Dataset Information

Creatine kinase B, a downstream effector of MYB, controls migration of osteosarcoma cells via regulation of N-cadherin

ABSTRACT: A study aimed at identification of proteins associated with CRISPR/Cas-induced depletion of creatine kinase B (CKB) in SAOS-LM5 metastatic osteosarcoma cell line using LC-MS/MS in data-independent acquisition (DIA)-parallel accumulation serial fragmentation (diaPASEF) mode. Here we prepared two KO cell lines, SAOS-LM5 CKB KO 6C and SAOS-LM5 CKB KO 11B, as well as control SAOS-LM5 scrambled cell line. After filter-aided sample preparation (FASP) protein digestion and peptide desalting, the samples were conducted to total proteome analysis. The data acquisition was performed in diaPASEF mode on timsTOF Pro 2 mass spectrometer. Data were processed in Spectronaut 19.0 in directDIA mode. This project covers the raw files from the diaPASEF measurements as well as search results from the Spectronaut 19.0 software.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

DISEASE(S): Osteosarcoma

SUBMITTER: Pavel Bouchal

LAB HEAD: Pavel Bouchal

PROVIDER: PXD065263 | Pride | 2026-01-23

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	6136_BRIMS1_DIA_RSLC_2col-138min_TFA_11B1_ID_1_GE6_1_18050.d.zip	Other
	6136_BRIMS1_DIA_RSLC_2col-138min_TFA_11B2_ID_1_GE7_1_18098.d.zip	Other
	6136_BRIMS1_DIA_RSLC_2col-138min_TFA_11B3_ID_1_GE8_1_18158.d.zip	Other
	6136_BRIMS1_DIA_RSLC_2col-138min_TFA_6C1_ID_1_BA1_1_18038.d.zip	Other
	6136_BRIMS1_DIA_RSLC_2col-138min_TFA_6C2_ID_1_BA2_1_18062.d.zip	Other

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Publications

Creatine kinase B, a downstream effector of c-Myb, controls migration of osteosarcoma cells via regulation of N-cadherin.

Pokludová Jana J Lapčík Petr P Zambo Iva Staniczková IS Kohoutek Jiří J Zapletalová Danica D Múdry Peter P Adámková Dagmar D Červinka Jakub J Loja Tomáš T Lexa Matej M Verner Jan J Šmarda Jan J Bouchal Pavel P Knopfová Lucia L Beneš Petr P

Cancer cell international 20251205 1

<h4>Background</h4>We have recently identified transcription factor c-Myb as a negative prognostic factor in osteosarcoma (OSA) patients associated with metastatic disease. Transcriptomic analysis identified creatine kinase B (CKB) as one of the most deregulated genes in OSA cell lines with depleted MYB. CKB is a component of the creatine/phosphocreatine system that plays a key role in maintaining cellular energy homeostasis and energy transport to sites with high demand. This study was therefor ...[more]

PMID: 41345636

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Project description:Data independent acquisition (DIA or DIA/SWATH ) mass spectrometry has emerged as a primary measurement strategy in the field of quantitative proteomics. diaPASEF is a recent adaptation that leverages trapped ion mobility spectrometry (TIMS) to improve selectivity and increase sensitivity. The complex fragmentation spectra generated by co-isolation of peptides in DIA mode are most typically analyzed with reference to prior knowledge in the form of spectral libraries. The best established method for generating libraries uses data dependent acquisition (DDA) mode, or DIA mode if appropriately deconvoluted, often including offline fractionation to increase depth of coverage,to create spectral libraries. More recently strategies for spectral library generation based on gas phase fractionation (GPF), where a representative sample is injected serially using narrow window DIA methods designed to cover different slices of the precursor space, have been introduced and performed comparably to deep offline fractionation-based libraries for DIA data analysis. Here, we investigated whether an analogous GPF-based library building approach that accounts for the ion mobility (IM) dimension is useful for the analysis of diaPASEF data and can remove the need for offline fractionation. To enable a rapid library development approach for diaPASEF we designed a GPF acquisition scheme covering the majority of multiply charged precursors in the m/z vs 1/K0 space requiring 7 injections of a representative sample and compared this with libraries generated by direct deconvolution-based analysis of diaPASEF data or by deep offline fractionation and ddaPASEF. . We found that the GPF based library outperformed library generation by direct deconvolution of the diaPASEF data, and performed comparably to deep offline fractionation libraries, when analysing diaPASEF data acquired from 200ng of commercial HeLa digest. With the ion mobility integrated GPF scheme we establish a pragmatic approach to rapid and comprehensive library generation for the analysis of diaPASEF data.