# Laura’s Notebook: 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 + 2 blanks | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | |—|——–|——–|——|——|——|——–|——|——| | A | | | | | | | | | | B | G041 | G066 | G105 | G032 | G129 | G054 | G081 | G003 | | C | G074 | G014 | G049 | G053 | G104 | G055 | G042 | G064 | | D | G073 | G057 | G007 | G070 | G001 | G071-B | G062 | | | E | GBlank | OBlank | | | | | | | | F | | | | | | | | |

#### Plate 1 – run 1 – 1 sample I didn’t re-run | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | |—|——|——-|——|——|——|——–|——|——| | A | | | | | | | | | | B | | | | | | | | | | C | | | | | | | | | | D | | | | G128 | | | | | | E | | | | | | | | | | F | | | G122 | | | | | |

#### NOTE:

• 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

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