Protein Identification

Current Prices (Updated Jan 2015)

Protein ID
Service University of California Non-Profit For-Profit
Protein ID Solution LC-MS/MS Q-Exactive $179.00 $252.00 $310.00
Protein ID Gel Band LC-MS/MS Q-Exactive $150.00 $234.00 $287.00
Raw Data Only $73.00 $114.00 $140.00

* These are bundled prices, for our official prices please see

*A note about our prices: If you can do the digestion or the database searching, it can be considerably cheaper. It’s really not that hard, and we can teach you how to do it if you are on campus or local to the area.
This Service includes prot id

  • A Quality Control run @ 125 fmol
  • Proteolytic Digestion
  • LC-MS/MS Analysis
  • Database Search
  • Results Returned via Scaffold

We Identify proteins by digesting them into peptides, analyzing the peptides using Sensitive liquid chromatography tandem mass spectrometry (LC-MS/MS), and then reassembling the identified peptides into proteins. Results are searched using X!tandem and results are returned using the Scaffold software. Want to know how to decrease your costs? You can lower the costs substantially (down to 73.00 per sample) if you do the digestion and database search. Basically the more you do, the less we have to charge you for. Not sure how to do a protein digestion or database search? Not to worry, we can teach you how to do that. Just give us a call and let us know and we can set up a time to walk you through the digestion protocol. The only caviot is that we will have to charge you a small amount if you want to put your results in Scaffold as it is commercial software that we have to pay for. If you want to just search your results with x!tandem than that would be totally free as that is open source software. We can also show you how to search your results and analyze your data during one of our free monthly data analysis classes

We are please to announce that we just installed our 2nd Q-Exactive benchtop orbitrap mass spectrometer. This is a very sensitive and fast mass spectrometer. We have been identifying over 1,000-2,000 proteins per analysis in samples that had really nice sample prep. You’re results may vary of course.


← Faqs

Protein ID

This used to be a problem when we had a large variety of instrumentation. Nowadays we use Q-Exactives for or identification and most of our Quantiation. For Targeted proteomics applications we have the TSA Vantage triple quadrupole. We have found that out Q-exactives can do about 70-80% of what the TSQ can provide.  The TSQ has a faster scan speed and it’s response is probably more linear than the Q-Exactives, although this is at the expense of greater method development

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Results are usually returned with some sort of probability estimate (depending on the software we use) and usually a false discovery rate (FDR).  You can have a look at our Scaffold Quick Start Guide 4.0  for some more info.  To make a long story short, we cannot guarantee the results you get are 100% correct. No one really can with this type of data unfortunately. The best advice is to please call before you spend a lot of money making an antibody or designing expensive experiments if you are not really familiar with this type of data.

Here is an excellent paper that explains multiple testing correction, FDR’s, p-values and q-values

How does multiple testing correction work?


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Glad you asked, we offer monthly free Data analysis classes and a yearly paid week long hands on class. Please see our web site (put in Link) for details and updates.

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We do a large amount of work to decrease the Keratin contamination in our laboratory, having said that it is possible it is coming from us, but more often than not it comes from the submitted samples. Not to worry, most of the time Keratin can be ignored if it is not at a large level. We can work with you to decrease Keratin contamination on future samples.

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Actually this hardly ever happens especially on organisms with completed genomes. On the off chance it does happen (very faint sypro band for example) we will re-verify all of our instruments were working properly and work with you to find the best solution

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Certainly, we can provide you with the mass spectrometry vendor specific file or a converted mzXML or mzML file. The later two are open source file formats that can be analyzed using a variety of open source and commercial programs.

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One misconception about proteomics (at least bottom up proteomics) is that we can identify your protein sequence directly from the data we generate from our mass spectrometers. Although this is technically possible using something called de novo sequencing, in practice it still does not work very well.

What we really do is match MS/MS patterns we generate in the mass spectrometer  with theoretical MS/MS pattern from existing sequences. Usually these sequences are stored in a FASTA formatted text file. Sometimes people refer to this as a database, which it really isn’t.

So where do we get this FASTA file? There are a few good places to look

There are a few others too

Another option is to generate your own transcriptome if you cannot find any available protein sequences.

Here is a good article that can get you started

I’ll add more to this  section hopefully soon

Please contact me if you can’t find a good database 530-754-5298. Usually we can find if one exists.

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← Faqs

Some Papers to get you Started (will put in more soon!)

Protein ID reference papers