DNR Speed Vacuum Round 2

Yaamini vs. CentriVap: The Sequel

Armed with leftover donuts and mini muffins, I spent my Saturday dueling my old nemesis, the CentriVap speed vacuum. Last time I used it, it kept me up late. This time I was prepared. I came in on a weekend and loaded my samples before anyone else could use the machine.

Step 1: Obtain digested samples from -80ºC

I got samples from both round 2 and round 3 of trypsin digestion.

Step 2: Load samples into speed vacuum

  • Make: CentriVap (R) Refrigerated Centrifugal Concentrators
  • Model: 7310021
  • Program Number: 4
    • Temperature: 4ºC
    • Refrigeration: Yes
  • Ensure samples are balanced

Step 3: Start speed vacuum

At 11 a.m., Genn needed to use the speed vacuum for 1.5 hours. She placed my samples in the fridge while she used the machine She also noted that some of my centrifuge tubes were colored, which could lead to some dye residue in the mass spectrometer. Emma believes that this should be taken care of with desalting. Additionally, there was no evidence of any dye contaminant in our previous run, so I think we’ll be fine. It’s just something to know for later!

Step 4: Remove samples

I let the speed vacuum run until there was only 20 µL of liquid left in snaptop centrifuge tubes.

Table 1. Time I removed samples from the speed vacuum from Round 2 of extractions. Samples were placed back in the -80ºC immediately. Most samples were removed at 8:11 p.m.

Time Samples
7:29 p.m. O39, O71, O90, O147
7:51 p.m. O26, O31, O32, O46, O66, O118
8:11 p.m. O01, O12, O14, O17, O40, O64, O100, O101, O103, O124, O128
8:26 p.m. O08, O137
8:40 p.m. OBLNK2
8:51 p.m. O145
9:05 p.m. O60

Table 2. Time I removed samples from the speed vacuum from Round 3 of extractions. Samples were placed back in the -80ºC immediately. These samples had an etra 20 µL of IAA in them.

Time Samples
7:29 p.m. O40, O52
7:51 p.m. O10, O35, O43, O49, O102, O113, O122
8:11 p.m. O78, O91, O106
8:26 p.m. O06, O24, O56, O131
8:40 p.m. O04
8:51 p.m. O96, O99
9:05 p.m. O21, O22, O30, O51, O121

One thing I noticed was that some of my samples had a black precipitate on the bottom. This was true for samples from both rounds.

Figure 1. Black precipitate after speed vacuuming samples. The sample shown is O31 from Round 2, but samples from Round 3 also had this precipitate.


Another thing I noticed was that I only speed vacuumed 24 of my Round 3 samples instead of 26 (25 samples + 1 blank)! My hunch is that I misplaced them and put them in with Laura’s samples. The ones I am missing are O144 and OBLNK3. I will check for these samples in the freezer when I get the chance.

At some point next week, I’ll desalt my samples. Then I’ll be all set for the mass spec!

Written on June 3, 2017