PXD032019

PXD032019 is an original dataset announced via ProteomeXchange.

Title	A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics
Description	Effective nanoscale phosphoproteome analysis remains a daunting task, primarily due to significant sample loss associated with non-specific surface adsorption during phosphopeptide enrichment and other sample processing steps. To address this issue, we have developed a tandem tip-based C18-IMAC-C18 method which significantly reduces not only sample loss but also sample transfer steps and processing time for phosphopeptide enrichment (to <20 min). The tandem tip method enables identification of >3,000 and >9,500 phosphopeptides from 1 and 10 µg of cell lysate inputs using the label-free method without the spectral library, respectively. Integration of the tandem tip method with our recently developed SOP (Surfactant-assisted One-Pot sample preparation; for nanoscale processing) and iBASIL (improved Boosting to Amplify Signal with Isobaric Labeling; for enhanced detection sensitivity and sample throughput) approaches into a streamlined tandem tip-based workflow enables rapid and sensitive nanoscale phosphoproteome measurements. This streamlined workflow allows for precise quantification of ~600 phosphopeptides from 100 MCF10A cells sorted by FACS, and robust separation of EGF-treated and nontreated MCF10A cells. This workflow opens new avenues for nanoscale phosphoproteome profiling of small numbers of cells and mass-limited samples at the low nanogram levels, which cannot be accessed by current proteomics platforms.
HostingRepository	jPOST
AnnounceDate	2023-01-27
AnnouncementXML	Submission_2023-01-27_23:51:50.740.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chia-Feng Tsai
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide; O-phospho-L-serine; O-phospho-L-threonine; O4'-phospho-L-tyrosine; alpha-amino acetylated residue; unknown modification; unknown modification; unknown modification; unknown modification
Instrument	LTQ Orbitrap; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-03-02 15:49:35	ID requested
⏵ 1	2023-01-27 23:51:51	announced

Tsai CF, Wang YT, Hsu CC, Kitata RB, Chu RK, Velickovic M, Zhao R, Williams SM, Chrisler WB, Jorgensen ML, Moore RJ, Zhu Y, Rodland KD, Smith RD, Wasserfall CH, Shi T, Liu T, A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics. Commun Biol, 6(1):70(2023) [pubmed]

submitter keyword: Tip IMAC, Boosting to Amplify the Signal with Isobaric Labeling, near single-cell, phosphoproteome, Surfactant-assisted One-Pot sample preparation

Chia-Feng Tsai
lab head
Chia-Feng Tsai
contact affiliation	Pacific Northwest National Laboratory
dataset submitter

jPOST dataset URI

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