

Submission Date

09/10/2013

Tissue

Not available

Instrument

LTQ Orbitrap Velos

Software

Not available

Quantification

Not available

Experiment Type

Bottom-up proteomics

Publication

    Lichtman JS, Marcobal A, Sonnenburg J, Elias JE; Host-centric proteomics of stool: A novel strategy focused on intestinal responses to the gut microbiota., Mol Cell Proteomics, 2013 Aug 27, PubMed(s) : 23982161

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