# US 12,110,314 B2 · PepCon proteomics standards and methods of use > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 12,110,314 B2 - Document ID: US12110314B2 - Status: Granted - Kind: B2 - Application number: 17/955,214 - Filed: 2022-09-28 - Published: 2023-06-22 - Granted: 2024-10-08 - Earliest claimed: 2019-07-24 - Assignees: Lawrence Livermore National Security, LLC - Applicants: Lawrence Livermore National Security, LLC - Inventors: Mathew Gerald Lyman; Deon S. Anex; Bonnee Rubinfeld - Web page: https://patentgrep.com/patent/US12110314B2 ## CPC - C07K 14/245: Escherichia (G) - C07K 7/08: having 12 to 20 amino acids (gastrins C07K14/595; somatostatins C07K14/655; melanotropins C07K14/68) - G01N 33/6848: {Methods of protein analysis involving mass spectrometry} - C07K 2319/036: targeting to the medium outside of the cell, e.g. type III secretion - C07K 2319/20: containing a tag with affinity for a non-protein ligand - C07K 2319/50: containing protease site - C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00) - G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q) ## Abstract Described are methods, compositions, and devices for a concatemeric protein standard that behaves as a protein but transforms into single peptides upon digestion, which is optimized to function as a non-obtrusive process control for mass spectrometry analysis. ## Claims ### Claim 1 A method of using a qualitative control for protein mass spectrometry, comprising: (a) generating an analysis sample by combining a protein sample with a peptide concatemer (“PepCon”), wherein the PepCon comprises two or more copies of a peptide linked by a cleavage site and the peptide comprises the sequence set forth in SEQ ID NO. 7 or a variant thereof which is at least 80% homologous to the SEQ ID NO. 7; and (b) digesting the analysis sample with an agent capable of cleaving at the cleavage site. ### Claim 2 (depends on 1) The method of claim 1, further comprising analyzing the analysis sample by mass spectrometry. ### Claim 3 (depends on 1) The method of claim 1 wherein cleavage site includes a protease cleavage site. ### Claim 4 (depends on 3) The method of claim 3 wherein the protease cleavage site includes an aminopeptidase M, bromelain, carboxypeptidase A, carboxypeptidase B, carboxypeptidase P, carboxypeptidase Y, cathepsin C, chymotrypsin, collagenase, dispase, elastase, endoproteinase, Arg-C, endoproteinase Asp-N, endoproteinase Glu-C, endoproteinase Lys-C, enterokinase, factor Xa, ficin, human rhinovirus (HRV) 3C protease (or its GST fusion, PreScission protease), kallikrein, papain, pepsin, plasmin, pronase, proteinase K, subtilisin, TEV, thermolysin, thrombin, or trypsin cleave site. ### Claim 5 (depends on 1) The method of claim 1 wherein digesting the analysis sample generates the two or more copies of the peptide. ### Claim 6 (depends on 5) The method of claim 5 wherein the two or more copies of the peptide include at least 15 copies of the peptide. ### Claim 7 (depends on 5) The method of claim 5 wherein the two or more copies of the peptide include at least 30 copies of the peptide. ### Claim 8 (depends on 1) The method of claim 1 wherein the peptide includes a single peptide. ### Claim 9 (depends on 1) The method of claim 1 wherein the peptide is a non-natural peptide. ### Claim 10 (depends on 9) The method of claim 9 wherein the peptide is optimized for electrospray ionization. ### Claim 11 A method of performing protein mass spectrometry, the method comprising: preparing an analysis sample containing a protein sample and a peptide concatemer (“PepCon”) for mass spectrometry, wherein the PepCon includes a protein structure having two or more copies of a peptide linked together and the peptide comprises the sequence set forth in SEQ ID NO. 7 or a variant thereof which is at least 80% homologous to the SEQ ID NO. 7, and wherein preparing the analysis sample includes digesting the PepCon to produce at least two unlinked copies of the peptide; and subjecting the analysis sample to mass spectrometry, wherein the at least two peptides act as a qualitative control for mass spectrometry analysis. ### Claim 12 (depends on 11) The method of claim 11 wherein the PepCon has 10 or more copies of the peptide, and wherein digesting the PepCon produces at least 10 unlinked copies of the peptide. ### Claim 13 (depends on 11) The method of claim 11 wherein the PepCon has 50 or more copies of the peptide, and wherein digesting the PepCon produces at least 50 unlinked copies of the peptide. ### Claim 14 (depends on 11) The method of claim 11 wherein digesting the PepCon includes mixing a cleavage agent with the analysis sample. ### Claim 15 (depends on 11) The method of claim 11 wherein the peptide is a non-natural peptide. ### Claim 16 A method of performing protein mass spectrometry using a qualitative control, the method comprising: subjecting an analysis sample containing a protein sample and two or more copies of a control peptide to mass spectrometry, wherein the two or more copies of the control peptide include a common sequence and were sourced from a peptide concatemer (“PepCon”) containing the two or more copies of the control peptide linked at a cleavage site and the control peptide comprises the sequence set forth in SEQ ID NO. 7 or a variant thereof which is at least 80% homologous to the SEQ ID NO. 7. ### Claim 17 (depends on 16) The method of claim 16, further comprising cleaving the PepCon to unlink the two or more copies of the control peptide before subjecting the analysis sample to mass spectrometry. ### Claim 18 (depends on 16) The method of claim 16 wherein analysis sample includes 15 or more copies of the control peptide, and wherein the 15 or more copies of the control peptide were sourced from a PepCon containing the 15 or more copies of the control peptide.