Mass Spectrometry : I'M Looking For A Web Service

Question

[Pierre Lindenbaum]

Hi all,

First and foremost, I must say that I am a complete ignorant regarding mass spectrometry.

A colleague of mine has received some masspec data. It looks like this:

m/z    Intensity    Relative    Charge
812.41    205053.5    100    3
812.75    147485.1    71.93    3
812.08    126367.7    61.63    3
(... many ...)

As far as I understand, for each row, she fills the following form http://prospector.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msproduct and tries to locate the m/z in the resulting HTML table.

Do you know if there would be a WEBService for this kind of data ? Apart from creating a robot filling the form, how would you suggest to speed up the process ?

Thanks

UPDATE: I had a closer look at her data. She uses this HTML form to get the molecular weights of a petide with/without some post transcriptional modifications. She then tries to find the predicted weights in the output of the MALDI.

At the end, I created a robot to query the HTML form. The form accepts the GET method:

curl "http://prospector.ucsf.edu/prospector/cgi-bin/mssearch.cgi?s=1&nterm=&sequence=SAMPLER&cterm=&s2=1&nterm2=&sequence2=&cterm2=&s3=1&nterm3=&sequence3=&cterm3=&s4=1&nterm4=&sequence4=&cterm4=&s5=1&nterm5=&sequence5=&cterm5=&s6=1&nterm6=&sequence6=&cterm6=&user_aa_composition=C2+H3+N1+O1&user_aa_2_composition=&user_aa_3_composition=&user_aa_4_composition=&it=b&it=y&it=P&display_graph=1&max_charge=3&count_pos_z=Count+Basic+AA&max_losses=1&output_type=XML&output_filename=lastres&parent_mass_convert=monoisotopic&fragment_masses_tolerance=300&fragment_masses_tolerance_units=ppm&instrument_name=ESI-Q-TOF&data_format=PP+M%2FZ+Charge&data=&data_source=Data+Paste+Area&ms_mass_exclusion=0&ms_matrix_exclusion=0&ms_peak_exclusion=0&msms_deisotope=0&msms_join_peaks=0&msms_mass_exclusion=0&msms_matrix_exclusion=0&msms_peak_exclusion=0&report_title=MS-Product&search_name=msproduct&version=5.7.2"

It works fine, nevertheless I would be happy to know if there would be a web service executing this task.

[Michael]

I think I didn't quite get what the aim of this analysis is. Can you specify what you wish. The only application that comes to my mind is peptide mass fingerprinting, or is it something else?

[Thaman]

What kind of analysis you want to do with these mass spectra data?

[Pierre Lindenbaum]

as I wrote a robot to solve my problem, I'll validate the answer with the highest number of votes next week.

Answer 1

[Delagoya]

Pierre is right. You need to give us more information on what you are trying to do. If I understand this right, you are entering peptide sequences into a form to see if the resulting m/z value is in your file, which looks like MS1 data.

This is the reverse of what most folk would do, which is to use the m/z values that you have to look for the candidate peptides and proteins best represented by the data point. For that use MS-Fit

http://prospector.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msfitstandard

Or Mascot peptide mass fingerprint search

http://www.matrixscience.com/cgi/search_form.pl?FORMVER=2&SEARCH=PMF

Answer 2

[Neilfws]

There are so few web services for bioinformatics, so few of them are very good and proteomics in general is so far behind the curve when it comes to modern practice: I feel confident in saying no, there would not be a web service.

So apart from creating a robot I'd suggest...creating a robot :-) But specifically, I'd use Ruby's Mechanize, which actually makes this type of task a joy, achievable using very little code.

[Michael]

sorry, but refuted

[Neilfws]

Hardly. Link to a service which does exactly what Pierre asks?

[Michael]

uh, I somehow automatically assumed that the intention was to identify protein by peptide mass fingerprinting. Didn't really look at that link, and must admit that I don't really understand what the MS-product does. So, sorry. However, what is the use of the mass-spec analyses then?

Answer 3

[Michael]

In my former group they developed the Qupe software. It's a software-as-service web app. So not a web-service in the strict sense. I think, all the software we did in our group included SAOP web-services for parts of the functionality, it depends on what you wish to with the service.

Afaik, the standard software for this kind of queries is Mascot which is a commercial product. Btw. also, for this kind of analyses it's important what kind of instrument you are using e.g. a MALDI-TOF (which is most common, again afaik).

The emowse software from the emboss package is another open source alternative: here is the EBI web-service to it: http://www.biocatalogue.org/services/245 you can also search in http://www.biocatalogue.org/ for such services e.g. "mass spectrometry" which yields 6 hits. So there exist such services!

[Niallhaslam]

Plus one for biocatalogue - great place to find webservices.

Answer 4

[Ayaz]

Hello there,

I would like to suggest http://www.ProteinGURU.com. It provides an instant online analysis of MassFingerPrinting data via its OLMAT tool.

Good luck! Ayaz