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“ramifarawi” committed Feb 1, 2024
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137 changes: 137 additions & 0 deletions protocols/00c517multi1-pt2/00c517multi1-pt2.ot2.apiv2.py
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import math

metadata = {
'protocolName': 'VIB UGENT - Multi-channel Workflow Part 2',
'author': 'Rami Farawi <[email protected]>',
'source': 'Custom Protocol Request',
'apiLevel': '2.15'
}


def run(ctx):

[num_samp, m300_mount] = get_values( # noqa: F821
"num_samp", "m300_mount")

# m300_mount = 'left'
# num_samp = 96

# labware
c_18_tiprack = ctx.load_labware('agilent_96_c18omix_200ul', 1)
agilent_1200 = ctx.load_labware('agilent_96_wellplate_1200ul', 2)

waste_res = ctx.load_labware('nest_1_reservoir_195ml', 5)
wash_buff_res = ctx.load_labware('nest_12_reservoir_15ml', 10) # up to number of columns of sample # noqa: E501
reagent_plate = ctx.load_labware('nest_12_reservoir_15ml', 4)
agilent_500 = [ctx.load_labware('agilent_96_wellplate_500ul', slot)
for slot in [7, 8, 9]]

tips300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)
for slot in [6, 11]]

# pipettes
m300 = ctx.load_instrument('p300_multi_gen2', m300_mount,
tip_racks=tips300)

# mapping
# trypsin = reagent_plate.rows()[0][0]
acn = reagent_plate.rows()[0][0]
equil_buffer = reagent_plate.rows()[0][1:3]
eb = reagent_plate.rows()[0][3:5]
waste = waste_res['A1']
wash_buff_plate = agilent_500[0]
elution_buff_plates = agilent_500[1:3]

num_col = math.ceil(num_samp/8)
sample_cols = agilent_1200.rows()[0][:num_col]

tip_ctr = 0

def pick_up_c18():
nonlocal tip_ctr
m300.pick_up_tip(c_18_tiprack.rows()[0][tip_ctr])
tip_ctr += 1

ctx.pause('''
Place the following labware on deck:
Opentrons tip rack with C18 OMIX tips on slot 1,
Agilent plate (round wells, 1200 µl) containing dried peptides on slot 2,
a 12 column reservoir containing 12 ml 2%ACN 0.1% TFA (column 1),
20 ml equilibration buffer (column 2, 3), and 10mL elution buffer
in columns 4, 5
a 12 column reservoir containing 8mL wash buffer in each column up to
the number of sample columns
and 20 ml elution buffer (column 8) in slot 4,
a one well reservoir on slot 5 (for waste),
a 300 µl tiprack on slot 6
and 3 96-well plates (Agilent 500 µl) in slots 7, 8 & 9.
''')

# protocol
ctx.comment('\n---------------43 - ADD ACN----------------\n\n')
for col in sample_cols:
m300.pick_up_tip()
m300.aspirate(100, acn)
m300.dispense(100, col)
m300.mix(5, 80, col)
m300.drop_tip()

ctx.pause('''
Add sample to lunatic chip manually to measure peptide concentration
''')

ctx.comment('\n---------------46 - ADDING WASH BUFFER----------------\n\n')
m300.pick_up_tip()
for wash_well, col in zip(wash_buff_res.rows()[0],
wash_buff_plate.rows()[0][:num_col]):
m300.transfer(400, wash_well, col, new_tip='never')
m300.drop_tip()

ctx.comment('\n-------------46 - ADDING ELUTION BUFFER--------------\n\n')
m300.pick_up_tip()
for eb_well, plate in zip(eb, elution_buff_plates):
for col in plate.rows()[0][:num_col]:
m300.aspirate(100, eb_well)
m300.dispense(100, col)
m300.drop_tip()

ctx.comment('\n-------------46 - WASH STEPS--------------\n\n')
for i, (wash_buff_res_col,
wash_buff_col,
eb1_col,
eb2_col,
sample_col) in enumerate(
zip(wash_buff_res.rows()[0],
wash_buff_plate.rows()[0],
elution_buff_plates[0].rows()[0][:num_col],
elution_buff_plates[0].rows()[0][:num_col],
sample_cols,
)):
pick_up_c18()
for _ in range(3):
m300.aspirate(100, equil_buffer[0 if i < 6 else 1], rate=0.2) # ONE COLUMN PER 6 SAMPLES
m300.dispense(100, waste.top())

for _ in range(5):
m300.aspirate(100, wash_buff_res_col)
m300.dispense(100, waste.top(), rate=0.2)

m300.mix(20, 100, sample_col, rate=0.2)
m300.aspirate(100, sample_col)
m300.dispense(100, waste.top())

for _ in range(3):
m300.aspirate(100, wash_buff_col)
m300.dispense(100, waste.top())

m300.mix(10, 100, eb1_col, rate=0.2)
m300.mix(10, 100, eb2_col, rate=0.2)
m300.aspirate(100, eb2_col)
m300.dispense(100, eb1_col)

m300.drop_tip()

ctx.comment('\n\n\n')
17 changes: 17 additions & 0 deletions protocols/00c517multi1-pt2/fields.json
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[
{
"type": "int",
"label": "Number of samples (8-96)",
"name": "num_samp",
"default": 96
},
{
"type": "dropDown",
"label": "P300 Multi-Channel Mount",
"name": "m300_mount",
"options": [
{"label": "Left", "value": "left"},
{"label": "Right", "value": "right"}
]
}
]
1 change: 1 addition & 0 deletions protocols/00c517multi1-pt2/labware/3DPrint 96 Tube Rack with Nippon 0.2 mL.json
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