Dataset Information

Secretome Processing for Proteomics: A Methods Comparison

ABSTRACT: The cancer cell secretome comprises a treasure-trove for biomarkers since it reflects cross-talk between tumor cells and their surrounding environment. In this study, we evaluated six secretome sample processing workflows coupled to single-shot mass spectrometry: 1. Protein concentration by ultrafiltration with a molecular weight cut-off (MWCO) filter and sample preparation through in-gel digestion (IGD); 2. Acetone protein precipitation coupled to IGD; 3. MWCO filter-based protein concentration followed by to in-solution digestion (ISD); 4. Acetone protein precipitation coupled to ISD; 5. Direct ISD; 6. Secretome lyophilization and ISD. To this end, we assessed workflow triplicates in terms of total number of protein identifications, unique identifications, reproducibility of protein identification and quantification and detectability of small proteins with important functions in cancer biology such as cytokines, chemokines and growth factors.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Thang Pham

LAB HEAD: Connie Jimenez

PROVIDER: PXD043014 | Pride | 2024-02-12

REPOSITORIES: Pride

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			Action	DRS
	QE1_220131_OPL1036_CdAM_SP4P_dda_A.raw	Raw
	QE1_220131_OPL1036_CdAM_SP4P_dda_B.raw	Raw
	QE1_220131_OPL1036_CdAM_SP4P_dda_C.raw	Raw
	QE1_220131_OPL1036_CdAM_SP4P_dda_D.raw	Raw
	QE1_220131_OPL1036_CdAM_SP4P_dda_E.raw	Raw

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Publications

Secretome processing for proteomics: A methods comparison.

Almeida-Marques Catarina C Rolfs Frank F Piersma Sander R SR Bijnsdorp Irene V IV Pham Thang V TV Knol Jaco C JC Jimenez Connie R CR

Proteomics 20240114 7

The cancer cell secretome comprises a treasure-trove for biomarkers since it reflects cross-talk between tumor cells and their surrounding environment with high detectability in biofluids. In this study, we evaluated six secretome sample processing workflows coupled to single-shot mass spectrometry: (1) Protein concentration by ultrafiltration with a molecular weight cut-off (MWCO) filter and sample preparation through in-gel digestion (IGD); (2) Acetone protein precipitation coupled to IGD; (3) ...[more]

PMID: 38221716

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