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Minimizing technical variation during sample preparation prior to label-free quantitative mass spectrometry

Ellen Scheerlinck (UGent) , Maarten Dhaenens (UGent) , Ann Van Soom (UGent) , Luc Peelman (UGent) , Petra De Sutter (UGent) , Katleen Van Steendam (UGent) and Dieter Deforce (UGent)
(2015) ANALYTICAL BIOCHEMISTRY. 490. p.14-19
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Organization
Abstract
Sample preparation is the crucial starting point to obtain high-quality mass spectrometry data and can be divided into two main steps in a bottom-up proteomics approach: cell/tissue lysis with or without detergents and a(n) (in-solution) digest comprising denaturation, reduction, alkylation, and digesting of the proteins. Here, some important considerations, among others, are that the reagents used for sample preparation can inhibit the digestion enzyme (e.g., 0.1% sodium dodecyl sulfate [SDS] and 0.5 M guanidine HCl), give rise to ion suppression (e.g., polyethylene glycol [PEG]), be incompatible with liquid chromatography tandem mass spectrometry (LC MS/MS) (e.g., SDS), and can induce additional modifications (e.g., urea). Taken together, all of these irreproducible effects are gradually becoming a problem when label-free quantitation of the samples is envisioned such as during the increasingly popular high-definition mass spectrometry (HDMSE) and sequential window acquisition of all theoretical fragment ion spectra (SWATH) data-independent acquisition strategies. Here, we describe the detailed validation of a reproducible method with sufficient protein yield for sample preparation without any known LC MS/MS interfering substances by using 1% sodium deoxycholate (SDC) during both cell lysis and in-solution digest.
Keywords
TRYPSIN, PEPTIDES, PROTOCOLS, OPTIMIZATION, MEMBRANE PROTEOME, PROTEIN DIGESTION, SHOTGUN PROTEOMICS, Sample preparation, SDC, HDMSE, DIGESTION EFFICIENCY, COMPATIBLE SURFACTANT

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Chicago
Scheerlinck, Ellen, Maarten Dhaenens, Ann Van Soom, Luc Peelman, Petra De Sutter, Katleen Van Steendam, and Dieter Deforce. 2015. “Minimizing Technical Variation During Sample Preparation Prior to Label-free Quantitative Mass Spectrometry.” Analytical Biochemistry 490: 14–19.
APA
Scheerlinck, Ellen, Dhaenens, M., Van Soom, A., Peelman, L., De Sutter, P., Van Steendam, K., & Deforce, D. (2015). Minimizing technical variation during sample preparation prior to label-free quantitative mass spectrometry. ANALYTICAL BIOCHEMISTRY, 490, 14–19.
Vancouver
1.
Scheerlinck E, Dhaenens M, Van Soom A, Peelman L, De Sutter P, Van Steendam K, et al. Minimizing technical variation during sample preparation prior to label-free quantitative mass spectrometry. ANALYTICAL BIOCHEMISTRY. 2015;490:14–9.
MLA
Scheerlinck, Ellen, Maarten Dhaenens, Ann Van Soom, et al. “Minimizing Technical Variation During Sample Preparation Prior to Label-free Quantitative Mass Spectrometry.” ANALYTICAL BIOCHEMISTRY 490 (2015): 14–19. Print.
@article{7019773,
  abstract     = {Sample preparation is the crucial starting point to obtain high-quality mass spectrometry data and can be divided into two main steps in a bottom-up proteomics approach: cell/tissue lysis with or without detergents and a(n) (in-solution) digest comprising denaturation, reduction, alkylation, and digesting of the proteins. Here, some important considerations, among others, are that the reagents used for sample preparation can inhibit the digestion enzyme (e.g., 0.1\% sodium dodecyl sulfate [SDS] and 0.5 M guanidine HCl), give rise to ion suppression (e.g., polyethylene glycol [PEG]), be incompatible with liquid chromatography tandem mass spectrometry (LC MS/MS) (e.g., SDS), and can induce additional modifications (e.g., urea). Taken together, all of these irreproducible effects are gradually becoming a problem when label-free quantitation of the samples is envisioned such as during the increasingly popular high-definition mass spectrometry (HDMSE) and sequential window acquisition of all theoretical fragment ion spectra (SWATH) data-independent acquisition strategies. Here, we describe the detailed validation of a reproducible method with sufficient protein yield for sample preparation without any known LC MS/MS interfering substances by using 1\% sodium deoxycholate (SDC) during both cell lysis and in-solution digest.},
  author       = {Scheerlinck, Ellen and Dhaenens, Maarten and Van Soom, Ann and Peelman, Luc and De Sutter, Petra and Van Steendam, Katleen and Deforce, Dieter},
  issn         = {0003-2697},
  journal      = {ANALYTICAL BIOCHEMISTRY},
  keyword      = {TRYPSIN,PEPTIDES,PROTOCOLS,OPTIMIZATION,MEMBRANE PROTEOME,PROTEIN DIGESTION,SHOTGUN PROTEOMICS,Sample preparation,SDC,HDMSE,DIGESTION EFFICIENCY,COMPATIBLE SURFACTANT},
  language     = {eng},
  pages        = {14--19},
  title        = {Minimizing technical variation during sample preparation prior to label-free quantitative mass spectrometry},
  url          = {http://dx.doi.org/10.1016/j.ab.2015.08.018},
  volume       = {490},
  year         = {2015},
}

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