| Biological samples |
|
|
| Primary human lung cells |
University of Rochester Medical Center |
Donor D011, Provided by Dr.Gloria Pryjuber |
|
| Chemicals, peptides, and recombinant proteins |
|
|
| Fetal bovine serum |
Thermo Fisher Scientific |
10–082-147 |
| RPMI-1641 |
Thermo Fisher Scientific |
11875093 |
| Dulbecco’s Modified Eagle Medium (DMEM) |
Thermo Fisher Scientific |
11965092 |
| Lipopolysaccharides (LPS) from Escherichia coli
|
Sigma Aldrich |
L2630–10MG |
| Calcein AM |
Thermo Fisher Scientific |
C3100MP |
| UREA |
Sigma Aldrich |
U5128 |
| Ammonium bicarbonate (NH4HCO3) |
Sigma Aldrich |
S2454 |
| Dithiothreitol (DTT) No-Weigh™ |
Thermo Fisher Scientific |
A39255 |
| Iodoacetate (IAA), Single-Use |
Thermo Fisher Scientific |
A39271 |
| Formic acid, LC-MS grade |
Thermo Fisher Scientific |
28905 |
| Lys-C, Mass Spectrometry Grade |
Promega |
V1671 |
| Trypsin, Mass Spectrometry Grade |
Promega |
V5280 |
| n-Dodecyl β-D-maltoside (DDM) |
Sigma Aldrich |
D4641–1G |
| 10x phosphate buffered saline (PBS) |
Sigma Aldrich |
P5493–1 L |
|
| Critical commercial assays |
|
|
| Pierce™ BCA Protein Assay Kit |
Thermo Fisher Scientific |
23225 |
|
| Deposited data |
|
|
| Proteomics RAW files |
MassIVE |
MSV000085937; https://doi.org/10.25345/C5PR1P
|
|
| Experimental models: Cell lines |
|
|
| K-562 human cell line |
Oregon Health & Science University |
Provided by Dr.Anupriya Agarwal, originally obtained from ATCC (CCL-243) |
| MOLM-14 human cell line |
Oregon Health & Science University |
Provided by Dr.Anupriya Agarwal, originally established from the peripheral blood of a patient at relapse of acute monocytic leukemia by Dr. Matsuo et al. at Fujisaki Cell Center in Japan |
| CMK human cell line |
Oregon Health & Science University |
Provided by Dr.Anupriya Agarwal, originally obtained from the German National Resource Center for Biological Material |
| RAW 264.7 mouse cell line |
ATCC |
TIB-71 |
| HeLa human cell line |
ATCC |
CCL-2 |
|
| Software and algorithms |
|
|
| MaxQuant (Ver 1.6.2.10) |
Max Planck Institute of Biochemistry |
https://www.maxquant.org/
|
| Perseus (Ver 1.6.12.0) |
Max Planck Institute of Biochemistry |
https://www.maxquant.org/perseus/
|
| FAIMS MzXML converting tool |
PNNL |
https://github.com/PNNL-Comp-Mass-Spec/FAIMS-MzXML-Generator/releases
|
| RomicsProcessor R package |
PNNL |
https://github.com/PNNL-Comp-Mass-Spec/RomicsProcessor
|
| GraphPad Prism Ver.8.3.0 |
GraphPad Software |
https://www.graphpad.com/scientific-software/prism/
|
