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GarrettLab-UF / LipidMatch

R script using rule based feature identification for lipids
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SWATH #1

Closed VeryGenome closed 6 years ago

VeryGenome commented 6 years ago

Excuse me,can LipidMatch process data acquired from data independent acquisition (DIA) ,for example ,SWATH mode in an SCIEX 5600 machine?Thank you!

jeremykoelmel commented 6 years ago

We do have users who use the SCIEX 5600, although with iterative exclusion (IE) and DDA data. LipidMatch does not support SWATH (the only DIA approach it supports is AIF for thermo vendors).

One of our users uses SWATH and analyzes the data with MS-DIAL and IE-DDA and analyzes the data with LipidMatch:

"Combining dataset for each polarity using IE for DDA and MS-Dial for SWATH resulted in “identifying” a large number of lipids biomarkers in my untargeted approach... LipidMatch is definitely part of our lipidomics platform analysis now."

VeryGenome commented 6 years ago

Jeremy,thank you so much for your reply and advice.Our lab focus on the plant sphingolipid but I haven't got the experience for processing SWATH data before.I have read the manual of MS-DIAL and analysed the example data,that was OK,but when I try to analyse my data,I find that was so difficult for me to adjust the parameters,can you share some experience for analyzing the SWATH data in MS-DIAL?Appreciate for your help!Richard Liu

jeremykoelmel commented 6 years ago

Hiroshi may be able to help you (MS-DIAL developer): hiroshi.tsugawa@riken.jp

VeryGenome commented 6 years ago

Thanks again for your help!

JasonCochran commented 6 years ago

If you have any more questions you can open a new issue or email us! Thanks, Jason