Arginine limitation causes a directed DNA sequence evolution response in colorectal cancer cells

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UID: 11350

Author(s): Heissel, Soren, Tavazoie, Sohail F.* * MSK affiliated

Description: Description from PRIDE:

"Proteomic changes following arginine deprivation in colorectal cancer cells before/after starvation were quantified with TMT mass spec"

Sample Processing Protocol from PRIDE:

"RKO cells were plated in full media in quadruplicates. Once at 40% confluence, cells were washed with PBS and continued on either full media (condition “DF” 1-4) or low-arginine media (12.5 uM - condition “DL” 1-4), both supplemented with dialyzed fetal bovine serum. Cells were then collected at 24 hours using a lysis buffer consisting of 0.02 M Tris-HCl (pH 7.4), 0.1 M KCl, 0.001 M EDTA (pH 8), and 0.5 M NP-40, and cOmplete protease inhibitor (Roche). Cell lysates were precipiated and proteins were digested with trypsin and labeled with TMTpro. Peptides were analyzed with a Q-Exactive HF in MS2"

Subject of Study

Subject(s)

Access via PRIDE

Accession #: PXD036737
Access Restrictions: Free to All
Access Instructions: Available for download from PRIDE via a CC0 license.
Associated Publications: Hsu D, Gao J, Yamaguchi N, Pinzaru A, Wu Q, Mandayam N, Liberti M, Heissel S, Alwaseem H, Tavazoie S, Tavazoie S. Arginine limitation drives a directed codon-dependent DNA sequence evolution response in colorectal cancer cells. Science Advances. 2023; 9(1):eade9120.
Equipment Used: Q Exactive HF
Mass Spectrometer
Software Used: Andromeda
A Peptide Search Engine Integrated into the MaxQuant Environment

MaxQuant
A quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.
Dataset Format(s): RAW
Dataset Size: 18.9 GB

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