The growing use of selected reaction monitoring (SRM) mass spectrometry in proteomic analyses led us to investigate how to identify peptides by SRM using only a minimal number of fragment ions. By using a computational model of the SRM work flow we computed the potential interferences from other peptides in a given proteome. From these results, we selected the deterministic SRM addresses that contained sufficient information to confer peptide and protein identity that we termed unique ion signatures (UIS). We computationally showed that UIS comprised of only two transitions are diagnostic for >99% of Escherichia coli proteins and >96% of human proteins that possess a sequence-unique peptide. We demonstrated an example of experimental use of UIS using a modified SRM methodology to profile the E. coli tricarboxylic acid cycle from a single injection of cell lysate. In addition, we showed the potential of UIS to form the first functionally orthogonal approach to validate peptide assignments obtained from conventional analyses of MS/MS spectra. The UIS methodology is a novel deterministic peptide identification method for MS/MS spectra based on information content. These robust theoretical assays will have widespread use when integrated with previously collected MS/MS data and conventional proteomics technologies. The growing use of selected reaction monitoring (SRM) mass spectrometry in proteomic analyses led us to investigate how to identify peptides by SRM using only a minimal number of fragment ions. By using a computational model of the SRM work flow we computed the potential interferences from other peptides in a given proteome. From these results, we selected the deterministic SRM addresses that contained sufficient information to confer peptide and protein identity that we termed unique ion signatures (UIS). We computationally showed that UIS comprised of only two transitions are diagnostic for >99% of Escherichia coli proteins and >96% of human proteins that possess a sequence-unique peptide. We demonstrated an example of experimental use of UIS using a modified SRM methodology to profile the E. coli tricarboxylic acid cycle from a single injection of cell lysate. In addition, we showed the potential of UIS to form the first functionally orthogonal approach to validate peptide assignments obtained from conventional analyses of MS/MS spectra. The UIS methodology is a novel deterministic peptide identification method for MS/MS spectra based on information content. These robust theoretical assays will have widespread use when integrated with previously collected MS/MS data and conventional proteomics technologies. Shotgun proteomic analyses using multidimensional LC/MS/MS show great capacity for rapid protein analysis. This is arguably the most prevalent work flow for high throughput comparative proteomics, utilizing information-dependent acquisition (IDA) 1The abbreviations used are:IDAinformation-dependent acquisitionMIDASMRM-initiated detection and sequencingSRMselective reaction monitoringUISunique ion signature(s) (a combination of ions generated by a peptide that maps exclusively to one peptide in the proteome being analyzed)UIS|rUIS composed of r SRM scans, meaning one Q1 value and r Q3 valuesIAAiodoacetamideXICextracted ion chromatogram. 1The abbreviations used are:IDAinformation-dependent acquisitionMIDASMRM-initiated detection and sequencingSRMselective reaction monitoringUISunique ion signature(s) (a combination of ions generated by a peptide that maps exclusively to one peptide in the proteome being analyzed)UIS|rUIS composed of r SRM scans, meaning one Q1 value and r Q3 valuesIAAiodoacetamideXICextracted ion chromatogram. to acquire MS/MS triggered by the signals generated from incoming peptides (1Wolters D.A. Washburn M.P. Yates 3rd, J.R. An automated multidimensional protein identification technology for shotgun proteomics.Anal. Chem. 2001; 73: 5683-5690Crossref PubMed Scopus (1557) Google Scholar, 2Aebersold R. Mann M. Mass spectrometry-based proteomics.Nature. 2003; 422: 198-207Crossref PubMed Scopus (5540) Google Scholar, 3Domon B. Aebersold R. Mass spectrometry and protein analysis.Science. 2006; 312: 212-217Crossref PubMed Scopus (1584) Google Scholar). Despite the utility and widespread use of this approach, there remain inherent problems including a relatively high level of ambiguous and false peptide assignments (∼5%) as well as high numbers of unassigned mass spectra (4Eriksson J. Fenyö D. A model of random mass-matching and its use for automated significance testing in mass spectrometric proteome analysis.Proteomics. 2002; 2: 262-270Crossref PubMed Scopus (31) Google Scholar, 5Cargile B.J. Bundy J.L. Stephenson Jr., J.L. Potential for false positive identifications from large databases through tandem mass spectrometry.J. Proteome Res. 2004; 3: 1082-1085Crossref PubMed Scopus (173) Google Scholar, 6Marcotte E.M. How do shotgun proteomics algorithms identify proteins?.Nat. Biotechnol. 2007; 25: 755-757Crossref PubMed Scopus (73) Google Scholar). The reason for this level of ambiguity stems in part from the non-deterministic nature of the identification algorithms. Without the use of reference standards the only way to know a spectrum was generated by a given peptide with absolute certainty is for the spectrum to contain a fragment pattern that conclusively demonstrates the presence of each amino acid. Unfortunately this level of coverage is extremely rare in proteomics data.More recently, selected reaction monitoring (SRM) or multiple reaction monitoring (MRM) mass spectrometry methods have been deployed for proteomic analyses (7Gerber S.A. Rush J. Stemman O. Kirschner M.W. Gygi S.P. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS.Proc. Natl. Acad. Sci. U.S.A. 2003; 100: 6940-6945Crossref PubMed Scopus (1534) Google Scholar, 8Anderson N.L. Anderson N.G. Haines L.R. Hardie D.B. Olafson R.W. Pearson T.W. Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA).J. Proteome Res. 2004; 3: 235-244Crossref PubMed Scopus (692) Google Scholar, 9Barnidge D.R. Goodmanson M.K. Klee G.G. Muddiman D.C. Absolute quantification of the model biomarker prostate-specific antigen in serum by LC-Ms/MS using protein cleavage and isotope dilution mass spectrometry.J. Proteome Res. 2004; 3: 644-652Crossref PubMed Scopus (243) Google Scholar, 10Cox D.M. Zhong F. Du M. Duchoslav E. Sakuma T. McDermott J.C. Multiple reaction monitoring as a method for identifying protein posttranslational modifications.J. Biomol. Tech. 2005; 16: 83-90PubMed Google Scholar, 11Kirkpatrick D.S. Gerber S.A. Gygi S.P. The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications.Methods. 2005; 35: 265-273Crossref PubMed Scopus (475) Google Scholar, 12Unwin R.D. Griffiths J.R. Leverentz M.K. Grallert A. Hagan I.M. Whetton A.D. Multiple reaction monitoring to identify sites of protein phosphorylation with high sensitivity.Mol. Cell. Proteomics. 2005; 4: 1134-1144Abstract Full Text Full Text PDF PubMed Scopus (186) Google Scholar, 13Lin S. Shaler T.A. Becker C.H. Quantification of intermediate-abundance proteins in serum by multiple reaction monitoring mass spectrometry in a single-quadrupole ion trap.Anal. Chem. 2006; 78: 5762-5767Crossref PubMed Scopus (83) Google Scholar, 14Anderson L. Hunter C.L. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins.Mol. Cell. Proteomics. 2006; 5: 573-588Abstract Full Text Full Text PDF PubMed Scopus (1076) Google Scholar, 15Stahl-Zeng J. Lange V. Ossola R. Eckhardt K. Krek W. Aebersold R. Domon B. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites.Mol. Cell. Proteomics. 2007; 6: Full Text Full Text PDF PubMed Scopus Google Scholar, T. M. E. S.A. assays for proteins in plasma by mass spectrometry and isotope Cell. Proteomics. 2007; 6: Full Text Full Text PDF PubMed Scopus Google Scholar, A. S. D.A. Multiple reaction monitoring for robust proteomic of Natl. Acad. Sci. U.S.A. 2007; PubMed Scopus Google Scholar, M. J. M. M. S. M. The of multiple reaction monitoring assays for plasma 2007; PubMed Scopus Google Scholar, S. J. A. of shotgun proteomic for monitoring in Proteome Res. PubMed Scopus Google Scholar, V. J. N.L. J. J. C.H. L. Domon B. Aebersold R. of by multiple reaction Cell. Proteomics. Full Text Full Text PDF PubMed Scopus Google Scholar). This as proteomics from a a and The method is using mass two of mass and sensitivity to one or peptides in the of a as a cell lysate. this approach the mass the selected ion and a ion from the SRM used to of these ions in an to the that the Q1 Q3 transitions the with A of with is the to for This by data from or by in as detection and D.M. Zhong F. Du M. Duchoslav E. Sakuma T. McDermott J.C. Multiple reaction monitoring as a method for identifying protein posttranslational modifications.J. Biomol. Tech. 2005; 16: 83-90PubMed Google Scholar, 12Unwin R.D. Griffiths J.R. Leverentz M.K. Grallert A. Hagan I.M. Whetton A.D. Multiple reaction monitoring to identify sites of protein phosphorylation with high sensitivity.Mol. Cell. Proteomics. 2005; 4: 1134-1144Abstract Full Text Full Text PDF PubMed Scopus (186) Google Scholar). the of SRM in proteomics is that the selected of and ions contain sufficient information to for the peptide and its protein of that proteomics SRM are with a minimal of one that a of in the of this been This a with of MS/MS triggered by SRM as these are sensitivity that contain data to conclusively confer peptide of is in SRM sensitivity a large Q1 is This in other peptides with Q1 and to with detection of the The of these interferences as the of the a of false this is an as conventional peptide identification utilizing tandem in false to that SRM assays that ions MS/MS J. K. M.P. How is The of and ion PubMed Scopus Google this we the information of SRM assays and in the potential of the us to that of SRM and ions the of by ion that to peptides the of the We used these unique ion signatures in a of to SRM data acquisition for the detection of in the Escherichia coli tricarboxylic acid In addition, given that UIS have been to peptides in the experimental we demonstrated the of UIS as an orthogonal of peptide identity for MS/MS methods for peptide identification are to proteomics of the of data generated by We used computational and experimental to show that the of to proteins in a proteome will in a of assays with ambiguous of from peptides that the we demonstrated by using generated by experimental that a to this is approach was to use the in the as a for the of the proteome. that is to the experimental in the as are to the of the UIS that are to false the and the UIS high in each detection of one peptide in and >96% of the E. coli and human We that these this coverage using only two transitions A of is being is robust method that ion we do have the to UIS ions will there are that to the of including use of of of peptide and based on these M. D. J. B. R. T. B. Aebersold R. of peptides for Biotechnol. 2007; 25: PubMed Scopus Google Scholar, of spectra of Chem. 2004; PubMed Scopus Google Scholar, of spectra of peptides with or Chem. 2005; PubMed Scopus Google use of data A. D.M. B. B. S. the of SRM using data from shotgun proteomics to method Proteome Res. PubMed Scopus Google or approach to ions based on in multiple By this we the ions that are in multiple a level of the UIS of a given do an ion by the number of transitions by one the that an of addresses are one that is a peptide ions and using two ions in or for the is The significance of these are for large proteome and given a high of UIS this the that a of the proteome will using the detection methodology by these UIS a peptide as are only sequence-unique are in the for a given that there is utility in using UIS for of peptide obtained from conventional of MS/MS this approach is functionally orthogonal to conventional methods to assignments that are these of the two methods is for the conventional given that ions are used in these a UIS in the MS/MS we demonstrated in UIS used to spectra from assignments that are that the spectra contain peptide assignments for peptides that have This of value for proteome given that that to of MS/MS spectra are unassigned E.M. How do shotgun proteomics algorithms identify proteins?.Nat. Biotechnol. 2007; 25: 755-757Crossref PubMed Scopus (73) Google is to that the are only in the of the a of is the a protein in the is composed exclusively of peptides in the there are UIS for to the presence of each peptide in the proteome is a that ion from UIS this the in an method to for and to the this We have previously the of using to SRM J. K. M.P. How is The of and ion PubMed Scopus Google Scholar). we an to the of or use of an SRM Q3 ion to peptide in the and each of these was to the use of a peptide This that use of is to the use of an Q3 a is an of using a one to peptide to this to as is an in proteomic a rapid to UIS the use of with MS/MS reference and peptide reference peptides for are to peptide and information content. The of the work addresses information content. of peptide identification from from for from the of A. A. S. and Scholar, A. R. J. Scholar). methods to with will in UIS identification and are an that will Shotgun proteomic analyses using multidimensional LC/MS/MS show great capacity for rapid protein analysis. This is arguably the most prevalent work flow for high throughput comparative proteomics, utilizing information-dependent acquisition (IDA) 1The abbreviations used are:IDAinformation-dependent acquisitionMIDASMRM-initiated detection and sequencingSRMselective reaction monitoringUISunique ion signature(s) (a combination of ions generated by a peptide that maps exclusively to one peptide in the proteome being analyzed)UIS|rUIS composed of r SRM scans, meaning one Q1 value and r Q3 valuesIAAiodoacetamideXICextracted ion chromatogram. 1The abbreviations used are:IDAinformation-dependent acquisitionMIDASMRM-initiated detection and sequencingSRMselective reaction monitoringUISunique ion signature(s) (a combination of ions generated by a peptide that maps exclusively to one peptide in the proteome being analyzed)UIS|rUIS composed of r SRM scans, meaning one Q1 value and r Q3 valuesIAAiodoacetamideXICextracted ion chromatogram. to acquire MS/MS triggered by the signals generated from incoming peptides (1Wolters D.A. Washburn M.P. Yates 3rd, J.R. An automated multidimensional protein identification technology for shotgun proteomics.Anal. Chem. 2001; 73: 5683-5690Crossref PubMed Scopus (1557) Google Scholar, 2Aebersold R. Mann M. Mass spectrometry-based proteomics.Nature. 2003; 422: 198-207Crossref PubMed Scopus (5540) Google Scholar, 3Domon B. Aebersold R. Mass spectrometry and protein analysis.Science. 2006; 312: 212-217Crossref PubMed Scopus (1584) Google Scholar). Despite the utility and widespread use of this approach, there remain inherent problems including a relatively high level of ambiguous and false peptide assignments (∼5%) as well as high numbers of unassigned mass spectra (4Eriksson J. Fenyö D. A model of random mass-matching and its use for automated significance testing in mass spectrometric proteome analysis.Proteomics. 2002; 2: 262-270Crossref PubMed Scopus (31) Google Scholar, 5Cargile B.J. Bundy J.L. Stephenson Jr., J.L. Potential for false positive identifications from large databases through tandem mass spectrometry.J. Proteome Res. 2004; 3: 1082-1085Crossref PubMed Scopus (173) Google Scholar, 6Marcotte E.M. How do shotgun proteomics algorithms identify proteins?.Nat. Biotechnol. 2007; 25: 755-757Crossref PubMed Scopus (73) Google Scholar). The reason for this level of ambiguity stems in part from the non-deterministic nature of the identification algorithms. Without the use of reference standards the only way to know a spectrum was generated by a given peptide with absolute certainty is for the spectrum to contain a fragment pattern that conclusively demonstrates the presence of each amino acid. Unfortunately this level of coverage is extremely rare in proteomics information-dependent acquisition detection and reaction monitoring unique ion signature(s) (a combination of ions generated by a peptide that maps exclusively to one peptide in the proteome being UIS composed of r SRM scans, meaning one Q1 value and r Q3 ion chromatogram. information-dependent acquisition detection and reaction monitoring unique ion signature(s) (a combination of ions generated by a peptide that maps exclusively to one peptide in the proteome being UIS composed of r SRM scans, meaning one Q1 value and r Q3 ion chromatogram. recently, selected reaction monitoring (SRM) or multiple reaction monitoring (MRM) mass spectrometry methods have been deployed for proteomic analyses (7Gerber S.A. Rush J. Stemman O. Kirschner M.W. Gygi S.P. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS.Proc. Natl. Acad. Sci. U.S.A. 2003; 100: 6940-6945Crossref PubMed Scopus (1534) Google Scholar, 8Anderson N.L. Anderson N.G. Haines L.R. Hardie D.B. Olafson R.W. Pearson T.W. Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA).J. Proteome Res. 2004; 3: 235-244Crossref PubMed Scopus (692) Google Scholar, 9Barnidge D.R. Goodmanson M.K. Klee G.G. Muddiman D.C. Absolute quantification of the model biomarker prostate-specific antigen in serum by LC-Ms/MS using protein cleavage and isotope dilution mass spectrometry.J. Proteome Res. 2004; 3: 644-652Crossref PubMed Scopus (243) Google Scholar, 10Cox D.M. Zhong F. Du M. Duchoslav E. Sakuma T. McDermott J.C. Multiple reaction monitoring as a method for identifying protein posttranslational modifications.J. Biomol. Tech. 2005; 16: 83-90PubMed Google Scholar, 11Kirkpatrick D.S. Gerber S.A. Gygi S.P. The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications.Methods. 2005; 35: 265-273Crossref PubMed Scopus (475) Google Scholar, 12Unwin R.D. Griffiths J.R. Leverentz M.K. Grallert A. Hagan I.M. Whetton A.D. Multiple reaction monitoring to identify sites of protein phosphorylation with high sensitivity.Mol. Cell. Proteomics. 2005; 4: 1134-1144Abstract Full Text Full Text PDF PubMed Scopus (186) Google Scholar, 13Lin S. Shaler T.A. Becker C.H. Quantification of intermediate-abundance proteins in serum by multiple reaction monitoring mass spectrometry in a single-quadrupole ion trap.Anal. Chem. 2006; 78: 5762-5767Crossref PubMed Scopus (83) Google Scholar, 14Anderson L. Hunter C.L. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins.Mol. Cell. Proteomics. 2006; 5: 573-588Abstract Full Text Full Text PDF PubMed Scopus (1076) Google Scholar, 15Stahl-Zeng J. Lange V. Ossola R. Eckhardt K. Krek W. Aebersold R. Domon B. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites.Mol. Cell. Proteomics. 2007; 6: Full Text Full Text PDF PubMed Scopus Google Scholar, T. M. E. S.A. assays for proteins in plasma by mass spectrometry and isotope Cell. Proteomics. 2007; 6: Full Text Full Text PDF PubMed Scopus Google Scholar, A. S. D.A. Multiple reaction monitoring for robust proteomic of Natl. Acad. Sci. U.S.A. 2007; PubMed Scopus Google Scholar, M. J. M. M. S. M. The of multiple reaction monitoring assays for plasma 2007; PubMed Scopus Google Scholar, S. J. A. of shotgun proteomic for monitoring in Proteome Res. PubMed Scopus Google Scholar, V. J. N.L. J. J. C.H. L. Domon B. Aebersold R. of by multiple reaction Cell. Proteomics. Full Text Full Text PDF PubMed Scopus Google Scholar). This as proteomics from a a and The method is using mass two of mass and sensitivity to one or peptides in the of a as a cell lysate. this approach the mass the selected ion and a ion from the SRM used to of these ions in an to the that the Q1 Q3 transitions the with A of with is the to for This by data from or by in as detection and D.M. Zhong F. Du M. Duchoslav E. Sakuma T. McDermott J.C. Multiple reaction monitoring as a method for identifying protein posttranslational modifications.J. Biomol. Tech. 2005; 16: 83-90PubMed Google Scholar, 12Unwin R.D. Griffiths J.R. Leverentz M.K. Grallert A. Hagan I.M. Whetton A.D. Multiple reaction monitoring to identify sites of protein phosphorylation with high sensitivity.Mol. Cell. Proteomics. 2005; 4: 1134-1144Abstract Full Text Full Text PDF PubMed Scopus (186) Google Scholar). the of SRM in proteomics is that the selected of and ions contain sufficient information to for the peptide and its protein of that proteomics SRM are with a minimal of one that a of in the of this been This a with of MS/MS triggered by SRM as these are sensitivity that contain data to conclusively confer peptide The of is in SRM sensitivity a large Q1 is This in other peptides with Q1 and to with detection of the The of these interferences as the of the a of false this is an as conventional peptide identification utilizing tandem in false to that SRM assays that ions MS/MS J. K. M.P. How is The of and ion PubMed Scopus Google Scholar). In this we the information of SRM assays and in the potential of the us to that of SRM and ions the of by ion that to peptides the of the We used these unique ion signatures in a of to SRM data acquisition for the detection of in the Escherichia coli tricarboxylic acid In addition, given that UIS have been to peptides in the experimental we demonstrated the of UIS as an orthogonal of peptide identity for MS/MS methods for peptide identification are to proteomics of the of data generated by We used computational and experimental to show that the of to proteins in a proteome will in a of assays with ambiguous of from peptides that the we demonstrated by using generated by experimental that a to this is approach was to use the in the as a for the of the proteome. that is to the experimental in the as are to the of the UIS that are to false the and the UIS high in each detection of one peptide in and >96% of the E. coli and human We that these this coverage using only two transitions A of is being is robust method that ion we do have the to UIS ions will there are that to the of including use of of of peptide and based on these M. D. J. B. R. T. B. Aebersold R. of peptides for Biotechnol. 2007; 25: PubMed Scopus Google Scholar, of spectra of Chem. 2004; PubMed Scopus Google Scholar, of spectra of peptides with or Chem. 2005; PubMed Scopus Google use of data A. D.M. B. B. S. the of SRM using data from shotgun proteomics to method Proteome Res. PubMed Scopus Google or approach to ions based on in multiple By this we the ions that are in multiple a level of the UIS of a given do an ion by the number of transitions by one the that an of addresses are one that is a peptide ions and using two ions in or for the is The significance of these are for large proteome and given a high of UIS this the that a of the proteome will using the detection methodology by these UIS a peptide as are only sequence-unique are in the for a given that there is utility in using UIS for of peptide obtained from conventional of MS/MS this approach is functionally orthogonal to conventional methods to assignments that are these of the two methods is for the conventional given that ions are used in these a UIS in the MS/MS we demonstrated in UIS used to spectra from assignments that are that the spectra contain peptide assignments for peptides that have This of value for proteome given that that to of MS/MS spectra are unassigned E.M. How do shotgun proteomics algorithms identify proteins?.Nat. Biotechnol. 2007; 25: 755-757Crossref PubMed Scopus (73) Google is to that the are only in the of the a of is the a protein in the is composed exclusively of peptides in the there are UIS for to the presence of each peptide in the proteome is a that ion from UIS this the in an method to for and to the this We have previously the of using to SRM J. K. M.P. How is The of and ion PubMed Scopus Google Scholar). we an to the of or use of an SRM Q3 ion to peptide in the and each of these was to the use of a peptide This that use of is to the use of an Q3 a is an of using a one to peptide to this to as is an in proteomic a rapid to UIS the use of with MS/MS reference and peptide reference peptides for are to peptide and information content. The of the work addresses information content. of peptide identification from from for from the of A. A. S. and Scholar, A. R. J. Scholar). methods to with will in UIS identification and are an that will methods for peptide identification are to proteomics of the of data generated by We used computational and experimental to show that the of to proteins in a proteome will in a of assays with ambiguous of from peptides that the we demonstrated by using generated by experimental that a to this is approach was to use the in the as a for the of the proteome. that is to the experimental in the as are to the of the UIS that are to false the and the UIS high in each detection of one peptide in and >96% of the E. coli and human We that these this coverage using only two transitions A of is being is robust method that ion we do have the to UIS ions will there are that to the of including use of of of peptide and based on these M. D. J. B. R. T. B. Aebersold R. of peptides for Biotechnol. 2007; 25: PubMed Scopus Google Scholar, of spectra of Chem. 2004; PubMed Scopus Google Scholar, of spectra of peptides with or Chem. 2005; PubMed Scopus Google use of data A. D.M. B. B. S. the of SRM using data from shotgun proteomics to method Proteome Res. PubMed Scopus Google or approach to ions based on in multiple By this we the ions that are in multiple a level of the UIS of a given do an ion by the number of transitions by one the that an of addresses are one that is a peptide ions and using two ions in or for the is The significance of these are for large proteome and given a high of UIS this the that a of the proteome will using the detection methodology by these UIS a peptide as are only sequence-unique are in the for a given We that there is utility in using UIS for of peptide obtained from conventional of MS/MS this approach is functionally orthogonal to conventional methods to assignments that are these of the two methods is for the conventional given that ions are used in these a UIS in the MS/MS we demonstrated in UIS used to spectra from assignments that are that the spectra contain peptide assignments for peptides that have This of value for proteome given that that to of MS/MS spectra are unassigned E.M. How do shotgun proteomics algorithms identify proteins?.Nat. Biotechnol. 2007; 25: 755-757Crossref PubMed Scopus (73) Google Scholar). is to that the are only in the of the a of is the a protein in the is composed exclusively of peptides in the there are UIS for to the presence of each peptide in the proteome is a that ion from UIS this the in an method to for and to the this We have previously the of using to SRM J. K. M.P. How is The of and ion PubMed Scopus Google Scholar). we an to the of or use of an SRM Q3 ion to peptide in the and each of these was to the use of a peptide This that use of is to the use of an Q3 a is an of using a one to peptide to this to as is an in proteomic a rapid to UIS the use of with MS/MS reference and peptide reference peptides for are to peptide and information content. The of the work addresses information content. of peptide identification from from for from the of A. A. S. and Scholar, A. R. J. Scholar). methods to with will in UIS identification and are an that will This was by to the Proteome the with with
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