Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics Based on Acid Extraction

被引:112
作者
Doellinger, Joerg [1 ]
Schneider, Andy [1 ]
Hoeller, Marcell [1 ]
Lasch, Peter [1 ]
机构
[1] Robert Koch Inst, Ctr Biol Threats & Special Pathogens Prote & Spec, Berlin, Germany
关键词
proteomics; sample preparation; lysis; TFA; digestion; mass spectrometry; label-free quantification; microbiome; bacteria; pathogens; automation; protein denaturation; detergent-free; ESCHERICHIA-COIL PROTEOME; MASS-SPECTROMETRY; PEPTIDE IDENTIFICATION; PHOSPHOPROTEOME; FRACTIONATION; MICROSCALE; SEPARATION; VIRULENCE; CELLS;
D O I
10.1074/mcp.TIR119.001616
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Sample Preparation by Easy Extraction and Digestion (SPEED) is a universal method for peptide generation from various sources. Because of its detergent-free chemistry, SPEED offers some inherent benefits for bottom-up proteomics sample preparation, including improved quantitative reproducibility, simple applicability and enhanced proteome coverage for lysis-resistant sample types as well as very rapid sample processing. SPEED has high automatization potential and can contribute to simplify and standardize sample preparation and thus enhance reproducibility in proteomics. The main challenge of bottom-up proteomic sample preparation is to extract proteomes in a manner that enables efficient protein digestion for subsequent mass spectrometric analysis. Today's sample preparation strategies are commonly conceptualized around the removal of detergents, which are essential for extraction but strongly interfere with digestion and LC-MS. These multi-step preparations contribute to a lack of reproducibility as they are prone to losses, biases and contaminations, while being time-consuming and labor-intensive. We report a detergent-free method, named Sample Preparation by Easy Extraction and Digestion (SPEED), which consists of three mandatory steps, acidification, neutralization and digestion. SPEED is a universal method for peptide generation from various sources and is easily applicable even for lysis-resistant sample types as pure trifluoroacetic acid (TFA) is used for highly efficient protein extraction by complete sample dissolution. The protocol is highly reproducible, virtually loss-less, enables very rapid sample processing and is superior to the detergent/chaotropic agent-based methods FASP, ISD-Urea and SP3 for quantitative proteomics. SPEED holds the potential to dramatically simplify and standardize sample preparation while improving the depth of proteome coverage especially for challenging samples.
引用
收藏
页码:209 / 222
页数:14
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