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Table 2 Final optimized SWATH acquisition method

From: Robust optimization of SWATH-MS workflow for human blood serum proteome analysis using a quality by design approach

Factor

Level

Critical

Protein amount

400 µg

No

Gradient length

30 min

No

MS acc. time

50 ms

No

MS range

400–800 m/z

No

MS/MS range

400–1200 m/z

No

SWATH windows

Variable

No

Number of SWATH windows

100

Yes

MS/MS accumulation time

40 ms

Yes

  1. The number of SWATH Windows and MS/MS accumulation time were chosen based on the CCD results. The 6 non-significant parameters were set to the level that produced the best response in the screening design
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Clinical Proteomics

ISSN: 1559-0275