MassIVE MSV000083561

Complete Public PXD008493

Assessment of sample preparation bias in mass spectrometry-based proteomics


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. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: nasal polyps ; parotid gland ; palatine tonsils ; proteomics ; sample preparation


Principal Investigators: Peter Horvatovich, University of Groningen Faculty of Mathematics and Natural Sciences Department of Pharmacy Analytical Biochemistry Building 3226, Room 6.9 Antonius Deusinglaan 1 9713 AV Groningen Internal Zip Code XB20 P.O. Box 196 9700 AD Groningen The Netherlands Telephone: +31-(0)50-363 3341 Fax: +31 (0)50 363 7582 Mobile: +31 (0)6 2459 7203 Email: Homepage:, N/A
Submitting User: ccms


Klont F, Bras L, Wolters JC, Ongay S, Bischoff R, Halmos GB, Horvatovich P.
Assessment of Sample Preparation Bias in Mass Spectrometry-Based Proteomics.
Anal. Chem. 2018 Apr 17;90(8):5405-5413. Epub 2018 Apr 6.

Number of Files:
Total Size:
Owner Reanalyses
Proteins (reported):
Variant Peptides:
FTP Download Browse Results
FTP Download Link (click to copy):

- Dataset Reanalyses

+ Dataset History

Click here to queue conversion of this dataset's submitted spectrum files to open formats (e.g. mzML). This process may take some time.

When complete, the converted files will be available in the "ccms_peak" subdirectory of the dataset's FTP space (accessible via the "FTP Download" link to the right).
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.
Proteins identified by originally submitted search results.