Proteomic Profiling of Human Samples

The proteins in each sample were reduced, alkylated and digested with trypsin according to the FASP protocol.^{[63 (link)]} The peptides were analyzed by nano-LC-MS/MS, and peptide identification as previously described with the following modifications.^{[64 (link)]} Reverse phase chromatography was performed using an in-house packed column (40 cm long X 75 μm ID X 360 OD, Dr. Maisch GmbH ReproSil-Pur 120 C18-AQ 1.9 μm beads) and a 120 min gradient. The Raw files were searched using the Mascot algorithm (ver. 2.5.1) against a protein database constructed by combining the human UniProt protein database (downloaded April 24, 2018, 20,303 entries), and a contaminant database (cRAP, downloaded 11–21-16 from http://www.thegpm.org) via Proteome Discoverer 2.1. Only peptide-spectrum matches with expectation value of less than 0.01 (“High Confidence”) were used. ^{[64 (link)]}

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Liu A., Yu T., Young K., Stone N., Hanasoge S., Kirby T.J., Varadarajan V., Colonna N., Liu J., Raj A., Lammerding J., Alexeev A, & Sulchek T. (2019). Cell Mechanical and Physiological Behavior in the Regime of Rapid Mechanical Compressions that Lead to Cell Volume Change. Small (Weinheim an der Bergstrasse, Germany), 16(2), e1903857.

Publication 2019

ReproSil-Pur 120 C18-AQ 1.9 μm beads

A protein Crap Human Ms ms Peptide Proteins Proteome Pur 1 Reprosil Reverse phase chromatography Trypsin

Corresponding Organization : Georgia Institute of Technology

Other organizations : The Wallace H. Coulter Department of Biomedical Engineering, Cornell University

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Variable analysis

independent variables

None explicitly mentioned

dependent variables

Peptide identification

control variables

Proteins in each sample were reduced, alkylated and digested with trypsin according to the FASP protocol
Reverse phase chromatography was performed using an in-house packed column (40 cm long X 75 μm ID X 360 OD, Dr. Maisch GmbH ReproSil-Pur 120 C18-AQ 1.9 μm beads) and a 120 min gradient
The Raw files were searched using the Mascot algorithm (ver. 2.5.1) against a protein database constructed by combining the human UniProt protein database (downloaded April 24, 2018, 20,303 entries), and a contaminant database (cRAP, downloaded 11–21-16 from http://www.thegpm.org)

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