User: Jdnavarro

gravatar for Jdnavarro
Jdnavarro410
Reputation:
410
Status:
Trusted
Location:
Sevilla, Spain
Website:
http://http:/dannynava...
Last seen:
7 years ago
Joined:
8 years, 5 months ago
Email:
j@dannynavarro.net

Posts by Jdnavarro

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Library To Generate Theoretical Tandem Mass Spectra From Arbitrary Peptide Seque
... That script is quite straightforward to port to my current application. I'll try to release my ported version as a Python library. ...
written 8.2 years ago by Jdnavarro410
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Library To Generate Theoretical Tandem Mass Spectra From Arbitrary Peptide Sequences
... I know there are some desktop applications where you can input some peptide sequences and it generates the coordinates of the expected fragments for a tandem MS/MS spectrum (normally y and b ions fragmented with CID). I would like to embed that functionality in a program I'm writing. Does anyone kno ...
proteomics library written 8.2 years ago by Jdnavarro410 • updated 4.3 years ago by Laurent1.6k
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Comment: C: Proteolysis Of A Protein Sequence
... What's your input file? FASTA? ...
written 8.2 years ago by Jdnavarro410
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Comment: C: How Wouid You Analyse Electron Transfer Dissociation (Etd) Mass Spectra?
... Well, in the paper I linked to they are claiming they designed a new scoring scheme for ETD from scratch. I never tried ProteinProspector but they claim very good restuls. ...
written 8.3 years ago by Jdnavarro410
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Answer: A: How Wouid You Analyse Electron Transfer Dissociation (Etd) Mass Spectra?
... The most popular search engines are optimized for CID. I would give a try to new search engines that claim better performance with ETD. Off the top of my head: MS-GFDB (open source) ZCore (commercial) http://www.biomedcentral.com/1471-2105/11/S1/S4 (ETD scoring function) ProteinProspector (web app? ...
written 8.3 years ago by Jdnavarro410
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Comment: C: What Are The Big Problems/Current Trends In Proteomics?
... I deliberately ommited top down proteomics in my reply. I think it's really hard to separate entire proteins as you do with peptides. However I agree with absolute quantifitacion, that could have a huge impact. ...
written 8.4 years ago by Jdnavarro410
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Answer: A: What Are The Big Problems/Current Trends In Proteomics?
... Protein inference from peptides. It's an old problem that still is not solved (and don't think won't be in a long time). There is no one solution but there should be more choices at how to look at the peptides in order to mine more meaningful information. Missing spectra. In an average experiment L ...
written 8.4 years ago by Jdnavarro410
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Comment: C: Open Source Mass Spec Search Engines?
... Nice, didn't know about that one. Looking forward for the code release. ...
written 8.4 years ago by Jdnavarro410
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Comment: C: Why There Are No Proteomics Questions In Biostar?
... I used to follow that group some time ago. I found it too specific of TPP but will give it a try again. Thanks for reminding me that one.. ...
written 8.4 years ago by Jdnavarro410
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Comment: C: Why There Are No Proteomics Questions In Biostar?
... I think nobody in bioinformatics expects to find proteomics informatics currently trained in the market. AFAIK most proteomics labs hire bioinformaticians that will be trained in proteomics data. But still there are not that many proteomics informaticians. Do you think it's a problem of recruitment ...
written 8.4 years ago by Jdnavarro410

Latest awards to Jdnavarro

Teacher 8.4 years ago, created an answer with at least 3 up-votes. For A: What Are The Big Problems/Current Trends In Proteomics?
Appreciated 8.4 years ago, created a post with more than 5 votes. For A: What Are The Big Problems/Current Trends In Proteomics?
Good Answer 8.4 years ago, created an answer that was upvoted at least 5 times. For A: What Are The Big Problems/Current Trends In Proteomics?
Student 8.4 years ago, asked a question with at least 3 up-votes. For Open Source Mass Spec Search Engines?
Good Question 8.4 years ago, asked a question that was upvoted at least 5 times. For Open Source Mass Spec Search Engines?
Appreciated 8.4 years ago, created a post with more than 5 votes. For Open Source Mass Spec Search Engines?
Student 8.4 years ago, asked a question with at least 3 up-votes. For Why There Are No Proteomics Questions In Biostar?
Appreciated 8.4 years ago, created a post with more than 5 votes. For Why There Are No Proteomics Questions In Biostar?
Good Question 8.4 years ago, asked a question that was upvoted at least 5 times. For Why There Are No Proteomics Questions In Biostar?

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