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In contrast, we are also less likely to believe weak hits that are found by only one search engine. For high-throughput analysis, it is not realistic to review every spectrum, but a selection of spectra should be scrutinized, particularly any that yield particularly important or unexpected findings.

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In these, the signal-to-noise ratio should be examined, the presence of appropriate isotope peaks should be confirmed, and the isotope spacing should be checked to establish that charge states and mass assignments are correct. However, this will only be meaningful if the raw data can be examined, rather than smoothed, de-isotoped, or otherwise manipulated versions of the spectrum.


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The information derived from search results will depend on the nature of the sample, the techniques used, and the particular search engine, but there are some general principles to consider. For peptide mass fingerprinting, there should be adequate sequence coverage for the peptides identified.

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At this level, there is no definitive rule so users should err on the side of caution, and bearing in mind the ever-increasing size of databases and the risk of ambiguous or incorrect results, it should be considered essential to obtain corroborating data from at least one CID spectrum. For protein identifications based on CID data, it is important to appreciate that the first step requires correct peptide identifications.


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Only if this is achieved can protein identifications have any relevance. Hopefully, there will be some chemical logic to the spectrum and the fragmentation, e. Then it must be appreciated that the protein is a gene product that may represent one of a number of forms.

If it is truncated, this will be revealed only if the appropriate terminus is identified in a peptide, and then it is important to consider that this peptide could correspond to a nonspecific cleavage.

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Alternative splice variants will only be established unambiguously if an amino acid sequence corresponding to the actual splice point is observed in a peptide. No structural or sequence inferences can be based on the failure to observe a specific peptide; such a peptide may arise from proteolysis but simply not be detected, it may have an unexpected mass due to one or more modifications, or the residues may indeed be present in the sequence but the proteolysis may not proceed as anticipated.

It is equally important to note that the absence of evidence for the presence of a particular protein does not definitively establish the absence of the protein. Even though a protein may be found in one sample but not another, it is not correct to describe this as being present in sample A but not sample B. This is something that simply cannot be proved by MS.

Hardware-accelerated protein identification for mass spectrometry.

Then there is the question of supporting information. Until recently, most mass spectrometric experiments were directed toward identifying small numbers of proteins. In such cases, it would be conventional to confirm any identification by obtaining an appropriate antibody and running a Western blot. Finally, the creation of a knockout mouse might be necessary to ascertain whether there was any biological relevance, which for the identification of neural cell adhesion molecule 1 as a binding partner of the prion protein proved not to be the case Such confirmations are impossible in high-throughput proteomic experiments, therefore researchers have a responsibility to either discard marginal results or to present the full details of the search output so that others can make their own evaluations.

Although many experiments in proteomics only require that proteins be identified, quantitation can also be important, particularly for differential analysis, such as in comparisons of samples from diseased and healthy states. Prior to the widespread adoption of MS, comparison of the intensity of staining of spots on two-dimensional gels by densitometry was a common approach to this problem.

The use of gels continued with mass spectrometric analysis and was extensively automated by some workers Nevertheless, this approach to quantitation may suffer from limited dynamic range for staining, uncertainties in protein identifications, and the danger that the darkening of a spot could be due to the presence of a new protein rather than up-regulation of the protein believed to be responsible.

Although it is now commonplace to use mass spectrometric analysis of spots that show differential staining, problems with the identification of low-level proteins in mixtures may persist. With differential gel electrophoresis 53 , which is commercially available as the DIGE system Amersham Biosciences, Piscataway, NJ , the use of spectrally resolvable fluorescent dyes may separate and quantitiate up to three samples on a single two-dimensional gel.

This employs software that automatically locates and analyzes protein spots, assigning statistical confidence to observed differences.

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A different approach relies on the power of MS to separate and identify differentially isotopically labeled species. Some researchers have compared proteins from cells grown in different isotopic environments, e. Another isotope used in the MS analysis of peptides for at least 20 years is 18 O Digestion of a protein in 18 O-enriched water results in the heavy isotope being incorporated at the C terminus of each new peptide formed, with the exception of the pre-existing protein C terminus. The use of a 1: A complicating factor is further exchange of isotopically labeled oxygen catalyzed by the protease that can lead to the presence of two 18 O per carboxyl group, rather than one.

However, this can be decoupled from proteolysis 58 and is advantageous as it gives a mass difference of 4 Da rather than 2, thereby ensuring more effective separation of the natural isotopic clusters. Another method to introduce stable isotopes is to differentially label a specific amino acid such as cysteine with a chemical reagent containing light or heavy isotopes.

Such reagents may incorporate an isotope-coded affinity tag ICAT to enable enrichment of the labeled peptides, as well as to permit measurement of relative abundance The strength of the isotope labeling strategy is that it allows specific markers to be incorporated into two populations of proteins that can then be mixed together before any extraction, digestion, peptide separation, and analysis is undertaken.

As long as peptides incorporating the different isotopes have virtually identical physical and chemical properties, the ratios of peak heights or areas from MS experiments will be proportional to the relative amounts of each protein.

TMT Tags and Cutting-edge Mass Spec Technology Multiplexing Protein Research

In practice some isotopes are better than others, e. Because there is a distribution of naturally occurring heavy isotopes in all peptides, it is necessary to add the heavy isotope in sufficient numbers to completely separate the isotopic patterns for the peptides derivatized with light and heavy reagents. Special software for quantitation is becoming available from instrument manufacturers and on the websites that provide MS proteomics tools.

ICAT methodology is applicable to high-throughput experiments and can be combined with statistical methods that optimize protein identification 61 as has been described for a dataset derived from lipid raft-associated proteins Such peptides are designed to mimic the peptides formed by proteolysis of the proteins of interest and can carry chemical modifications to simulate modified proteins such as phosphoproteins MS is ideal for the study of covalent modifications as all such modifications involve a change in molecular mass, which is reflected in the mass of any peptide carrying the modified amino acid s.

It is also uncertain whether this is a posttranslational modification or a chemical change occurring during sample processing. Other mass changes may be more ambiguous, e. Some modifications may be quite heterogeneous, as with N -glycosylation, although enzymatic removal of the modified group can give a more defined change, e.

The major difficulties arise with the search for transient modifications of low stoichiometry, such as phosphorylation occurring in a regulatory role. Affinity methods have been employed to enrich phosphopeptides such as immobilized metal ion chromatography but with mixed success 68 , The difficulties are exacerbated when the modification is labile, either during chemical separation or in the mass spectrometer.

In general, peptide mass mapping alone cannot be used for identification of posttranslational modifications. Based on MS data alone, a search can be made for phosphopeptide mass values that are 80 Da higher in mass than calculated for the amino acid sequence or Da, etc. Other more labile modifications requiring special techniques for detection are sulfation 70 and O -GlcNAc 71 , It is clear that the field of proteomic analysis by MS continues to be in a very dynamic state, making it presently difficult to specify absolute standards for analytical protocols and subsequent interpretative judgments.

Furthermore, it is strongly recommended that authors take the risk of presenting too much information in describing their experiments, their data, and its interpretation. It will then be incumbent on journal editors and reviewers to determine what fraction of this information is relevant and is required for publication. Proteins were separated by MW during size exclusion chromatography followed by pI separation using IEF capillary electrophoresis.

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Immuno-selective columns, where monoclonal or polyclonal antibodies are covalently linked to the inside surface of the column. Composition and influence of the blotting buffer and solvents Buffers are crucial during the electroblotting operation tank or semi-dry. Buffer creates the electric field that is the active process for protein migration and carries ions from the anode to the cathode to maintain the electrical neutrality of the system. An aqueous buffer is generally used but it usually contains a low concentration of organic solvents.

Buffers composition A large number of buffering substances are used. Field programmable gate arrays FPGAs are used to create hardware-accelerated algorithms that reduce operating costs and improve search speed compared to large clusters. We present a novel hardware design that takes full spectra and computes 6-frame translation word searches on DNA databases at a rate of approximately 3 billion base pairs per second, with queries of up to 10 amino acids in length and arbitrary wildcard positions.

Hardware post-processing identifies in silico tryptic peptides and scores them using a variety of techniques including mass frequency expected values.