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UnknownEvaluation of Protein Identification and Quantification by the diaPASEF Method on timsTOF SCP.
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S-EPMC12379512 | biostudies-literature
ProteomicsLessons learned in label free single cell proteomics on a TIMSTOF SCP system
This repository is an amalgamation of different single cells analyzed using label free approaches (both DDA/PASEF and DIAPASEF) on a TIMSTOF SCP system. Cells analyzed including multiple immoratalized cancer cell lines and primary human hepatocytes isolated from a single donor
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2024-08-17 | MSV000095633 | MassIVE
ProteomicsBenchmarking of single cell proteomics data analysis workflows
Single cell proteomics data containing quantitative information of THP1 and U937 monocytes that were treated or not to undergo a macrophage-like differentiation. Dataset also contains "Mix" samples generated by mixing in equal proportions THP1 and U937 peptides in the single-cell range or by process...
ORGANISM(S): Homo sapiens (Human) 
2024-02-02 | PXD046211 | Pride
Single cell Macrophage Benchmarking Monocyte Mix Scp 
ProteomicsDemocratised single cell proteomics uncovers tumor associated macrophage signature in CYLD cutaneous syndrome skin tumors
Single-cell proteomics (SCP) reveals heterogeneity and biological insights inaccessible to bulk analysis. Key limitations are cost, sample loss during processing, and accessibility to state-of-the-art instrumentation. We describe a label free SCP methodology in human tissue, combining fluorescence a...
ORGANISM(S): Homo sapiens (Human) 
2026-06-18 | PXD073250 | Pride
Scp Skin tumor Ccs Tam 
ProteomicsOvercoming preservation challenges to enable single-cell proteomics of fixed cell and tissue samples with retained proteome integrity
Recent advances in single-cell proteomics (SCP) now enable the unbiased quantification of the proteome to a depth of several thousand proteins across hundreds of cells. Yet the broader adoption beyond specialised groups remains limited due to the need for specific equipment and expertise. A major ch...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) 
2025-05-23 | PXD061710 | Pride
Human Pancreas Mouse Lc-ms/ms Scp 
ProteomicsHLA class I MAPPs Assay in 10 mono-allelic cell lines transfected with SaCas9, AsCas12a and CasΦ
MHC-associated peptide proteomics (MAPPs) enables direct identification of intracellular peptides naturally processed and presented by cells, providing experimental evidence for antigen processing and HLA class I presentation. In this dataset an HLA-A/B/C-focused MAPPs workflow was used on 10 mono-a...
ORGANISM(S): Homo sapiens (Human) 
2026-09-14 | PXD073207 | Pride
ProteomicsHLA-DR MAPPs Assay in moDCs From 8 Donors Loaded With Infliximab
MHC-associated peptide proteomics (MAPPs) enables direct identification of peptides naturally processed and presented by APCs, providing experimental evidence for antigen processing and HLA class II presentation. In this dataset published in PMID: 41085630, an HLA-DR–focused MAPPs workflow was used ...
ORGANISM(S): Homo sapiens (Human) 
2026-02-13 | PXD074155 | Pride
ProteomicsSingle Skeletal Muscle Fiber Proteomics with timsTOF SCP
The following files are located in this repository: 1) Raw mass spectrometry output for 53 skeletal muscle fibers 2) Spectral library used in library-free search 3) UniProt FASTA file used for initial library-free search and reannotation in second search 4) Final peptide output from DIA-NN 5) Final ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2023-02-14 | MSV000091282 | MassIVE
ProteomicsSingle cell proteomics of an HDAC inhibitor by label free proteomics
NCI-H-358 cancer cells were treated with the HDAC inhibitor mocetinostat for 24 hours. Single cells were isolated by FACs and prepared in a single well prior to diaPASEF analysis on a TIMSTOF SCP. A 40cm column was used for all analysis using a 200nL/min active gradient of 180 minutes. Library runs ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2024-05-05 | MSV000094678 | MassIVE
ProteomicsSubsection and proteomic analysis of single algael cells on multiple TOF mass spectrometers
Single cells were physically sectioned into 6 distinct fractions, processed and analyzed on a TIMSTOF Flex, TIMSTOF SCP and ZenoTOF mass analyzer using both DDA and DIA methods.
ORGANISM(S): Caulerpa Taxifolia (ncbitaxon:76313) 
2024-03-22 | MSV000094383 | MassIVE
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