{"database":"iProX","file_versions":[],"scores":null,"additional":{"omics_type":["Proteomics"],"submitter":["Yun Yang"],"species":["Homo Sapiens","Mus Musculus"],"full_dataset_link":["http://www.iprox.org/page/project.html?id=IPX0013448000"],"submitter_email":["yangyunwww@126.com"],"submitter_affiliation":["International Academy of Phronesis Medicine (Guang Dong)"],"sample_protocol":[""],"repository":["iProX"],"data_protocol":[""],"pubmed_abstract":["Large-scale tissue proteomics requires workflows that are efficient, rapid, and repeatable across diverse samples. Herein, we present a Simple Workflow for Integrated and Fast Tissue-preparation (SWIFT), which enables complete processing of fresh-frozen (FF) and formalin-fixed, paraffin-embedded (FFPE) tissues in either one- or two-step formats while maintaining deep proteome coverage with high repeatability from low- to microgram-level tissues. For FF tissues, an incubation process integrating lysis, reduction, alkylation, and digestion generates peptide samples directly from tissues in ≤1.5 h. For FFPE tissues, concurrent deparaffinization, rehydration, and de-cross-linking are achieved within 0.5 h, followed by one-step peptide preparation. Furthermore, our workflows eliminate desalting and offline cleanup steps, thereby reducing variability and total processing time. Using our methods, we identified up to ∼10,000 protein groups and ∼150,000 peptides across multiple mouse organs on the timsTOF Pro. Repeatability was high (pairwise Pearson's <i>r</i> > 0.96 across six experimental replicates), with dynamic ranges spanning 6-7 orders of magnitude. Organ-enriched protein analysis identified functionally distinct proteins unique to each tissue. Paired FF and FFPE analyses revealed preservation-induced shifts, with FFPE tissues showing reduced detection of membrane-associated and respiratory proteins, including mitochondrial Complex I. Together, our fast and simplified workflows enable deep tissue proteomics for large-scale clinical and translational studies in a cost-effective and widely accessible manner."],"pubmed_title":["Simple, Fast, and Highly Efficient One- or Two-Step Proteomic Preparation Enables Deep Profiling of Microgram-Level FF and FFPE Tissues."],"pubmed_authors":["Wei Chuping C, Zhang Qiuxia Q, Fu Changying C, Leng Yeye Y, Huang Chuanxi C, He Fuchu F, Yang Yun Y"],"additional_accession":[]},"is_claimable":false,"name":"Simple Workflow for Integrated and Fast Tissue-preparation for microgram-level FF and FFPE Tissues Proteomics Analysis","description":"We present Simple Workflow for Integrated and Fast Tissue-preparation (SWIFT) workflows, enabling complete processing of fresh-frozen (FF) and formalin-fixed, paraffin-embedded (FFPE) tissues in one- or two-step formats, while maintaining deep proteome coverage with good repeatability. For FF tissues, an incubation process integrating lysis, reduction, alkylation, and digestion can generate peptide samples directly from tissues in ≤ 1.5 h. For FFPE tissues, simultaneous deparaffinization, rehydration, and de-crosslinking was achieved within 0.5 h, followed by one-step pretreatment to obtain peptides.","dates":{"publication":"Mon Apr 27 00:00:00 BST 2026"},"accession":"PXD077679","cross_references":{"TAXONOMY":["10090","9606"],"pubmed":["42046375"]}}