Evaluation of the reliability of MS1-based approach to profile naturally occurring peptides with clinical relevance in urine samples

Jialu Jiang; Lingpeng Zhan; Liuyan Dai; Xiaopeng Yao; Yao Qin; Zhongqin Zhu; Mei Zhang; Wenjun Tong; Guanbo Wang

doi:10.1002/rcm.9369

Evaluation of the reliability of MS1-based approach to profile naturally occurring peptides with clinical relevance in urine samples

Rapid Commun Mass Spectrom. 2022 Jul 29:e9369. doi: 10.1002/rcm.9369. Online ahead of print.

Authors

Jialu Jiang^{1

2}, Lingpeng Zhan², Liuyan Dai³, Xiaopeng Yao^{1

2}, Yao Qin³, Zhongqin Zhu^{1

2}, Mei Zhang³, Wenjun Tong¹, Guanbo Wang^{2

4}

Affiliations

¹ School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, China.
² Shenzhen Bay Laboratory, Institute for Cell Analysis, Shenzhen, China.
³ Department of Endocrinology, The First Affiliated Hospital with Nanjing Medical University, Nanjing Medical University, Nanjing, China.
⁴ Biomedical Pioneering Innovation Centre, Peking University, Beijing, China.

PMID: 35906701
DOI: 10.1002/rcm.9369

Abstract

Rationale: The profiling of natural urinary peptides is a valuable indicator of kidney condition. While front-end separation limits the speed of peptidomic profiling, MS1-based results suffer from limited peptide coverage and specificity. Clinical studies on chronic kidney disease require an effective strategy to balance the trade-off between identification depth and throughput.

Methods: CKD273, a urinary proteome classifier associated with chronic kidney disease, in samples from diabetic nephropathy patients was profiled in parallel using capillary electrophoresis-mass spectrometry (CE-MS), liquid chromatography with mass spectrometry (LC-MS), and matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS). Through cross-comparison of results from MS1 of unfractionated peptides and elution-time-resolved MS1 as well as MS/MS in LC- and CE-MS approaches, we evaluated the contribution of false-positive identification to MS1-based identification and quantitation, and analyzed the benefit of front-end separation in terms of accuracy and efficiency.

Results: In LC- and CE-MS, although MS1 data resulted in higher number of identifications than MS/MS, elution-time-dependent analysis revealed extensive interference by non-CKD273 peptides, which would contribute up to 50% to quantitation if they are not separated from genuine CKD273 peptides. In the absence of separation, MS1 data resulted in lower numbers of identifications and abundance pattern that significantly deviated from those by liquid chromatography with tandem mass spectrometry (LC-MS/MS) or capillary electrophoresis with tandem mass spectrometry (CE-MS/MS). CE showed higher identification efficiency even when less sample was used or achieved faster separation.

Conclusions: To ensure the reliability of MS1-based urinary peptide profiling, front-end separation should not be omitted, and elution time should be used in addition to intact mass for identification. Including MS/MS in data acquisition does not compromise the speed or identification number, while benefiting data reliability by providing real-time sequence verification.

Abstract

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