Protein Prospector

Freely available PMF search engines include Mascot from Matrix Science (http / /www.matrixscience.com/cgi/search form.pl FORMVER=2 SEARCH=PMF), MS-Fit from Protein Prospector (http //prospector.ucsf.edU/ucsfhtml4.0/msfit. htm), and Peptldent from ExPaSy (http //us.expasy.org/tools/peptident.html). 

Thirteen ions were selected from the spectrum shown in Fig. 6 and used to search the SwissProt protein sequence database. The results of this search are shown in Table 1. The program MS-Fit, which is part of the Protein Prospector... 

The methods for each study are divided into the initial protein separation step, a second separation step if applicable, the type of mass analysis, and the software used for peptide identification. ID = one dimensional polyacrylamide gel electrophoresis, 2D = two dimensional polyacrylamide gel electrophoresis, MS = mass spectrometry (peptide mass fingerprinting), MS/MS = tandem mass spectrometry, MALDI-TOF = matrix assisted laser desorption/ionization-time of flight, MS FIT = software from Protein Prospector, http //prospector.ucsf edu/, ESI = electrospray ionization, Q-TOF = quadrupole-time of flight, PPSS2 =Protana s Proteomic Software Suite (ProtanaEngineering, Odense, Denmark), Mascot = Matiix Science, http //www.matrixscience.com/, TOF-TOF = MALDI plus TOF tandem mass spectrometry, RP-HPLC = reverse phase high performance liquid chromatography, Q-IT = quadrupole ion trap, LIT = linear ion trap. Bioworks = Thermo Electron Corporation. 

The combination of MALDI-TOF MS and capillary LC/MS/MS was recently described for the identification of disease state markers in human urine. In this study, urine proteins obtained from emphysema patients were separated on 2-D gels and selected spots were digested with trypsin and analyzed by MALDI-TOF. A database search using Protein Prospector identified a potential biomarker for emphysema as human alpha-1-antitrypsin (AlAT). The corresponding MALDI spectrum contained nine out of 18 peptides with masses that match the expected tryptic digest fragments for AlAT. 

PE Corp http //WWW.pecorporation.com http //www.appliedbiosystems.com Symbiot workstation Voyager STR MALDI-TOF MS, the Voyager DE-PRO or the Mariner API-TOF LC-MS Protein Solution 1, SQL-LiMS, ProteinKeeper (under development)and Protein Prospector... 

International Protein Index database for the species studied (available online at http //www.ebi.ac. uk/IPI) and its sequence-reversed version with the Mascot (Matrix Science, Boston, MA) search algorithm. Equivalent search software (Proteome Discoverer [Thermo Fisher Scientific], Protein Prospector [http //prospector.ucsf.edu/prospector/ mshome.htm], Phenyx [GeneBio, Geneva, Switzerland], XlTandem [http //www.thegpm.org/tandem/], etc.) may also be used. 

In our first example we use a low-performance mass spectrometer. Assuming that five peptides (m/z 729.86,818.95,1072.32,1253.49, and 1530.65) appear in the mass spectrum (e.g., as commonly observed, due to the ion-suppression effect we do not detect all tryptic peptides), the average masses are determined with 2000 ppm mass accuracy, and the search in the SwissProt database is restricted to the proteins of Homo sapiens, the MS-Fit searching tool of Protein Prospector [11] finds 114 entries that are more or less consistent with this data. The relevant section of the mass spectrum is shown in Fig. 2. Note that in this example no impurities complicate the spectrum. 

The mass differences in the b series reveal the presence of L/I followed by S in the sequence. This information is sufficient to attempt a sequence tag search. Searching the SwissProt database for H. sapiens proteins by entering m/z 1833.9 for the parent ion and 1108.5, 1021.5, and 908.4 for the b series fragments in the MS-Seq searching tool of Protein Prospector [11] turns up a single protein, human hemoglobin a subunit with primary accession number P69905. 

The MS-Tag program, implemented in Protein Prospector, was the first to identify proteins from MS/MS spectra by searching sequence databases. Unlike the other database-searching programs, MS-Tag does not calculate a score. Instead, it simply ranks peptides by the number of fragment ions that match to a sequence in the database. Oftentimes, this method of ranking peptides is too low-resolution to differentiate between the top-ranking peptides and is supplemented with a method to score the peptides. ... 

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