PXD081138

PXD081138 is an original dataset announced via ProteomeXchange.

Title	LC-SWATH-MS-Based Proteomic Analysis of Non-Malignant and Malignant FFPE Cervical Samples
Description	We analyzed FFPE (Formalin-Fixed Paraffin-Embedded)samples from healthy (non-cancerous), pre-malignant, in situ, and invasive cervical cancer subjects using mass spectrometry-based proteomics. Proteins were extracted from FFPE following standar protocols, including deparaffinization with xylene, rehydration (ethanol-based), and assisted by lysis buffer and sonication. Soluble proteins were then reduced, alkylated and digested using the Pierce Mass Spec Sample Prep Kit for Cultured Cells (Cat. No. 84840) as per the manufacturers instructions. Tryptic peptides were dried down by SpeedVac and reconstituted in water/acetonitrile 95:5 v/v with 0.1% formic acid. The peptide concentration was analyzed by using the Pierce Quantitative Colorimetric Peptide Assay kit (Cat. No. 23275) as per the manufacturers instructions. Data from DDA samples were processed using ProteinPilot software version 4.2 (AB Sciex, Foster City, CA, USA) with the Paragon algorithm. MS/MS data were searched against a SwissProt Homo sapiens database containing 20,360 reviewed proteins (downloaded in September 2018). The parameters used were as follows: Sample type, Identification; Cys Alkylation, Iodoacetamide; digestion, trypsin; Instrument, TripleTOF 5600; Special Factors, none; Species, Homo sapiens; ID Focus, Biological modifications, and amino acid substitutions; Search Effort, Thorough ID. False discovery rate analysis was also performed. Targeted data extraction of SWATH files was done using the SWATH Acquisition MicroApp 2.0 in PeakView version 1.2 (AB Sciex, Foster City, CA, USA) along with the spectral library generated by DDA. Retention time calibration among samples was done manually using two endogenous peptides (>10,000 intensity) every 10 minutes throughout the LC gradient. The parameters used were as follows: Number of peptides per protein, 6; Number of transitions per peptide, 6; Peptide confidence threshold, 99%; False discovery rate threshold, 1%; exclude modified peptides, checked; XIC extraction window, 10 min, and; XIC width, 50 ppm. Protein peak areas were exported to Markerview (AB Sciex, Foster City, CA, USA) for further processing. The reversed and common contaminants hits were removed and then the protein abundance quantification table exported as a .tsv file. The filtered protein abundance table was exported as a .tsv file and then quantile-normalized using NormalyzerDE version 1.3.4 (https://normalyzerde.serve.scilifelab.se/). For all univariate and multivariate statistical analyses, the quantitative table was imputed for missing values (one-fifth minimum value imputation) and log2-transformed.
HostingRepository	MassIVE
AnnounceDate	2026-07-15
AnnouncementXML	Submission_2026-07-15_14:56:58.307.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Aldo Moreno
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 5600+

Revision	Datetime	Status	ChangeLog Entry
0	2026-07-15 14:49:41	ID requested
⏵ 1	2026-07-15 14:56:58	announced

no publication

submitter keyword: SWATH, Cervical cancer, Proteomics, DatasetType:Proteomics

Aldo Moreno Ulloa
contact affiliation	Centro de Investigacion Cientifica y de Educacion Superior de Ensenada
contact email	amoreno@cicese.mx
lab head
Aldo Moreno
contact affiliation	CICESE
contact email	amoreno@cicese.mx
dataset submitter

MassIVE dataset URI

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