PXD064088

PXD064088 is an original dataset announced via ProteomeXchange.

Title	AUTO-SP: automated sample preparation for analyzing proteins and protein modifications
Description	Liquid chromatography (LC) tandem mass spectrometry (MS/MS) is one of the widely used proteomic techniques to study the alterations occurred at protein level as well as post-translation modifications (PTMs) of proteins that are relevant to different physiological or pathological statuses. The mass spectrometric analysis of peptides digested from proteins (bottom-up proteomics) has emerged as one of the major approaches for proteomics. In this approach, proteins are first cleaved by one or more proteases into peptides for MS analysis and peptides with PTMs are further enriched followed by the LC-MS/MS analysis. To achieve a reproducible and quantitative proteomic characterization, a well-established protease digestion and PTM peptide enrichment protocol is critical. In this study, we developed AUTO-SP, a sample preparation platform providing automated protocols for BCA analysis, protein digestion and PTM enrichment for protein and PTM analyses. We utilized patient-derived xenograft (PDX) breast cancer tumor tissues (basal-like and luminal subtypes) to demonstrate the efficacy of AUTO-SP. The protein amount was quantified and proteins were further digested by using AUTO-SP for each PDX sample. Based on the data-independent acquisition (DIA)-MS data, we observed samples of the same breast cancer subtypes were highly correlated (≥0.98). Additionally, >25,000 phosphopeptides and >14,000 ubiquitinated peptides were identified in the PDX samples when using AUTO-SP for PTM enrichment, while unique pathways were enriched from the differentially expressed ubiquitinated peptides of basal-like and luminal subtypes. AUTO-SP demonstrated its efficacy to provide reliable and reproducible sample preparation procedure for MS-based proteomic and PTM analyses.
HostingRepository	PRIDE
AnnounceDate	2026-03-16
AnnouncementXML	Submission_2026-03-16_07:06:29.394.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tung-Shing Lih
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	ubiquitinylated lysine; phosphorylated residue
Instrument	timsTOF HT

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-20 00:53:26	ID requested
⏵ 1	2026-03-16 07:06:30	announced

10.1021/acs.analchem.5c00886;

Lih TM, Jiao L, Chen L, Woo J, Wang Y, Zhang H, AUTO-SP: Automated Sample Preparation for Analyzing Proteins and Protein Modifications. Anal Chem, 97(31):16751-16758(2025) [pubmed]

submitter keyword: proteomics,automation, mass spectrometry, sample preparation, protein modifications

T. Mamie Lih
contact affiliation	Johns Hopkins University
contact email	tlih1@jhmi.edu
lab head
Tung-Shing Lih
contact affiliation	Johns Hopkins University
contact email	tlih1@jhmi.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD064088
     1. Label: PRIDE project
     2. Name: AUTO-SP: automated sample preparation for analyzing proteins and protein modifications