Aug 14, 2024

Public workspaceproteomics (mitochondria)

DOI
https://dx.doi.org/10.17504/protocols.io.36wgqny15gk5/v1
  • Livia Hecke Morais1,
  • Baiyi Quan1,
  • Tsui-fen Chou1
  • 1California Institute of Technology
Livia Hecke Morais
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DOI: https://dx.doi.org/10.17504/protocols.io.36wgqny15gk5/v1
Protocol Citation: Livia Hecke Morais, Baiyi Quan, Tsui-fen Chou 2024. proteomics (mitochondria). protocols.io https://dx.doi.org/10.17504/protocols.io.36wgqny15gk5/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: August 14, 2024
Last Modified: August 14, 2024
Protocol Integer ID: 105242
Keywords: ASAPCRN, proteomics experiment with isolated mitochondrial extract, proteome exploration laboratory, proteomics experiment, proteomic, mitochondria, isolated mitochondrial extract, fen chou in collaboratin, collaboratin, laboratory
Funders Acknowledgements:
ASAP
Abstract
Here we describe proteomics experiment with isolated mitochondrial extracts at the Proteome exploration laboratory (PEL) at Caltech by Baiyi Quan, Jeff Jones and Tsui-Fen Chou in collaboratin with Livia Hecke Morais and Sarkis Mazmanian.
Troubleshooting
Sample Preparation

  1. Proteins extracted from mitochondria are reduced using a final concentration of 5 mM of TCEP (tris(2-carboxyethyl)phosphine) at room temperature for 10 min.
  2. The proteins are further alkylated using a final concentration of 20 mM of CAA (chloro-acetamide) at room temperature for 15 min.
  3. A 25 ul aliquot of the lysate is acidified using 2.5 ul of 12% phosphoric acid. Using a pH test paper to make sure solution pH< 2.
  4. Combine 165 ul of the S-trap buffer (90% MeOH with 100 mM triethylammonium bicarbonate) with the acidified lysate.
  5. Transfer the combined colloid into the S-trap micro (Protifi, NY).
  6. Centrifuge the S-trap micro at 4000 g for 1 min at room temperature.
  7. Using 150 ul of the S-trap buffer to wash the S-trap and centrifuge at 4000 g for 1 min. Repeat the step two more times.
  8. Add 20 ul of 100 mM triethylammonium bicarbonate containing 20 ug of Trypsin into S-trap micro. Allow the incubation stay overnight (14-16 hr) at 37 C.
  9. After overnight incubation, directly adding 40 ul of the 50 mM triethylammonium bicarbonate and centrifuge at 4000 g for 1 min.
  10. Add 40 ul of 2% formic acid in water to the S-trap, and centrifuge at 4000 g for 1 min.
  11. Add 40 ul of 50% acetonitrile in water to the S-trap, and centrifuge at 4000 g for 1 min.
  12. Speedvac the sample.
  13. The sample is reconstituted in 20 ul of 2% acetonitrile and 0.2% formic acid in water and 500 ug of the peptide is used for LC-MS/MS analysis.
LC-MS/MS
  1. An aliquot of sample containing 500 ug of the peptides is subjected to the LC-MS/MS analysis. The sample is separated on an Aurora UHPLC Column (25 cm × 75 μm, 1.6 μm C18, AUR2-25075C18A, Ion Opticks) using an Easy-nLC 1200 liquid chromatography system. The gradient settings follows Table 1.
Time Duration Flow (nl/min) %B
0:00 0:00 350 3
1:00 1:00 350 3
73:00 72:00 350 19
101:00 28:00 350 29
121:00 20:00 350 41
124:00 3 350 95
131:00 7 350 98
Table 1. LC gradient for the sample

Mobile Phase A: 0.2% formic acid, 2% acetonitrile, and 97.8% water.
Mobile Phase B: 0.2% formic acid, 80% acetonitrile, and 19.8% water.
  1. The sample is analyzed on a Thermo Q-Exactive HF mass spectrometer using a data-dependent acquisition method. Detailed parameters of the scans are listed in Table 2.
Global settings
Ion source type NSI
Spray voltage 2000 V
Ion transfer tube temperature 300 C
Polarity Positive
MS1 scan settings
Resolution 60000
AGC target 3e6
Maximum IT 15 ms
Scan range 375-1500 m/z
MS2 scan settings
Resolution 30000
AGC target 1e5
Maximum IT 45 ms
Loop count 12
Isolation window 1.2 m/z
NCE 28
Spectrum data type Centroid
Fixed first mass 100 m/z
Table 2. MS settings for the run.

Proteomic Data analysis
  1. The raw data generated by mass spectrometer is analyzed using Proteome Discoverer 2.5. The data is searched using the mouse proteome achieved from UniprotKB on 10/26/2020 (swissprot + trembl). The processing and consensus workflow are set according to Figure 1 and 2. The parameters are listed below in Table 3. All the parameters that are not mentioned are left defaulted.

Figure1. Processing workflow of the PD analysis.


Figure 2. Consensus workflow of the PD analysis.

SequestHT settings
Enzyme name Trypsin (Full)
Max. missed cleavage 2
Min. peptide length 6
Max. peptide length 144
Precursor mass tolerance 10 ppm
Fragment mass tolerance 0.02 Da
Max. equal modification 3
Dynamic modification Oxidation/ +15.995 Da (M)
Dynamic modification (protein terminus) Acetyl/ + 42.011 Da (N-Terminal)
Dynamic modification (protein terminus) Met-loss/ - 131.040 Da (M)
Dynamic modification (protein terminus) Met-loss+Acetyl/ - 89.030 Da (M)
Static modification Carbamidomethyl/ + 57.021 Da (C)
Percolator
Target/Decoy selection Concatenated
Validation based on q-Value
Target FDR (Strict) 0.01
Target FDR (Relaxed) 0.05
Feature Mapper settings
Maximum RT shift (min) 2
Mass tolerance 5 ppm
Table 3. Parameters for PD searching

  1. The protein list exported from PD results are further analyzed using R scripts based on the TidyProteomics package (jeffsocal.github.io/tidyproteomics/articles/overview.html).