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Items: 1 to 50 of 78

1.

Hybrid Search: A Method for Identifying Metabolites Absent from Tandem Mass Spectrometry Libraries.

Cooper BT, Yan X, Simón-Manso Y, Tchekhovskoi DV, Mirokhin YA, Stein SE.

Anal Chem. 2019 Oct 10. doi: 10.1021/acs.analchem.9b03415. [Epub ahead of print]

PMID:
31600070
2.

NIST Interlaboratory Study on Glycosylation Analysis of Monoclonal Antibodies: Comparison of Results from Diverse Analytical Methods.

De Leoz MLA, Duewer DL, Fung A, Liu L, Yau HK, Potter O, Staples GO, Furuki K, Frenkel R, Hu Y, Sosic Z, Zhang P, Altmann F, Gruber C, Shao C, Zaia J, Evers W, Pangelley S, Suckau D, Wiechmann A, Resemann A, Jabs W, Beck A, Froehlich JW, Huang C, Li Y, Liu Y, Sun S, Wang Y, Seo Y, An HJ, Reichardt NC, Ruiz JE, Archer-Hartmann S, Azadi P, Bell L, Lakos Z, An Y, Cipollo JF, Pučić-Baković M, Štambuk J, Lauc G, Li X, Wang PG, Bock A, Hennig R, Rapp E, Creskey M, Cyr T, Nakano M, Sugiyama T, Leung PA, Link-Lenczowski P, Jaworek J, Yang SJ, Zhang H, Kelly T, Klapoetke S, Cao R, Kim JY, Lee HK, Lee J, Yoo JS, Kim SR, Suh SK, de Haan N, Falck D, Lageveen-Kammeijer GSM, Wuhrer M, Emery RJ, Kozak RP, Liew LP, Royle L, Urbanowicz PA, Packer N, Song X, Everest-Dass A, Lattová E, Cajic S, Alagesan K, Kolarich D, Kasali T, Lindo V, Chen Y, Goswami K, Gau B, Amunugama R, Jones R, Stroop CJM, Kato K, Yagi H, Kondo S, Yuen CT, Harazono A, Shi X, Magnelli P, Kasper BT, Mahal LK, Harvey DJ, O'Flaherty RM, Rudd P, Saldova R, Hecht ES, Muddiman DC, Kang J, Bhoskar P, Menard D, Saati A, Merle C, Mast S, Tep S, Truong J, Nishikaze T, Sekiya S, Shafer A, Funaoka S, Toyoda M, de Vreugd P, Caron C, Pradhan P, Tan NC, Mechref Y, Patil S, Rohrer JS, Chakrabarti R, Dadke D, Lahori M, Zou C, Cairo CW, Reiz B, Whittal RM, Lebrilla C, Wu LD, Guttman A, Szigeti M, Kremkow BG, Lee K, Sihlbom C, Adamczyk B, Jin C, Karlsson NG, Örnros J, Larson G, Nilsson J, Meyer B, Wiegandt A, Komatsu E, Perreault H, Bodnar ED, Said N, Francois YN, Leize-Wagner E, Maier S, Zeck A, Heck AJR, Yang Y, Haselberg R, Yu YQ, Alley W, Leone JW, Yuan H, Stein SE.

Mol Cell Proteomics. 2019 Oct 7. pii: mcp.RA119.001677. doi: 10.1074/mcp.RA119.001677. [Epub ahead of print]

3.

Mass Spectrometry Fingerprints of Small-Molecule Metabolites in Biofluids: Building a Spectral Library of Recurrent Spectra for Urine Analysis.

Simón-Manso Y, Marupaka R, Yan X, Liang Y, Telu KH, Mirokhin Y, Stein SE.

Anal Chem. 2019 Sep 17;91(18):12021-12029. doi: 10.1021/acs.analchem.9b02977. Epub 2019 Aug 30.

PMID:
31424920
4.

False Discovery Rate Estimation for Hybrid Mass Spectral Library Search Identifications in Bottom-up Proteomics.

Burke MC, Zhang Z, Mirokhin YA, Tchekovskoi DV, Liang Y, Stein SE.

J Proteome Res. 2019 Sep 6;18(9):3223-3234. doi: 10.1021/acs.jproteome.8b00863. Epub 2019 Aug 14.

PMID:
31364354
5.

Cross-Ring Fragmentation Patterns in the Tandem Mass Spectra of Underivatized Sialylated Oligosaccharides and Their Special Suitability for Spectrum Library Searching.

De Leoz MLA, Simón-Manso Y, Woods RJ, Stein SE.

J Am Soc Mass Spectrom. 2019 Mar;30(3):426-438. doi: 10.1007/s13361-018-2106-8. Epub 2018 Dec 18.

6.

The challenge of implant integration in partial meniscal replacement: an experimental study on a silk fibroin scaffold in sheep.

Stein SEC, von Luebken F, Warnecke D, Gentilini C, Skaer N, Walker R, Kessler O, Ignatius A, Duerselen L.

Knee Surg Sports Traumatol Arthrosc. 2019 Feb;27(2):369-380. doi: 10.1007/s00167-018-5160-7. Epub 2018 Sep 27.

7.

Creating a Mass Spectral Reference Library for Oligosaccharides in Human Milk.

Remoroza CA, Mak TD, De Leoz MLA, Mirokhin YA, Stein SE.

Anal Chem. 2018 Aug 7;90(15):8977-8988. doi: 10.1021/acs.analchem.8b01176. Epub 2018 Jul 17.

PMID:
29969231
8.

The NISTmAb tryptic peptide spectral library for monoclonal antibody characterization.

Dong Q, Liang Y, Yan X, Markey SP, Mirokhin YA, Tchekhovskoi DV, Bukhari TH, Stein SE.

MAbs. 2018 Apr;10(3):354-369. doi: 10.1080/19420862.2018.1436921. Epub 2018 Mar 6.

9.

Reverse and Random Decoy Methods for False Discovery Rate Estimation in High Mass Accuracy Peptide Spectral Library Searches.

Zhang Z, Burke M, Mirokhin YA, Tchekhovskoi DV, Markey SP, Yu W, Chaerkady R, Hess S, Stein SE.

J Proteome Res. 2018 Feb 2;17(2):846-857. doi: 10.1021/acs.jproteome.7b00614. Epub 2018 Jan 11.

PMID:
29281288
10.

Combining Fragment-Ion and Neutral-Loss Matching during Mass Spectral Library Searching: A New General Purpose Algorithm Applicable to Illicit Drug Identification.

Moorthy AS, Wallace WE, Kearsley AJ, Tchekhovskoi DV, Stein SE.

Anal Chem. 2017 Dec 19;89(24):13261-13268. doi: 10.1021/acs.analchem.7b03320. Epub 2017 Dec 1.

11.

Collision-Induced Dissociation of Deprotonated Peptides. Relative Abundance of Side-Chain Neutral Losses, Residue-Specific Product Ions, and Comparison with Protonated Peptides.

Liang Y, Neta P, Yang X, Stein SE.

J Am Soc Mass Spectrom. 2018 Mar;29(3):463-469. doi: 10.1007/s13361-017-1842-5. Epub 2017 Nov 15.

PMID:
29143271
12.

Extending a Tandem Mass Spectral Library to Include MS2 Spectra of Fragment Ions Produced In-Source and MSn Spectra.

Yang X, Neta P, Stein SE.

J Am Soc Mass Spectrom. 2017 Nov;28(11):2280-2287. doi: 10.1007/s13361-017-1748-2. Epub 2017 Jul 18.

PMID:
28721670
13.

The Hybrid Search: A Mass Spectral Library Search Method for Discovery of Modifications in Proteomics.

Burke MC, Mirokhin YA, Tchekhovskoi DV, Markey SP, Heidbrink Thompson J, Larkin C, Stein SE.

J Proteome Res. 2017 May 5;16(5):1924-1935. doi: 10.1021/acs.jproteome.6b00988. Epub 2017 Apr 11.

PMID:
28367633
14.

Mass Spectral Library Quality Assurance by Inter-Library Comparison.

Wallace WE, Ji W, Tchekhovskoi DV, Phinney KW, Stein SE.

J Am Soc Mass Spectrom. 2017 Apr;28(4):733-738. doi: 10.1007/s13361-016-1589-4. Epub 2017 Jan 26.

15.

Analysis of human plasma metabolites across different liquid chromatography/mass spectrometry platforms: Cross-platform transferable chemical signatures.

Telu KH, Yan X, Wallace WE, Stein SE, Simón-Manso Y.

Rapid Commun Mass Spectrom. 2017 Jan 15;31(1):152. doi: 10.1002/rcm.7773. No abstract available.

PMID:
27943490
16.

Data quality issues in proteomics - there are many paths to enlightenment.

Haynes PA, Stein SE, Washburn MP.

Proteomics. 2016 Sep;16(18):2433-4. doi: 10.1002/pmic.201600277. No abstract available.

PMID:
27550836
17.

Interconversion of Peptide Mass Spectral Libraries Derivatized with iTRAQ or TMT Labels.

Zhang Z, Yang X, Mirokhin YA, Tchekhovskoi DV, Ji W, Markey SP, Roth J, Neta P, Hizal DB, Bowen MA, Stein SE.

J Proteome Res. 2016 Sep 2;15(9):3180-7. doi: 10.1021/acs.jproteome.6b00406. Epub 2016 Aug 8.

PMID:
27386737
18.

In-Depth Characterization and Spectral Library Building of Glycopeptides in the Tryptic Digest of a Monoclonal Antibody Using 1D and 2D LC-MS/MS.

Dong Q, Yan X, Liang Y, Stein SE.

J Proteome Res. 2016 May 6;15(5):1472-86. doi: 10.1021/acs.jproteome.5b01046. Epub 2016 Apr 19.

PMID:
26990841
19.

A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline.

Rudnick PA, Markey SP, Roth J, Mirokhin Y, Yan X, Tchekhovskoi DV, Edwards NJ, Thangudu RR, Ketchum KA, Kinsinger CR, Mesri M, Rodriguez H, Stein SE.

J Proteome Res. 2016 Mar 4;15(3):1023-32. doi: 10.1021/acs.jproteome.5b01091. Epub 2016 Feb 25.

20.

Analysis of human plasma metabolites across different liquid chromatography/mass spectrometry platforms: Cross-platform transferable chemical signatures.

Telu KH, Yan X, Wallace WE, Stein SE, Simón-Manso Y.

Rapid Commun Mass Spectrom. 2016 Mar 15;30(5):581-93. doi: 10.1002/rcm.7475. Erratum in: Rapid Commun Mass Spectrom. 2017 Jan 15;31(1):152.

21.

Reaction of arylium ions with the collision gas N2 in electrospray ionization mass spectrometry.

Liang Y, Neta P, Simón-Manso Y, Stein SE.

Rapid Commun Mass Spectrom. 2015 Apr 15;29(7):629-36. doi: 10.1002/rcm.7147.

PMID:
26212280
22.

Unexpected peaks in tandem mass spectra due to reaction of product ions with residual water in mass spectrometer collision cells.

Neta P, Farahani M, Simón-Manso Y, Liang Y, Yang X, Stein SE.

Rapid Commun Mass Spectrom. 2014 Dec 15;28(23):2645-60. doi: 10.1002/rcm.7055.

PMID:
25366411
23.

Creation of libraries of recurring mass spectra from large data sets assisted by a dual-column workflow.

Mallard WG, Andriamaharavo NR, Mirokhin YA, Halket JM, Stein SE.

Anal Chem. 2014 Oct 21;86(20):10231-8. doi: 10.1021/ac502379x. Epub 2014 Oct 1.

PMID:
25233296
24.

Loss of H2 and CO from protonated aldehydes in electrospray ionization mass spectrometry.

Neta P, Simón-Manso Y, Liang Y, Stein SE.

Rapid Commun Mass Spectrom. 2014 Sep 15;28(17):1871-82. doi: 10.1002/rcm.6968.

PMID:
25088131
25.

Quality control for building libraries from electrospray ionization tandem mass spectra.

Yang X, Neta P, Stein SE.

Anal Chem. 2014 Jul 1;86(13):6393-400. doi: 10.1021/ac500711m. Epub 2014 Jun 13.

PMID:
24896981
26.

Tandem mass spectral libraries of peptides in digests of individual proteins: Human Serum Albumin (HSA).

Dong Q, Yan X, Kilpatrick LE, Liang Y, Mirokhin YA, Roth JS, Rudnick PA, Stein SE.

Mol Cell Proteomics. 2014 Sep;13(9):2435-49. doi: 10.1074/mcp.O113.037135. Epub 2014 Jun 2.

27.

Improved normalization of systematic biases affecting ion current measurements in label-free proteomics data.

Rudnick PA, Wang X, Yan X, Sedransk N, Stein SE.

Mol Cell Proteomics. 2014 May;13(5):1341-51. doi: 10.1074/mcp.M113.030593. Epub 2014 Feb 21.

28.

QC metrics from CPTAC raw LC-MS/MS data interpreted through multivariate statistics.

Wang X, Chambers MC, Vega-Montoto LJ, Bunk DM, Stein SE, Tabb DL.

Anal Chem. 2014 Mar 4;86(5):2497-509. doi: 10.1021/ac4034455. Epub 2014 Feb 17.

29.

Quantitative bottom-up proteomics depends on digestion conditions.

Lowenthal MS, Liang Y, Phinney KW, Stein SE.

Anal Chem. 2014 Jan 7;86(1):551-8. doi: 10.1021/ac4027274. Epub 2013 Dec 9.

PMID:
24294946
30.

Metabolite profiling of a NIST Standard Reference Material for human plasma (SRM 1950): GC-MS, LC-MS, NMR, and clinical laboratory analyses, libraries, and web-based resources.

Simón-Manso Y, Lowenthal MS, Kilpatrick LE, Sampson ML, Telu KH, Rudnick PA, Mallard WG, Bearden DW, Schock TB, Tchekhovskoi DV, Blonder N, Yan X, Liang Y, Zheng Y, Wallace WE, Neta P, Phinney KW, Remaley AT, Stein SE.

Anal Chem. 2013 Dec 17;85(24):11725-31. doi: 10.1021/ac402503m. Epub 2013 Dec 3.

PMID:
24147600
31.

Comprehensive analysis of protein digestion using six trypsins reveals the origin of trypsin as a significant source of variability in proteomics.

Walmsley SJ, Rudnick PA, Liang Y, Dong Q, Stein SE, Nesvizhskii AI.

J Proteome Res. 2013 Dec 6;12(12):5666-80. doi: 10.1021/pr400611h. Epub 2013 Nov 14.

32.

The need for additional training for nutritional management of diabetes.

Carney T, Stein SE, Quinlan JJ.

Br J Nurs. 2013 May 9-22;22(9):512, 514-7.

PMID:
23752631
33.

Regional differences in rat vaginal smooth muscle contractility and morphology.

Skoczylas LC, Jallah Z, Sugino Y, Stein SE, Feola A, Yoshimura N, Moalli P.

Reprod Sci. 2013 Apr;20(4):382-90. doi: 10.1177/1933719112472733. Epub 2013 Jan 8.

34.

Characterizing Vaccinium berry Standard Reference Materials by GC-MS using NIST spectral libraries.

Lowenthal MS, Andriamaharavo NR, Stein SE, Phinney KW.

Anal Bioanal Chem. 2013 May;405(13):4467-76. doi: 10.1007/s00216-012-6610-6. Epub 2013 Jan 6.

PMID:
23291961
35.

Identification of unique food handling practices that could represent food safety risks for minority consumers.

Henley SC, Stein SE, Quinlan JJ.

J Food Prot. 2012 Nov;75(11):2050-4. doi: 10.4315/0362-028X.JFP-12-146.

PMID:
23127716
36.

Developing qualitative LC-MS methods for characterization of Vaccinium berry Standard Reference Materials.

Lowenthal MS, Phillips MM, Rimmer CA, Rudnick PA, Simón-Manso Y, Stein SE, Tchekhovskoi D, Phinney KW.

Anal Bioanal Chem. 2013 May;405(13):4451-65. doi: 10.1007/s00216-012-6346-3. Epub 2012 Sep 2.

PMID:
22941178
37.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR 3rd, Rodriguez H.

Proteomics Clin Appl. 2011 Dec;5(11-12):580-9. doi: 10.1002/prca.201100097.

PMID:
22213554
38.

Formation of y + 10 and y + 11 ions in the collision-induced dissociation of peptide ions.

Kilpatrick LE, Neta P, Yang X, Simón-Manso Y, Liang Y, Stein SE.

J Am Soc Mass Spectrom. 2012 Apr;23(4):655-63. doi: 10.1007/s13361-011-0277-7. Epub 2011 Dec 8.

PMID:
22161574
39.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H.

Proteomics. 2012 Jan;12(1):11-20. doi: 10.1002/pmic.201100562. Epub 2011 Dec 14.

PMID:
22069307
40.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H.

J Proteome Res. 2012 Feb 3;11(2):1412-9. doi: 10.1021/pr201071t. Epub 2011 Dec 8.

41.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR 3rd, Rodriguez H.

Mol Cell Proteomics. 2011 Dec;10(12):O111.015446. doi: 10.1074/mcp.O111.015446. Epub 2011 Nov 3.

42.

Repetitive mechanical stretch increases extracellular collagenase activity in vaginal fibroblasts.

Zong W, Jallah ZC, Stein SE, Abramowitch SD, Moalli PA.

Female Pelvic Med Reconstr Surg. 2010 Sep 1;16(5):257-262.

43.

Loss of 45 Da from a2 ions and preferential loss of 48 Da from a2 ions containing methionine in peptide ion tandem mass spectra.

Simón-Manso Y, Neta P, Yang X, Stein SE.

J Am Soc Mass Spectrom. 2011 Feb;22(2):280-9. doi: 10.1007/s13361-010-0025-4. Epub 2011 Jan 29.

PMID:
21472587
44.

Charge states of y ions in the collision-induced dissociation of doubly charged tryptic peptide ions.

Neta P, Stein SE.

J Am Soc Mass Spectrom. 2011 May;22(5):898-905. doi: 10.1007/s13361-011-0089-9. Epub 2011 Feb 25.

PMID:
21472524
45.

Electron ionization mass spectra of alkylated sulfabenzamides.

Todua NG, Tretyakov KV, Borisov RS, Zhilyaev DI, Zaikin VG, Stein SE, Mikaia AI.

Rapid Commun Mass Spectrom. 2011 Mar 30;25(6):750-4. doi: 10.1002/rcm.4918.

46.

Electrospray tandem quadrupole fragmentation of quinolone drugs and related ions. On the reversibility of water loss from protonated molecules.

Neta P, Godugu B, Liang Y, Simón-Manso Y, Yang X, Stein SE.

Rapid Commun Mass Spectrom. 2010 Nov 30;24(22):3271-8. doi: 10.1002/rcm.4769.

PMID:
20973001
47.

Unique para-effect in electron ionization mass spectra of bis(perfluoroacyl) derivatives of bifunctional aminobenzenes.

Tretyakov KV, Todua NG, Borisov RS, Zaikin VG, Stein SE, Mikaia AI.

Rapid Commun Mass Spectrom. 2010 Sep 15;24(17):2529-32. doi: 10.1002/rcm.4661.

48.

Depletion of abundant plasma proteins and limitations of plasma proteomics.

Tu C, Rudnick PA, Martinez MY, Cheek KL, Stein SE, Slebos RJ, Liebler DC.

J Proteome Res. 2010 Oct 1;9(10):4982-91. doi: 10.1021/pr100646w.

49.
50.

Effect of N-terminal glutamic acid and glutamine on fragmentation of peptide ions.

Godugu B, Neta P, Simón-Manso Y, Stein SE.

J Am Soc Mass Spectrom. 2010 Jul;21(7):1169-76. doi: 10.1016/j.jasms.2010.03.027. Epub 2010 Mar 27.

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