User: Craig

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Craig30
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Last seen:
8 years, 1 month ago
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9 years ago
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Posts by Craig

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Ms/Ms Peptide Identification - Please Clarify "Monoisotopic Vs Average" Paramete
... When you choose monoisotopic, you are telling the search algorithm that the input data contains monoisotopic experimental peaks so it should use monoisotopic theoretical peaks when it is doing comparisons. It doesn't necessarily mean the input data is de-isotoped. ...
written 8.9 years ago by Craig30
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Comment: C: Why Am I Getting An Error When Searching Mzml Data With Thermo Proteome Discover
... Do you happen to have a link to the Proteome Discoverer 1.3 Release Notes? I can't find them online. It is certainly interesting to hear that mzXML didn't work in 1.2 though. ...
written 8.9 years ago by Craig30
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Why Am I Getting An Error When Searching Mzml Data With Thermo Proteome Discoverer 1.3?
... I am trying to search mzML files with Thermo Proteome Discoverer 1.3 and I got the following error in the Spectrum Selector node: "Error: The number of spectrum data doesn't fit the expected value!" My mzML files were created with a very recent version of ProteoWizard and they worked fine in Mascot, ...
proteomics written 9.0 years ago by Craig30 • updated 9.0 years ago by User 317810
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Comment: C: Genbank,Ncbi Refseq Or Uniprot Protein Sequences
... Unfortunately I have never used NR so I can't answer this question. ...
written 9.0 years ago by Craig30
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Answer: A: Why Is Mass Accuracy Of Mass Spectrometers Typically Expressed In Ppm?
... I think scientists tend to like to work with numbers that range from low single digits to high triple digits. They often adjust the units they work with just to get numbers that fit into this range (I'm thinking mostly of spectroscopists, with crazy quantities like wavenumbers in units of cm[?]-1[?] ...
written 9.0 years ago by Craig30
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Answer: A: Which Mass-Spectrometry Search Algorithm Do You Use For Peptide/Protein Identifi
... I've had great success with OMSSA. Once you get past the command-line interface it is pretty simple to use. It provides good results and is multi-threaded so it's relatively fast. I've never had an issue with its results files being too big, although by default it does output the top 30 hits per spe ...
written 9.0 years ago by Craig30
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Comment: C: Open Source Mass Spec Search Engines?
... OMSSA is a great search algorithm, but not exactly the most readable. It is C++ and uses a lot of NCBI components. ...
written 9.0 years ago by Craig30
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Answer: A: Genbank,Ncbi Refseq Or Uniprot Protein Sequences
... For mass spectrometry–based proteomics, the International Protein Index (IPI, http://www.ebi.ac.uk/IPI/IPIhelp.html) has been a popular choice for common organisms. For some reason they don't have yeast but Saccharomyces Genome Database (SGD, http://www.yeastgenome.org/) fills in nicely there. Howev ...
written 9.0 years ago by Craig30
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Comment: C: Genbank,Ncbi Refseq Or Uniprot Protein Sequences
... When you go to download the FASTA (assuming that is what you are using), e.g. http://www.uniprot.org/uniprot/?query=organism%3a9606+keyword%3a181&format=*, you get a choice to download the canonical sequence data, or canonical and isoform sequence data. The latter presumably includes splice vari ...
written 9.0 years ago by Craig30 • updated 12 months ago by RamRS30k
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Answer: A: On Calculating I-Traq Ratio
... I am not 100% sure because I don't use Scaffold, but I have a pretty good guess based on my experience with isobaric tagging data analysis software. Usually for iTRAQ experiments you make the assumption that across all peptides, the median ratio will be 1:1. In other words, a typical peptide will ha ...
written 9.0 years ago by Craig30

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