Feature Changes - v1.0.2 Michael Degan  2015-06-24
 
Updates new in v1.0.2
 - Completed spectral library for Homo Sapiens All Tissues
    + Previously, since this organism did not have a complete spectral library, the plugin would reach a fail state. This addition addresses and corrects this issue, allowing users to investigate proteins from all tissues explored in http://www.nature.com/nature/journal/v509/n7502/abs/nature13302.html. Note: due to the large amount of data associated with this organism, calculating pathway coverage and generating the pathway images takes a significant amount of time.
 
 
Cheryl.Lichti responded:  2015-11-02
Hi Michael,

Thanks for your work - great plug-in with lots of potential!

I have a quick question for you: are the MS/MS spectra in this library ion trap spectra or HCD spectra? If they are trap spectra, is there any way we can add an option to use another spectral database?

Thanks,
Cheryl
 
Samuel Payne responded:  2015-11-03
Cheryl,

Are you referring to the human spectra? or the library in general?

For the human spectra, they all come from the Pandey lab publication (see link in Mike's comment). This publication has the following about data generation "Mass spectrometry analysis was carried out in a data dependent manner with full scans (350–1,800 m/z) acquired using an Orbitrap mass analyser at a mass resolution of 60,000 at 400 m/z in Velos and 120,000 in Elite at 400 m/z. Twenty most intense precursor ions from a survey scan were selected for MS/MS from each duty cycle and detected at a mass resolution of 15,000 at m/z of 400 in Velos and 30,000 at m/z of 400 in Orbitrap analyser. All the tandem mass spectra were produced by higher-energy collision dissociation (HCD) method."

So all that data is HCD.

As for the library in general, it is a real mixed bag. Please see our publication about the dataset (http://www.nature.com/articles/sdata201541). It is the collection of data from 15 years doing fun science here at PNNL. It comes from various instruments and fragmentation modalities. In supplemental table 2 in the manuscript we go over data generation details for the >35,000 .RAW files that make up the library.

Thanks for your interest. If you have any other questions, please let us know.

Sam Payne
 
Samuel Payne responded:  2015-11-03
Cheryl,

I should have addressed your question about adding other data to the database. What kind/type of data did you have in mind? We are open to adding new stuff, but it may require a bit of work.
 
Cheryl.Lichti responded:  2015-11-03
Hi Sam,

Sorry my question was so vague; I did mean the human database, so you gave me exactly what I needed to know. (And, gee, I should've followed the link! Somehow I missed that. Such a Monday thing to do.) I'm attempting to analyze SWATH data, so HCD spectra are much better than CID spectra from an ion trap. In terms of another database, I was wondering how easy/difficult it would be to allow the option to NOT export a corresponding spectral library and use a local library instead.

Are you currently working with anyone to optimize use of the Biodiversity plug-in for analyzing SWATH data? I'd be very interested in playing along. I think I've made a pretty good start on things, but it could be helpful to work with others. Multiple minds are usually better than one.

Cheryl
 
Samuel Payne responded:  2015-11-03
Cheryl,

This is a very interesting idea, to allow people to use a local library. There are a few requirements that would be needed in order to have things work, mostly bookkeeping stuff.

1. you have to use real accessions. This may sound simple, but it is an issue. We use accessions from either Uniprot or RefSeq to match things onto the KEGG pathways. If you're using something else, the plugin will fail.
2. you have to have a bibliospec library created in a certain way.

It would be good for us to think about the best way to enable this option. you can feel free to email me at first.lastname@pnnl.gov

Samuel Payne
 
Cheryl.Lichti responded:  2015-11-03
Will do! Thanks, Sam.