Fig 1.
Workflow of the current study.
Table 1.
Comparison of proteins identified using five different extraction buffers after LMD/MS analysis.
Fig 2.
LMD/MS results from the five different extraction buffers.
(a) Comparison of the three SDS-based extraction buffers (buffers 2, 3, 4). The number of unique identified proteins from the LMD kidney specimen was highest using buffer 4. (b) Comparison of the Zwittergent-containing buffer, the most efficient SDS-containing buffer (buffer 4), and the urea-containing buffer. The number of unique identified proteins from the LMD kidney specimen was highest using the Zwittergent-containing buffer. (c) Total iBAQ was comparable among buffers 1, 3, and 4, with the highest intensity found in proteins extracted using the Zwittergent-containing buffer.
Table 2.
Protein yield (μg) of extracts from FFPE tissue slices using different extraction buffers.
Fig 3.
Comparison of the electrophoretic patterns of proteins extracted from the kidney FFPE sample using different buffers.
a, extraction buffer 1; b, extraction buffer 4; c, extraction buffer 3; d, extraction buffer 5; e, extraction buffer 2.
Table 3.
Total number of identified proteins from tissue specimens using five different extraction buffers after LC-MS/MS analysis.
Fig 4.
MS results from FFPE samples using five different extraction buffers.
(a) When comparing the three SDS-containing extraction buffers (buffers 2, 3, 4), the number of unique identified proteins from the heart FFPE specimens was highest in the buffer 2 group. (b) When comparing the Zwittergent-containing buffer, the most efficient SDS-containing buffer (buffer 2), and the urea-containing buffer, the number of unique identified proteins from the heart FFPE specimen was highest in the Zwittergent-containing buffer group. (c) Total protein iBAQ of the Zwittergent-containing buffer was significantly lower than that of buffers 2 and 3, and was higher than that of buffers 4 and 5.