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Messages - Mary

1
Other / MSMS in-house library - open access txt
Hello Everyone
I have a question related to building an in-house library. I am doing one with MSMS spectras acquired on Triple TOF ABSciex 5600+ (IDA , not SWATH!! - nice clean MSMS).
I am running Sigma Aldrich LSMSMS Library (around 1000 metabolites) on 4 different LC columns (RP, HILIC, pZIC Hilic etc).
I started building an library on Library View Sciex software that I can export as ".lbp". I would like to open it and save as txt or whatever other open format, including info about MSMS fragmentation and different Rt associated with metabolites.

I was looking an alternative for some other way of creating this library, in a way it can be use in R later on. The good and bad point is the number of metablites (ca.1000 x two polarities x 4 Rt), and I am very careful about data curation, so I select manually "the good" spectra, nice intensity, no instrumental noise etc.
I would be very helpful if anyone could help in opening/converting .lbp file into whatever open stuff, or suggesting better way for in-house data creation. (I tested already MS-DIAL, mzMiNE, MLS Discovery as tools)

Thank you so much for your help.

Marynka
2
Vendor specific software / Sieve v2.2
Hello, 

I would like to ask if some of you is using Sieve? 
I have just installed Sieve 2.2 on VM with windows2010... (already this probably is a problem...)
So after installation, I cannot open any old files with data processing.   :-[
Secondly, Sieve let me start a new Experiment, let me chose what kind of experiment I want to perform, I can up load files, Sieve sees at least reference file, becuase takes correctly information regarding Rt and m/z range. Once I click on "Run As Workflow", it take 3 minutes to perform all analysis, and unfortunately I see 0 features. Sieve is not able to look for features from files. Allignment is limited to reference file only. I am not sure why this problem is occuring, I don't know how to resolve this problem. 
No allert or error appear on the screen. 
also no allert was appearing during installation on windows2010....

I would appreciate any help.

marynka
3
Other / Orbitrap AIF experiment - conversion of data to open format
Hi, 
I have a question related to conversion of raw file form Orbitrap Exactive into mzXML (or whatever).

I have files from MS experiment designed in a way: ScanEvent1 - FullScan; followed by ScanEvent2: In source fragmentation HCD30, followed by ScanEvent3: Ion source fragmentation HCD 60, followed by ScanEvent3: In source fragmentation HCD 90.  (nota bene: NO DATA DEPENDENT SCAN). This design was used for untargeted metabolomics experiment as reported in article by Bird et al 2011 (10.1021/ac102598u)
I have a problem with annotation, because I have no software that is able to group correctly full scan data - with the one coming from other three scan events. First data management and statistics was done using Progenesis and Sieve, however both softwares are using only information from FullScan Event 1, not from SC 2-4.
I am trying to convert these files, with msconverter, into mzXML (mzML), where I wish to obtain mzXML that contains information from all four scan evens, in order to perform afterwards alignment and pc grouping. However, results obtained from converting only Level 1,  or Levels 1 to 4, give me always the same file. I do believe that I am loosing information from scan event 2,3 and 4. 

Does anybody know how can I convert files into "whatever open format", that contains information from all four scan events. Does anybody have some other solutions, how to connect data from ScanEvent 1, with those from Scan Events 2-4?
Is my situation hopeless, or ... hopeless   :'( ?  

Marynka


4
Mass spectrometers / Re: QTRAP parameters for lipidomics
Hi Titan,
So regarding your untargeted experiment, what can I say, is that it is not good idea.... Not on this equipment. You will not obtain any reasonable info from that. Unfortunately it is the same for direct injection; DI is sth I would rather avoid - especially for lipidomix. There are so many isomers, so many isobaric stuff, lipids are very concentrated, so you should dilute them really much. I guess that you should take an article, as Jan suggested, and go through already set parameters for your equipment. QTrap 5500 is good for targeted very sensible profiling, take one or two families that you are the most interested in, and try to profile them nicely with all isomers on good LC column. Reasonable Rt sth between 7-30 minutes.

Good luck,

Mary
5
Compound identification / DataDependentScan analysis - screening for fragment ion
Dear All,
I have one emerging question regarding analysis of DDA raw files done with Orbitrap XL.
I have found one interesting fragment ion (not precursor, just one fragment), that repeats in many MS2 spectras along all retention time. I wish to screen  whole raw file in order to look for that fragment, as it is probably related to one metabolite-marker in my study.
I have MassFrontier 7.0, Sieve and XCalibur - which of them  would be the most suitable, and how to do it? Which option to use?
I was desperately looking for some on-line manual videos, or any step-by-step explanations, however could not find any.

I would be very appreciated for any help.
thank you
Marynka
6
Compound identification / I offer Jack Daniels/Gordon's/Blantons for good answer
Hi Guys
[attachment=0:1ne5lh95]XCMS3.jpg[/attachment:1ne5lh95]
I desperately need your help with my MSMS of one unknown compoud. None of databases bring me an answer, I cannot figure out the strucutre. I have pretty nice MS data in negative and positive ionization mode done on Orbitrap FT and IT.
I would need: the putative structure or smile(You can play with C, H, O, S, N, not K, Na, ecc
I can offer: Jack Daniels/ Gordon's/Blantons Straight/ any Vodka/ Barcelo Imperial or cell number....

Here we go with MS in NEG:
HR Full ScanNEG: 282.0482(100)[M-H]-; 283.0486(10.5); 284.0413(8); 78.9855 (12) [CH3O2S]-;
HR MS/MS2 282: 162.0226(100)[M-H-CH4SO2-C3H4]-; 153.0049(10); 202.0525(30)[M-H-CH4SO2]-; 194.0(20); 236.0(40); 263.2(40); 120.0690(15); 84.0460(15)[C4H6NO]-; 254.0(20); 78.9865(14) [CH3SO2]-
•   IT MS/MS3 282-162: 84.0(100) [C4H6NO]-; 120.0(20); 162.0(10);
•   IT MS/MS3 282-153: 78.9(100) [CH3SO2]-

AND in POS:
HR FullScan POS: 284.0602(100)[M+H]+; 285.0631(9.8); 286.0551(8.9); 242.0493 (30) [M+H-C2H2O]+; 306.0411 (20)[M+Na]+; 238.0543 (30),  329.12126 (30)
HR MS/MS2 284: 242.0502(100)[M+H-C2H2O]+; 238.0553(83.2)[M+H-CO-H2O]+; 266.0501(81.5)[M+H-H2O]+; 196.0441(10)[M+H-C2H2O-H2O-CO]+; 152.0302(40);  225.0235(30)[M+H-C2H2O-NH3]+; 74.0064(20)[C2H2O3]+; 84.0450(20); 130.0510(10); 88.0386(2.2);
•   IT MS/MS3 284-266: 238.0(100)[M+H-CO]+; 222.0 (20)[M+H-C2H4O]+; 196.0(20)[M+H-CO-COCH2]+;
•   IT MS/MS3 284-242: 225.0(100)[M+H-NH3]+; 196.0 (20)[M+H-NH3-CO-H2O]+; 153.0(10)
•   IT MS/MS3 284-238: 196.0 (100)[M+H-COCH2]+; 84.0(10); 116.0(10)
•   IT MS/MS3 284-130: 88.0(100)[M+H-COCH2]+; 84.0(30)[M+H-CO-H2O]+; 102.0(20); 112.0(20);

looking forward to get some answer!
Thank you :)

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