Remaining SRM Timeline
How many samples can I run?
@ 8:30am on Monday 7/24 I got my samples started again. I need to figure out how many more samples I can run within the given timeline. Here are the considerations:
- Running samples in batches of (5 samples) + (1 QC) + (1 blank) = 500 minutes total, so that’s 100 minutes / sample.
- We have until 10am on Friday 7/28
- Need 40 hrs for the dilution curve run
- So, need to be done with my samples by Wednesday 7/26 @ 6:00pm
- Time between this morning @ 8:30am when I re-started my samples & 7/26 @ 6pm = 57.5 hrs = 3450 minutes / 100 minutes/sample = 34.5 samples.
- I have 25 samples left to run, plus 2 blanks (Gblank & OBlank) which I could run twice.
- Should be done with my samples on Wednesday @ 5:30am, this includes 1 run of each blank.
Thoughts on whether or not to re-make samples
Up to this point I have 20 samples where a handful of peptides don’t show up from both PRTC and my samples. In PRTC there are 4/9 poor quality peptides, and in my samples 3/39 poor quality transitions. In an ideal world I would remake these ~20 samples, run the new batch twice while being careful with freeze/thaw and time out of the freezer. However, I don’t have time for 2 runs of remade samples. I could remake, then do 1 run of each in the hopes of capturing data on those 3 transitions. However, I think it’s best to have replicates of the 36 good quality transitions in my samples. Also, the 3 poor quality transitions were not in the sample proteins, so I can likely draw conclusions about protein quantification from the other 2 transitions. The differing rates of peptide degradation between samples does make me a little concerned; I’m wondering how folks take this into consideration.
Samples left to run:
#### Plate 2 - 23 samples + 2 blanks
#### Plate 1 - run 1 - 2 samples
- The following samples were put into the autosampler tray @ the following dates/times:
- 7/23 @ ~8pm: G041, G066, G105, G032, G129, G054, G081, G003, G074, G014, G049, G064, G073, G007, G001, G071-B, G062.
- 7/24 @ 2:25pm: G122
- 7/24 @ Xpm: TBD
- 7/25 @ Xpm: TBD