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Table 1 Timing and difficulty level of different sample preparation protocols for MS-based proteomics

From: Evaluation of sample preparation methods for mass spectrometry-based proteomic analysis of barley leaves

Procedurea

FASP

SDS-ISD

SDC-FASP

SDC-ISD

OP-ISD

Timing (h)

Difficulty levelb

Timing (h)

Difficulty level

Timing (h)

Difficulty level

Timing (h)

Difficulty level

Timing (h)

Difficulty level

Protein extraction

1.5

1.5

1.5

1.5

1.5

Protein quantification

1

0.5

1

1

1

Clean up at protein level

1.5

9

1

0

0

Reduction and alkylation

0.5

0.5

0.5

0.5

0

Clean up at peptide level

0

0

0.5

0.5

0.5

Digestion

7

6

7

6

6

Total

11.5

17.5

11.5

9.5

9

  1. aprotein quantification can be performed by several methods. The timing is calculated from the method that required least time to be done, i.e. BCA methods for FASP, SDC-FASP, SDC-ISD and OP-IS protocols and Qubit for SDS-ISD
  2. bThe difficulty level reflects the time required, the number of steps to be performed and the complexity of the steps; an open star indicates the easiest step, while the number of filled stars shows the level of difficulty of each step