Databehandling. 3. Mark e.g. the first fraction (1: 0-45 min, 2: min, 3; min, 4: min, 5: min, 6: min).

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1 Databehandling Data analysis 1. Choose Open in the Data analysis window. 2. Press the Open folder and choose the desired analysis. Click the + button, so that the Chromatograms line appears. Click the + on this line so the TIC±All line appears. 3. Mark e.g. the first fraction (1: 0-45 min, 2: min, 3; min, 4: min, 5: min, 6: min). 4. Check and mark TIC ± All. 1. Choose Find in the Toolbar parameters Parameters: a) AutoMS(n) parameters Intensity threshold: Retention time window (min): 0.75 (Note: computer might not understand comma, use period. ) Spectrum type (Line/Profile): Profile spectra only Background subtraction (MS only): None Do not choose Create individual AutoMS (n) chromatogram traces. b) Mass List parameters Choose Apex page Peak width (FWHM) (m/z): 0.1 S/N threshold: 0.1 Relative intensity threshold (base peak): 0 Absolute intensity threshold: 0.1 Choose Use peak finder to calculate peak position. c) Charge Deconvolute parameters

2 Choose peptide/small molecules Adduct ions: +H (first window) and H (second window) Deconvolute: choose Full scan, MS MaxRes Scan, MS(n) Low mass: High mass: (1500) Abundance cutoff (%): 5 2 Resolved-isotope deconvolution Maximum charge: Choose Related-ion deconvolution (MS full scan only). Max charge: 4 Min peak in set.3 MW agreement (0.01 %): 5 Choose clear previous results d) Mascot export options parameters Choose Set global charge limitation (2+ and 3+) Mixed list (non-deconvoluted and deconvoluted) Keep the other parameters unchecked! Press OK! 2) Choose Find in the toolbar Compounds-AutoMS(n) 3) Select and mark Compounds mass spectra so it is highlighted in blue 4) Choose Masslist in the toolbar Find 5) Choose Deconvolute Mass Spectra 6) In the downer left corner, all the peaks with selected information is displayed. If you want to select other information, right click in the window and choose layout, here you can choose between many different parameters (choose retention time and m/z in these experiments) 6) File Export Compounds and save the file as mgf. file 7) File Export Compounds and save the file as csv. File

3 Excel File Open and choose the csv.file The data will appear on the screen but in a messy way. Sort the data Mark the column Data in the upper toolbar Text to column make sure Delimited is checked Next Finish Remove the peak number so it wont disturb the comparison of the m/z Start at the top with the first mass find and replace (Ctrl H) are there many masses, then it is just garbage and not necessary to save replace them with 0 are there few peaks with that m/z and in several fractions compare the retention time approximately the same retention time it is probably a peptide mark the numbers red. When all fractions are compared and hopefully some m/z are marked red, go to the next step! Data analysis Mark the fraction you have found a potential peptide which is marked red (right click and drag, so the fraction is highlighted black). Choose Find in the toolbar Parameters (control that the parameters are set correctly, take a look in the upper section of this document to see the values of the Parameters). Choose Find CompoundsMS(n). The retention time and MS(n) isolation mass will appear down at the screen. If the data does not appear on the screen, choose Window Compounds List. In the left side of the screen under Analysis list, open the menu Compounds Mass Spectra and mark the Peak number with the m/z of interest and open the menu of that compound and mark e.g MS/MS (MS 2(631.4)) or mark the line with wanted retention time and m/z in the compound list.

4 Analysis list File Export Mass Spectrum Save as bsc.file (e.g. make a folder for each fraction and choose the m/z value as filename). Open BioTools! BioTools Open BioTools by Start All programs Bruker Daltonics BioTool File Open (open the wanted file) The mass spectrum will appear in a own window at the screen and some of the signals are marked red all of the signals must be marked red To mark the signals red: Right click in the window Choose Add peaks left click and drag over the black signals and they will become red. If you want to remove some red signals for some reasons Right click choose Remove peaks right click and drag to make red signals to black! Choose the MS icon MS If you have run a tryptic digestion choose MS (missing cleavage is normally 1 or 2).

5 In the page: a) URL: b) Taxonomy: Rodentia (Rodents) (limit the search to only some species). c) Database: MSDB (eller NCBInr) these are very broad and free databases and not that good. We are using MSDB! SwissProt: better database, but only for the human genome. d) Enzyme: None e) Fixed modification: No! Do not mark neither of these f) Variable modification: No! Do not mark neither of these g) Peptide tolerance: ± 2 Da h) MS/MS : ± 1.5 Da i) Protein mass: leave open j) Charge state: + 2 (this number is transferred to the software by it self) k) m/z : (this number is transferred to the software by it self) l) Inst: ESI-TRAP m) Report top: 20 hits (up to 100 hits, since we do not have the license). n) Press START and the data will be transferred to Mascot! Mascot 1) Format as: peptide summary 2) There will be a list with e.g. 20 proteins, depending on the parameters sat before the Mascot transfer (see BioTools part m), like this:

6 Search Selected Error tolerant 1. Q6WGI1_TRYBO Mass: Score: 61 Queries matched: 2 Heat shock protein 70 (Fragment).- Trypanoplasma borreli. Check to include this hit in error tolerant search Que ry Obser Mr(expMr(cal ved t) c) De Mi lta ss Sco re Exp Ra ect nk Peptide K.SQVFSTYADNQPGVHIQVYEGER.A K.MYQAGGGGGMPGGMPGGMPGGMPGGMP 153 GGIPGG Oxidation (M) BioTool If the program is not already open Start All programs Bruker Daltonics BioTool Open the spectrum (bsc.file) File Open Spectrum Open Sequence Editor in the upper Toolbar (Window Start Sequence editior).

7 Click on the icon at the left in the upper toolbar and the sequence will automatically be copied in the sequence editor page. If the sequence is not copied in the Sequence Editor automatically, copy the sequence, but not the flang amino acids, and paste it in the page. To get information about b and y-ions, press Bio at the toolbar (both a, b and y ions will appear). and if you get 5 b and/or y ions that is good! (You can trust the a,b and y-ions. If you have the a ion and not the b ion, just add 28 Da (C=O) to the a ion and you have the b-ion). R1-Rx are called w-ions 1) Tolerance: 2 (use 2 in these experiments, when the tolerance is increased the score of the result is also increased). When increasing the tolerance from 1 to 2, more y-ions were detected. 2) Calculate: Masses 3) Threshold: 0.0 4) Check Monoisotopic 5) Do not check Average

8 (Choose View in the toolbar View MS/MS results then you will obtain the new and perhaps increased score. According to Albena, this score is more reliable than the Mascot score.) Choose Window in the toolbar and Show/Hide Treeview. A window will appear in the left of the screen with the Biotools score If you want to examine if there are any a/b-17 (NH3) or a/b-18 (water), choose the y- and b- button in the toolbar The Biotool score can be improved by a) choosing Oxidation (M) and pyro-glu (N-term Q) and pyro-glu (Nterm E) (tar med begge fordi man vet ikke hva som er på hvilken ende) as variable modifications b) choosing Missing cleavage mix : 2 (it is normally 1) c) if Biotool detect phosphoro

9 Quantification Data analysis Open the TIC for the wanted analysis Open the SIM for the specific ion if there are several peaks with the specific m/z check the mass spectrum and if necessary send the MS/MS spectrum to Mascot and control if the same peptide sequence appear as the original m/z. If the peak shape is poor, improve the shape by changing the m/z value to the exact mass (e.g. SIM of but the chromatography shows that the most abundant m/z is make a SIM of and compare the peak shape). Mark the SIM file Integrate the peak manually, by choosing the icon then the peak area, retention time (RT) and range (pluss other parameters) appear at the end of the screen. Excel Open Excel Write the retention time and peak area of the internal standard (IS). If the compounds are separated into several peaks, sum the peak areas together and calculate the sample concentration by dividing the sample peak area with the area of the internal standard.

10 Normalize the concentration to 100 mg, then it is easier to compare the concentrations (e.g. µg/mg brain * 100 mg). If the retention time of the internal standard varies a lot, normalize the retention time as well ( e.g. tr/tr (IS)). Reporting Peak number Retention time m/z Concentration Normalized concentration Bartosz: m/z value and peptide sequence