Proteomics

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Isobaric tag-based protein profiling across eight human cell lines using high-Field Asymmetric Ion Mobility Spectrometry (FAIMS) and real-time database searching (RTS)


ABSTRACT: A vast assortment of human cell lines is available for cell culture model-based studies, and as such the potential exists for discrepancies in findings due to cell line selection. To investigate this concept, we determined the relative protein abundance profiles of a panel of eight diverse, but commonly studied, human cell lines. This panel includes: HAP1, HEK293T, HeLa, HepG2, Jurkat, Panc1, SH-SY5Y, and SVGp12. We use a mass spectrometry-based proteomics workflow designed to enhance quantitative accuracy while maintaining analytical depth. To this end, our strategy leverages TMTpro16-based sample multiplexing, high-Field Asymmetric Ion Mobility Spectrometry (FAIMS), and real-time database searching (RTS). The data show that cell line diversity was reflective of differences in the relative protein abundance profiles. We also determined that several hundred proteins were highly enriched for a given cell line and performed gene ontology and pathway analysis on these cell line-enriched proteins. We provide an R Shiny application to query protein abundance profiles and retrieve proteins with similar patterns. The workflows used herein can be applied to additional cell lines to aid cell line selection in addressing a given scientific inquiry or in improving an experimental design.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Joao Paulo  

LAB HEAD: Joao A. Paulo

PROVIDER: PXD020806 | Pride | 2020-10-19

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
448552_ea00599_812_Ecl_RTS.mzIdentML Mzid
448553_ea00600_812_Ecl_RTS.mzIdentML Mzid
448554_ea00601_812_Ecl_RTS.mzIdentML Mzid
448555_ea00602_812_Ecl_RTS.mzIdentML Mzid
448556_ea00603_812_Ecl_RTS.mzIdentML Mzid
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Publications

Isobaric Tag-Based Protein Profiling across Eight Human Cell Lines Using High-Field Asymmetric Ion Mobility Spectrometry and Real-Time Database Searching.

Liu Xinyue X   Gygi Steven P SP   Paulo Joao A JA  

Proteomics 20201026 1


A vast number of human cell lines are available for cell culture model-based studies, and as such the potential exists for discrepancies in findings due to cell line selection. To investigate this concept, the authors determine the relative protein abundance profiles of a panel of eight diverse, but commonly studied human cell lines. This panel includes HAP1, HEK293T, HeLa, HepG2, Jurkat, Panc1, SH-SY5Y, and SVGp12. A mass spectrometry-based proteomics workflow designed to enhance quantitative a  ...[more]

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