PXD021922-1

PXD021922 is an original dataset announced via ProteomeXchange.

Title	BoxCarmax: a novel high-selectivity data-independent acquisition mass spectrometry method for the analysis of protein turnover and complex samples
Description	The data-independent acquisition (DIA) mode performed in the latest high-resolution, high-speed mass spectrometers offers a powerful analytical tool for biological investigations. The DIA mass spectrometry (MS) combined with the isotopic labeling approach holds a particular promise for increasing the multiplexity of DIA-MS analysis, which could assist the relative protein quantification and the proteome-wide turnover profiling. However, the wide isolation windows employed in conventional DIA methods lead to a limited efficiency in identifying and quantifying isotope-labelled peptide pairs. Here, we optimized a high-selectivity DIA-MS named BoxCarmax that supports the analysis of complex samples, such as those generated from Stable isotope labeling by amino acids in cell culture (SILAC) and pulse SILAC (pSILAC) experiments. BoxCarmax enables multiplexed acquisition at both MS1- and MS2- levels, through the integration of BoxCar and MSX features, as well as a gas-phase separation strategy. We found BoxCarmax modestly increased the identification rate for label-free and labeled samples but significantly improved the quantitative accuracy in SILAC and pSILAC samples. We further applied BoxCarmax in studying the protein degradation regulation during serum starvation stress in cultured cells, revealing valuable biological insights. Our study offered a new and accurate approach for the MS analysis of protein turnover and complex samples.
HostingRepository	PRIDE
AnnounceDate	2021-02-02
AnnouncementXML	Submission_2021-02-02_00:08:17.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yansheng Liu
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-10-12 06:55:03	ID requested
⏵ 1	2021-02-02 00:08:17	announced
2	2024-10-22 05:18:29	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: PC12 cells, HeLa cells, human plasma, serum starvation, DIA

Yansheng Liu
contact affiliation	Yale University School of Medicine
contact email	yansheng.liu@yale.edu
lab head
Yansheng Liu
contact affiliation	Yale University School of Medicine
contact email	yansheng.liu@yale.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD021922
     1. Label: PRIDE project
     2. Name: BoxCarmax: a novel high-selectivity data-independent acquisition mass spectrometry method for the analysis of protein turnover and complex samples