PXD002895 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Standard Pressure LC-MS/MS Using 1.9um C18 Particles Column at Room Temperature |
Description | Although the benefits of reduction of the size of reversed phase particles are established to provide increased sequencing depth and improved chromatography in LCMS experiments, the wide-scale adoption of optimally sized small particles in reversed-phase columns has been hampered by the necessity for specialized equipment such as ultra-high pressure liquid chromatography or a customized column heating apparatus. Here, we introduce a new strategy to routinely fabricate a 50 cm-long, 1.9 µm particle C18 column and extensively characterize the performance of this column. This column was packed under 100 Bar and routinely utilized on a standard quarternary HPLC at pressures below 300 Bar. Expanding the depth of sequencing of peptides that show a statistically significant quantitative change arising from a biological stimulation is critical. Compared with traditional C18 columns packed with 3 µm particles, the column with the 1.9 µm particles operated with a standard HPLC could detect 330% more peptides with statistically significant changes from differentially stimulated T cells. This improved column fabrication methodology provides an inexpensive improvement for single-run LC-MS/MS analysis to optimize sequencing depth, dynamic range, sensitivity, and reproducibility. This study also highlights the importance of the statistical analysis of quantitative proteomic data instead of a sole focus on peptide spectrum match yields. |
HostingRepository | PRIDE |
AnnounceDate | 2022-02-28 |
AnnouncementXML | Submission_2022-02-28_02:24:55.569.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Zhuo Chen |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2015-09-11 03:57:00 | ID requested | |
⏵ 1 | 2022-02-28 02:24:57 | announced | |
Publication List
Ahsan N, Belmont J, Chen Z, Clifton JG, Salomon AR, Highly reproducible improved label-free quantitative analysis of cellular phosphoproteome by optimization of LC-MS/MS gradient and analytical column construction. J Proteomics, 165():69-74(2017) [pubmed] |
Keyword List
curator keyword: Technical |
submitter keyword: Jurkat, Fritless Column, LC-MS/MS, Single-run Proteomics |
Contact List
Arthur Salomon |
contact affiliation | Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, USA |
contact email | art@drsalomon.com |
lab head | |
Zhuo Chen |
contact affiliation | Brown University |
contact email | zhuo_chen@brown.edu |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD002895
- Label: PRIDE project
- Name: Standard Pressure LC-MS/MS Using 1.9um C18 Particles Column at Room Temperature