Proteomics

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Assessment of sample preparation bias in mass spectrometry-based proteomics


ABSTRACT: For mass spectrometry-based proteomics, the selected sample preparation strategy is a key determinant for information that will be obtained. However, the corresponding selection is often not based on a fit-for-purpose evaluation. Here we report a comparison of in-gel (IGD), in-solution (ISD), on-filter (OFD), and on-pellet digestion (OPD) workflows on the basis of targeted (QconCAT-multiple reaction monitoring (MRM) method for mitochondrial proteins) and discovery proteomics (data dependent acquisition, DDA) analyses using three different human head and neck tissues (i.e. nasal polyps, parotid gland, and palatine tonsils). Our study reveals differences between the sample preparation methods, for example with respect to protein and peptide losses, quantification variability, protocol-induced methionine oxidation and asparagine/glutamine deamidation as well as identification of cysteine containing peptides. Moreover, none of the methods performed best for all types of tissues, which seemingly argues against the existence of a universal sample preparation method for proteome analysis.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Nasal Polyp, Parotid Gland, Palatine Tonsil

SUBMITTER: Horvatovich Péter  

LAB HEAD: Peter Horvatovich

PROVIDER: PXD008493 | Pride | 2018-04-06

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
151029_IGD_NP_1d_151112210208.mzML Mzml
151029_IGD_NP_1d_151112210208.mzid.gz Mzid
151029_IGD_NP_1d_151112210208.pride.mztab.gz Mztab
151029_IGD_NP_1d_151112210208.raw Raw
151029_IGD_NP_2.mzML Mzml
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Publications

Assessment of Sample Preparation Bias in Mass Spectrometry-Based Proteomics.

Klont Frank F   Bras Linda L   Wolters Justina C JC   Ongay Sara S   Bischoff Rainer R   Halmos Gyorgy B GB   Horvatovich Péter P  

Analytical chemistry 20180406 8


For mass spectrometry-based proteomics, the selected sample preparation strategy is a key determinant for information that will be obtained. However, the corresponding selection is often not based on a fit-for-purpose evaluation. Here we report a comparison of in-gel (IGD), in-solution (ISD), on-filter (OFD), and on-pellet digestion (OPD) workflows on the basis of targeted (QconCAT-multiple reaction monitoring (MRM) method for mitochondrial proteins) and discovery proteomics (data-dependent acqu  ...[more]

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