TITLE: Whole-cell proteomics and Analysis by Tandem Mass Tagging-based proteomics
AUTHORS: Felix Kraus, Sharan Swarup, Vinay V. Eapen, J. Wade Harper wade_harper@hms.harvard.edu

[DESCRIPTION]
The analysis of relative protein abundance has emerged as an important tool in cell biology. Typically, it is possible to quantify >8000 proteins under standard conditions. Tandem Mass Tags (TMT) are isobaric reagents that contain a set of isotopically distinct reporter ions, which can be used to quantify individual peptides in distinct samples through multiplexing(McAlister et al., 2014). Because the TMT analysis is performed in multiplexed format (up to 18 plex), it is possible to examine the effect of different perturbations (treatments, time courses, etc) on the total abundance of the proteome and include replicate samples as desired. This protocol is applicable to many different cell types, although the number of proteins quantified may differ, depending on the complexity of the proteomes in individual cell types. The small amount of protein needed (50-100 ug) makes application of this approach simple for many different types of cells

[BEFORE_START]
WORKFLOW:
  


[GUIDELINES]
Mass spectrometry:
The analysis of TMT-labelled peptides by mass spectrometry will depend on the type of instrument/platform used. Typical instrument settings for analysis on a Thermo Fusion Lumos instrument are provided in the following section.

Inject 3 μl for each LC–MS/MS analysis using available mass spectrometer with a 120-minute online LC separation.

Search raw data against UniProt human protein database using any proteomic analysis software with the following parameters:
-Up to 3 missed cleavages allowed for trypsin/LysC digestion
-Carbamidomethyl (C), TMT (N-term peptide and K) set as a fixed modification
-Oxidation (M) and di-glycine (K) set as variable modifications

Extract signal to noise intensity values of each TMT reporter and identified proteins, and further calculate the ratio of each condition to the control sample’s intensity.

Instrument settings:
Mass spectrometry data were collected using an Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific, San Jose, CA) coupled to a Proxeon EASY-nLC1200 liquid chromatography (LC) pump (Thermo Fisher Scientific). Peptides were separated on a 100 μm inner diameter microcapillary column packed in house with ~35 cm of Accucore150 resin (2.6 μm, 150 Å, ThermoFisher Scientific, San Jose, CA) with a gradient consisting of 3%–26% (0-100 min), 26-32% (100-110min) (ACN, 0.1% FA) over a total 120 min run at ~400 nL/min.For analysis, we loaded 1/3 of each fraction onto the column. Each analysis used the Multi-Notch MS3-based TMT method(McAlister et al., 2014). The scan sequence began with an MS1spectrum (Orbitrap analysis; resolution 120,000 at 200 Th; mass range 400−1250 m/z; automatic gain control (AGC) target 1×106; maximum injection time 100 ms). Precursors for MS2analysis were selected using a Top 4 sec method. MS2analysis consisted of collision-induced dissociation (quadrupole Orbitrap analysis; AGC 1×105; isolation window 0.7 Th; normalized collision energy (NCE) 35; maximum injection time 300 ms resolution was 7,500 at 200 Th).Monoisotopic peak assignment was used, and previously interrogated precursors were excluded using a dynamic window (120 s ± 7 ppm).Following acquisition of each MS2spectrum, a synchronous-precursor-selection (SPS) MS3scan was collected on the top 10 most intense ions in the MS2spectrum(McAlister et al., 2014). MS3precursors were fragmented by high energy collision-induced dissociation (HCD) and analyzed using the Orbitrap (NCE 65; AGC 2×105;maximum injection time 500 ms, resolution was 50,000 at 200 Th).

[STEPS]
SECTION: Harvest, precipitation and digestion
1. For whole proteome analysis, 50 µg  is required for each replicate. Lyse cells in lysis buffer and pass them through a 21G needle 10 times. Alternatively, lyse cells by
sonication as per manufactures instructions.
SECTION: Harvest, precipitation and digestion
2. Centrifugate suspensions at 13000 rpm, 4 °C for 10 min  and collect the supernatant.
SECTION: Harvest, precipitation and digestion
3. Transfer quantified protein lysate concentration and 50 µg for each sample to a clean 1.5 mL protein Lo-Bind Eppendorf tubes. Reduce lysates for 20 min at Room temperature with 5 millimolar (mM) , and alkylate cysteine residues with 20 millimolar (mM)(Room temperature, 30 min).

SECTION: Harvest, precipitation and digestion
4. Extract protein content by methanol-chloroform precipitation and subsequent MeOH washes.
SECTION: Harvest, precipitation and digestion
4.1. Add 4x volumes of MeOH and vortex.

SECTION: Harvest, precipitation and digestion
5. Resuspend protein pellets  100 µL of 200 millimolar (mM)  (pH 8.5).

SECTION: Harvest, precipitation and digestion
6. Digest samples at 37 °C for 120 min with endoproteinase Lys-C (Wako, Japan) at a 1/200 enzyme/protein ratio.

SECTION: Harvest, precipitation and digestion
7. Digest with Trypsin (1:100) for 360 minat 37 °C.

SECTION: TMT-Labeling of samples
8.  Add 5 µL to each sample. Solubilize TMT reagents are in ACN as per manufacturer’s instructions and 5 µL  is used for every 50 µg. Performe TMT labeling in a final concentration of 20-25% ACN. Add 20 µL  to bring the reaction volume at 125 µL.The number of samples, and hence the number of individual TMT reagents, will depend upon the design of the experiment.

SECTION: TMT-Labeling of samples
9. Incubate for 60 minat 37 Room temperature to label the samples.
SECTION: Harvest, precipitation and digestion
4.2. Add 1x volume of chloroform and vortex.
SECTION: Harvest, precipitation and digestion
4.3. Add 3x volume of water and vortex.
SECTION: Harvest, precipitation and digestion
4.4. Spin down at Room temperature  for  5 min at high speed.

SECTION: Harvest, precipitation and digestion
4.5. Aspirate and discard the upper aqueous phase. Do not disturb the protein disc at the interface of the aqueous phase (top) and organic phase (bottom).
SECTION: Harvest, precipitation and digestion
4.6. Add 4x volumes of MeOH and vortex.
SECTION: Harvest, precipitation and digestion
4.7. Spin down at Room temperature  for 5 min  at high speed.

SECTION: Harvest, precipitation and digestion
4.10. Air dry (or speed-vac) protein pellet down to remove all traces of MeOH.
SECTION: Harvest, precipitation and digestion
4.9. Repeat MeOH wash.
SECTION: Harvest, precipitation and digestion
4.8. Aspirate and discard supernatant. Do not disturb the protein pellet at the bottom of the tube.
SECTION: TMT-Labeling of samples
10. Combine 1% of each labeled sample together in a tube, quench the reaction with 4 µL  for 15 min at 37 Room temperature, and dry down using the speed-vac. This combined sample is used to perform the ratio check to test labeling efficiency. The remaining amount of each sample can be stored in the freezer.
SECTION: Stage tip for Ratio Check
11. Resuspend the dried sample in 100 µL . Check to ensure that the pH of the sample is ~pH 3 (or lower) using pH strip.

SECTION: Stage tip for Ratio Check
12. Make stage tip by placing 6-8 “cookies” of C-18 embedded membranes in 200 µL.

SECTION: Stage tip for Ratio Check
13. Perform C-18 cleanup:
SECTION: Stage tip for Ratio Check
13.1. Equilibrate C-18 with 100 µL .

SECTION: Stage tip for Ratio Check
14. Dry down eluted peptides in speed-vac.
SECTION: Stage tip for Ratio Check
13.2. Wash C-18 with 50 µL .

SECTION: Stage tip for Ratio Check
13.3. Wash C-18 with 100 µL .

SECTION: Stage tip for Ratio Check
13.4. Load sample on to C-18 to bind peptides.
SECTION: Stage tip for Ratio Check
13.5. Wash bound peptides on C-18 with 50 µL .
SECTION: Stage tip for Ratio Check
13.6. Elute peptides off C-18 with 50 µL  into a mass spec vial.

SECTION: Stage tip for Ratio Check
15. Reconstitute peptides in 10 µL.

SECTION: Stage tip for Ratio Check
16. Perform ratio check by analyzing the total amount of reporter ions present, as measured by mass spectrometry, for each TMT reporter ion channel.
SECTION: Stage tip for Ratio Check
17. Quench the entire volume of each sample using 8 µL  for 15 min at 37 Room temperature. Combine samples in 2 ml Eppendorf tube to equal amounts, based on normalization values you obtain from the ratio check.

SECTION: Stage tip for Ratio Check
18. Dry down labeled, combined sample in speed-vac.
SECTION: Stage tip for Ratio Check
19. Re-constitute the sample in 750 µL.

SECTION: SepPak clean-up (C18 solid-phase extraction (SPE))
20. Place SepPak column into vacuum slot on a vacuum manifold.
SECTION: SepPak clean-up (C18 solid-phase extraction (SPE))
22. Start the vacuum, gently, try to ensure that the pressure gauge is below 10. This can be achieved by opening one of the valves gently. The fluid should pass through slowly, drop wise.
SECTION: SepPak clean-up (C18 solid-phase extraction (SPE))
23. Fill SepPak with 1 mL, Flow Liquid through.

SECTION: SepPak clean-up (C18 solid-phase extraction (SPE))
24. Fill SepPak with 1 mL , Flow Liquid through, repeat 2 more times.

SECTION: SepPak clean-up (C18 solid-phase extraction (SPE))
25. Replace tube with 2 ml collection tube.
SECTION: SepPak clean-up (C18 solid-phase extraction (SPE))
26. Add Peptides, Flow Liquid through (~ 750 µl).
SECTION: SepPak clean-up (C18 solid-phase extraction (SPE))
27. Wash with 1 mL, Flow Liquid through, 2 times.

SECTION: SepPak clean-up (C18 solid-phase extraction (SPE))
28. Replace 15 ml collection tube with 2 ml collection tube.
SECTION: SepPak clean-up (C18 solid-phase extraction (SPE))
29. Elute with 750 µL. Since there is residual liquid left in the SepPak, ensure that all the liquid flows through SepPak.

SECTION: SepPak clean-up (C18 solid-phase extraction (SPE))
30. Dry down in SpeedVac 37 Room temperature 15 min or 30 °C.

SECTION: SepPak clean-up (C18 solid-phase extraction (SPE))
21. Fill SepPak with 1 mL.
SECTION: Fractionation
31. Resuspend sample in 100 µL pH 8.

SECTION: Fractionation
32. Fractionate using pH reverse-phase HPLC:
SECTION: Fractionation
32.1. Fractionate samples by high-pH reverse-phase HPLC (Agilent LC1260) into 96 fractions over a 90 min run.

SECTION: Fractionation
32.2. Fractions are run through an Aeris peptide XB-c18 column (Phenomenex; 250 mm x 3.6 mm), with mobile phase A containing 5 1425 and 10 millimolar (mM) pH 8  and phase B containing 90 1425 and 10 millimolar (mM) pH 8  (all inLC-MS grade H20).

SECTION: Fractionation
33. Combine fractionated samples (either 12 or 24 fractions) in a non-continuous manner into individual 1.5 ml Eppendorf tube (see outline below form Paulo et al., 2016).
  

SECTION: Fractionation
34. Dry down in SpeedVac.
SECTION: Fractionation
35. Resuspend peptides in 100 µL.

SECTION: Fractionation
36. Check pH (~3.5) with pH indicator strips.
SECTION: Stage tip for proteomics sample
37. Stage tip each fraction.
SECTION: Stage tip for proteomics sample
37.1. Make stage tips and equilibrate. Spin down at 3000 rpm, 3 min .

SECTION: Stage tip for proteomics sample
37.2. Perform C-18 cleanup:
SECTION: Stage tip for proteomics sample
37.3. Wash with 50 µL.

SECTION: Stage tip for proteomics sample
37.4. Wash with 100 µL .

SECTION: Stage tip for proteomics sample
37.5. Load sample
SECTION: Stage tip for proteomics sample
37.6. Collect flow through and freeze.
SECTION: Stage tip for proteomics sample
37.7. Wash with 50 µL.
SECTION: Stage tip for proteomics sample
37.8. Elute with 50 µL in mass spec vial.

SECTION: Stage tip for proteomics sample
38. Dry down in SpeedVac.
SECTION: Stage tip for proteomics sample
39. Reconstitute pellet in 10 µL .

SECTION: Stage tip for proteomics sample
40. Freeze sample at --20 °C until ready to run proteomics.