Dataset Information

SPE optimization for peptide sample preparation for urine peptidomics

ABSTRACT: Development of a modified solid phase extraction (SPE) approach for improved peptide yield and analysis sensitivity with LC-MS based peptidomics of urine.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Urine

SUBMITTER: Matthew Monroe

LAB HEAD: Minnie M. Sarwal

PROVIDER: PXD003045 | Pride | 2015-10-16

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Urine_pep_MSAlign_Results_syn.txt	Txt
	Urine_pep_SEQUEST_Results_syn.txt	Txt
	Urine_pep_SEQUEST_Results_syn_metadata.txt	Txt
	Urine_pep_test_A2_velos_13Mar13_Cougar_12-12-36.mgf	Mgf
	Urine_pep_test_A2_velos_13Mar13_Cougar_12-12-36.pride.mgf.gz	Mgf

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Publications

Optimization for peptide sample preparation for urine peptidomics.

Sigdel Tara K TK Nicora Carrie D CD Hsieh Szu-Chuan SC Dai Hong H Qian Wei-Jun WJ Camp David G DG Sarwal Minnie M MM

Clinical proteomics 20140225 1

Analysis of native or endogenous peptides in biofluids can provide valuable insights into disease mechanisms. Furthermore, the detected peptides may also have utility as potential biomarkers for non-invasive monitoring of human diseases. The non-invasive nature of urine collection and the abundance of peptides in the urine makes analysis by high-throughput 'peptidomics' methods , an attractive approach for investigating the pathogenesis of renal disease. However, urine peptidomics methodologies ...[more]

PMID: 24568099

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Project description:Analysis of native or endogenous peptides in biofluids can provide valuable insights into disease mechanisms. Furthermore, the detected peptides may also have utility as potential biomarkers for non-invasive monitoring of human diseases. The non-invasive nature of urine collection and the abundance of peptides in the urine makes analysis by high-throughput 'peptidomics' methods , an attractive approach for investigating the pathogenesis of renal disease. However, urine peptidomics methodologies can be problematic with regards to difficulties associated with sample preparation. The urine matrix can provide significant background interference in making the analytical measurements that it hampers both the identification of peptides and the depth of the peptidomics read when utilizing LC-MS based peptidome analysis. We report on a novel adaptation of the standard solid phase extraction (SPE) method to a modified SPE (mSPE) approach for improved peptide yield and analysis sensitivity with LC-MS based peptidomics in terms of time, cost, clogging of the LC-MS column, peptide yield, peptide quality, and number of peptides identified by each method. Expense and time requirements were comparable for both SPE and mSPE, but more interfering contaminants from the urine matrix were evident in the SPE preparations (e.g., clogging of the LC-MS columns, yellowish background coloration of prepared samples due to retained urobilin, lower peptide yields) when compared to the mSPE method. When we compared data from technical replicates of 4 runs, the mSPE method provided significantly improved efficiencies for the preparation of samples from urine (e.g., mSPE peptide identification 82% versus 18% with SPE; p = 8.92E-05). Additionally, peptide identifications, when applying the mSPE method, highlighted the biology of differential activation of urine peptidases during acute renal transplant rejection with distinct laddering of specific peptides, which was obscured for most proteins when utilizing the conventional SPE method. In conclusion, the mSPE method was found to be superior to the conventional, standard SPE method for urine peptide sample preparation when applying LC-MS peptidomics analysis due to the optimized sample clean up that provided improved experimental inference from the confidently identified peptides.