Dataset Information

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

ACCESS DATA

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]

PMID: 29608294

Similar Datasets

Project description:Polyethylene glycol sorbitan monoacylates (Tween) are detergents of widespread use in plant sciences. We show them, notably Tween 20, to cause a rapid and complex change in transcript abundance which bears all characteristics of a PAMP / elicitor-induced defense response, and they do so at concentrations which cause no detectable deleterious effects on plant cellular integrity. The activity does not reside in the intact Tween molecule itself, but is caused by medium-chain fatty acids, notably lauric acid (LA), which are efficiently released from the Tween-backbone by the plant. The Tween / LA-response is independent of the jasmonate signalling system. Medium-chain fatty acids are thus novel elicitors/regulators of plant pathogen defense. The results also have several practical implications: (i) The use of Tweens and, as we show, several other detergents, as solvating/wetting agents on intact plants causes profound physiological changes which may mask actual effects of test compounds; (ii) Tweens by themselves can be regarded (and probably used) as economical, non-toxic, and safe-to-apply elicitors of inducible plant immunity against pathogens. Experiment Overall Design: In preliminary Northern blot experiments using the Arabidopsis thaliana genes OPR1 / OPR2, strongest responses were observed between 1 h and 2.5 h after foliar treatment with 0.2 % Tween 20 solution (approx. 1.6 mM). These conditions were thus chosen for the microarray experiments. Three experiments were carried out, two 1 h after the onset of the Tween treatment (expt. IA and IB which are biological repetitions; GSM126247, GSM126248; GSM126990, GSM126991 files) and one after 2.5 h (expt. II; GSM126244, GSM126246 files, c and t respectively) to allow a distinction between fast, transient and slower, more permanent responses. Experiment Overall Design: All the experiments were conducted at the same day time in the morning. For every experiment a total of three independent replicas (33 Arabidopsis thaliana Col-0 plants per experiment) were done. The plants used were 28 days old, growing under sterile conditions in 0.5 L glass jars containing MS medium. The controls were sprayed with water and the samples with 0.2 % (w/v) Tween 20 detergent. The plant material was collected in a random way from the different glass jars, the samples were dried in tissue paper, weighted (1 g) and immediately frozen in liquid nitrogen. This complete procedure took place in less than 1 min. Total RNA extraction from every individual experiment was made with TRIzol. Once the RNA quality of every independent induction experiment was satisfactory, the RNA samples were mixed. Experiment Overall Design: RNA quality and quantity control, cRNA labeling, hybridizations, expression data normalization and analysis were performed in collaboration with Carsten MÃ¼ssig and Thomas Altmann (Max-Planck-Institute for Molecular Plant Physiology, Golm) according to the Affymetrix manual. Clustering was performed using the Access and the MAPMAN program. Experiment Overall Design: The levels of 118 transcripts were elevated (2-fold) after 1 h, i.e., in both, the IA and IB arrays, but only 12 levels were reduced (by 2-fold). In the 2.5 h array the corresponding numbers were 137 and 11. The transcript levels of 38 genes were found elevated in all three arrays. The validity of the array data was checked for 25 randomly-picked genes out of the 38 genes by RT-PCR.

Dataset Information

Assessment of sample preparation bias in mass spectrometry-based proteomics

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure