A | |
50 mM Tris-HCl, pH 7.5 | |
10% (v/v) glycerol | |
150 mM NaCl | |
0.5 mM EDTA | |
1% (v/v) NP-40 Alternative (Merck #492016) | |
1X phosSTOP phosphatase inhibitor cocktail (PhosSTOP tablet: Roche, REF# 04906837001; to be added just before use) | |
1X protease inhibitor cocktail (cOmplete EDTA-free protease inhibitor cocktail tablet: Roche, REF# 11873580001; to be added just before use) |
A | B | |
Urea | 2 M | |
Tris-HCl pH 7.5 | 50 mM | |
DTT | 1 mM |
A | B | |
Urea | 2 M | |
Tris-HCl pH 7.5 | 50 mM | |
Iodoacetamide | 5 mM |
A | B | |
FLAG-LRRK2 [Y1699C] plasmid | 3 µg | |
wild type RILPL1-GFP or 2 µg [R293A] RILPL1-GFP plasmid | 2 µg | |
HA-Rab8A [Q67L] plasmid | 1 µg | |
1 mg/ml PEI Max 40K | 18 µl | |
OptiMem | 500 µl |
A | B | C | D | E | |
Elution solvent # (Fraction number) | Final ACN % in Elution solvent | Solvent A (ml) | Total volume (ml) | ||
8 | 100% | 100% ACN | 0 | N/A | |
7 | 17.5% | 0.7 ml Solvent B (50% ACN) | 1.3 | 2.0 | |
6 | 15.0% | 1.2 ml Elution solvent 7 (17.5% ACN) | 0.2 | 1.4 | |
5 | 12.5% | 1.0 ml Elution solvent 6 (15.0% ACN) | 0.2 | 1.2 | |
4 | 10.0% | 0.8 ml Elution solvent 5 (12.5% ACN) | 0.2 | 1.0 | |
3 | 7.5% | 0.6 ml Elution solvent 4 (10.0% ACN) | 0.2 | 0.8 | |
2 | 5.0% | 0.4 ml Elution solvent 3 (7.5% ACN) | 0.2 | 0.6 | |
1 | 2.5% | 0.2 ml Elution solvent 2 (5.0% ACN) | 0.2 | 0.4 |
A | B | |
Application Mode | Peptide | |
Method Duration (min) | 140 | |
Global Parameters | ||
Infusion Mode | Liquid Chromatography | |
Expected LC Peak Width (s) | 30 | |
Advanced Peak Determination | False | |
Default Charge State | 2 | |
Internal Mass Calibration | Off | |
Experiment#1 [MS] | ||
Start Time (min) | 0 | |
End Time (min) | 140 | |
Master Scan | ||
MS OT | ||
Detector Type | Orbitrap | |
Orbitrap Resolution | 120000 | |
Mass Range | Normal | |
Use Quadrupole Isolation | True | |
Scan Range (m/z) | 350-1500 | |
RF Lens (%) | 30 | |
AGC Target | Custom | |
Normalized AGC Target (%) | 50 | |
Maximum Injection Time Mode | Custom | |
Maximum Injection Time (ms) | 50 | |
Micro scans | 1 | |
Data Type | Profile | |
Polarity | Positive | |
Source Fragmentation | Disabled | |
Scan Description | ||
Filters | ||
MIPS | ||
Monoisotopic Peak Determination | Peptide | |
Charge State | ||
Include charge state(s) | 2-7 | |
Include undetermined charge states | False | |
Dynamic Exclusion | ||
Use Common Settings | False | |
Exclude after n times | 1 | |
Exclusion duration (s) | 45 | |
Mass Tolerance | ppm | |
Low | 10 | |
High | 10 | |
Exclude Isotopes | True | |
Perform dependent scan on single charge state per precursor only | True | |
Intensity | ||
Filter Type | Intensity Threshold | |
Intensity Threshold | 5.00E+03 | |
Data Dependent | ||
Data Dependent Mode | Number of Scans | |
Number of Dependent Scans | 10 | |
Scan Event Type 1 | ||
Scan | ||
ddMS² OT HCD | ||
Isolation Mode | Quadrupole | |
Isolation Window (m/z) | 0.7 | |
Isolation Offset | Off | |
Activation Type | HCD | |
Collision Energy Mode | Fixed | |
HCD Collision Energy (%) | 39 | |
Detector Type | Orbitrap | |
Orbitrap Resolution | 30000 | |
Mass Range | Normal | |
Scan Range Mode | Auto | |
AGC Target | Standard | |
Maximum Injection Time Mode | Custom | |
Maximum Injection Time (ms) | 96 | |
Micro scans | 1 | |
Data Type | Centroid | |
Use EASY-IC™ | False | |
Scan Description | ||
Filters | ||
Precursor Selection Range | ||
Selection Range Mode | Mass Range | |
Mass Range (m/z) | 400-1200 | |
Precursor Ion Exclusion | ||
Exclusion mass width | ppm | |
Low | 25 | |
High | 25 | |
Isobaric Tag Loss Exclusion | ||
Reagent | TMT | |
Data Dependent | ||
Data Dependent Mode | Scans Per Outcome | |
Scan Event Type 1 | ||
Scan | ||
ddMS3 OT HCD | ||
MSⁿ Level | 3 | |
Synchronous Precursor Selection | True | |
Number of SPS Precursors | 5 | |
MS Isolation Window (m/z) | 2 | |
MS2 Isolation Window (m/z) | 2 | |
Isolation Offset | Off | |
Activation Type | HCD | |
HCD Collision Energy (%) | 65 | |
Detector Type | Orbitrap | |
Orbitrap Resolution | 50000 | |
Mass Range | Normal | |
Scan Range Mode | Define m/z range | |
Scan Range (m/z) | 100-500 | |
AGC Target | Custom | |
Normalized AGC Target (%) | 200 | |
Maximum Injection Time Mode | Custom | |
Maximum Injection Time (ms) | 120 | |
Micro scans | 1 | |
Data Type | Profile | |
Use EASY-IC™ | False | |
Scan Description | ||
Number of Dependent Scans | 5 |
A | B | |
Parameter | Value | |
Version | 1.6.6.0 | |
User name | Rnirujogi | |
Machine name | SILAC-MRC0 | |
Date of writing | 10/23/2019 21:11:33 | |
Include contaminants | TRUE | |
PSM FDR | 0.01 | |
PSM FDR Crosslink | 0.01 | |
Protein FDR | 0.01 | |
Site FDR | 0.01 | |
Use Normalized Ratios For Occupancy | TRUE | |
Min. peptide Length | 7 | |
Min. score for unmodified peptides | 0 | |
Min. score for modified peptides | 40 | |
Min. delta score for unmodified peptides | 0 | |
Min. delta score for modified peptides | 6 | |
Min. unique peptides | 0 | |
Min. razor peptides | 1 | |
Min. peptides | 1 | |
Use only unmodified peptides and | TRUE | |
Modifications included in protein quantification | Oxidation (M);Acetyl (Protein N-term);Deamidation (NQ) | |
Peptides used for protein quantification | Razor | |
Discard unmodified counterpart peptides | TRUE | |
Label min. ratio count | 1 | |
Use delta score | FALSE | |
iBAQ | TRUE | |
iBAQ log fit | TRUE | |
Match between runs | TRUE | |
Matching time window [min] | 0.7 | |
Match ion mobility window [indices] | 0.05 | |
Alignment time window [min] | 20 | |
Alignment ion mobility window [indices] | 1 | |
Find dependent peptides | FALSE | |
Fasta file | D:\Database\HUMAN-Uniprot-150317_Custom7.FASTA | |
Decoy mode | revert | |
Include contaminants | TRUE | |
Advanced ratios | TRUE | |
Fixed andromeda index folder | ||
Temporary folder | ||
Combined folder location | ||
Second peptides | FALSE | |
Stabilize large LFQ ratios | FALSE | |
Separate LFQ in parameter groups | FALSE | |
Require MS/MS for LFQ comparisons | FALSE | |
Calculate peak properties | FALSE | |
Main search max. combinations | 200 | |
Advanced site intensities | FALSE | |
Write msScans table | TRUE | |
Write msmsScans table | TRUE | |
Write ms3Scans table | TRUE | |
Write allPeptides table | TRUE | |
Write mzRange table | TRUE | |
Write pasefMsmsScans table | TRUE | |
Write accumulatedPasefMsmsScans table | TRUE | |
Max. peptide mass [Da] | 4600 | |
Min. peptide length for unspecific search | 8 | |
Max. peptide length for unspecific search | 25 | |
Razor protein FDR | TRUE | |
Disable MD5 | FALSE | |
Max mods in site table | 3 | |
Match unidentified features | FALSE | |
Epsilon score for mutations | ||
Evaluate variant peptides separately | TRUE | |
Variation mode | None | |
MS/MS tol. (FTMS) | 20 ppm | |
Top MS/MS peaks per Da interval. (FTMS) | 12 | |
Da interval. (FTMS) | 100 | |
MS/MS deisotoping (FTMS) | TRUE | |
MS/MS deisotoping tolerance (FTMS) | 7 | |
MS/MS deisotoping tolerance unit (FTMS) | ppm | |
MS/MS higher charges (FTMS) | TRUE | |
MS/MS water loss (FTMS) | TRUE | |
MS/MS ammonia loss (FTMS) | TRUE | |
MS/MS dependent losses (FTMS) | TRUE | |
MS/MS recalibration (FTMS) | FALSE | |
MS/MS tol. (ITMS) | 0.5 Da | |
Top MS/MS peaks per Da interval. (ITMS) | 8 | |
Da interval. (ITMS) | 100 | |
MS/MS deisotoping (ITMS) | FALSE | |
MS/MS deisotoping tolerance (ITMS) | 0.15 | |
MS/MS deisotoping tolerance unit (ITMS) | Da | |
MS/MS higher charges (ITMS) | TRUE | |
MS/MS water loss (ITMS) | TRUE | |
MS/MS ammonia loss (ITMS) | TRUE | |
MS/MS dependent losses (ITMS) | TRUE | |
MS/MS recalibration (ITMS) | FALSE | |
MS/MS tol. (TOF) | 40 ppm | |
Top MS/MS peaks per Da interval. (TOF) | 10 | |
Da interval. (TOF) | 100 | |
MS/MS deisotoping (TOF) | TRUE | |
MS/MS deisotoping tolerance (TOF) | 0.01 | |
MS/MS deisotoping tolerance unit (TOF) | Da | |
MS/MS higher charges (TOF) | TRUE | |
MS/MS water loss (TOF) | TRUE | |
MS/MS ammonia loss (TOF) | TRUE | |
MS/MS dependent losses (TOF) | TRUE | |
MS/MS recalibration (TOF) | FALSE | |
MS/MS tol. (Unknown) | 0.5 Da | |
Top MS/MS peaks per Da interval. (Unknown) | 8 | |
Da interval. (Unknown) | 100 | |
MS/MS deisotoping (Unknown) | FALSE | |
MS/MS deisotoping tolerance (Unknown) | 0.15 | |
MS/MS deisotoping tolerance unit (Unknown) | Da | |
MS/MS higher charges (Unknown) | TRUE | |
MS/MS water loss (Unknown) | TRUE | |
MS/MS ammonia loss (Unknown) | TRUE | |
MS/MS dependent losses (Unknown) | TRUE | |
MS/MS recalibration (Unknown) | FALSE | |
Site tables | Deamidation (NQ)Sites.txt;Oxidation (M)Sites.txt;Phospho (STY)Sites.txt |