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

Abstract

RationaleThe 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.MethodsCKD273, 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.ResultsIn 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.ConclusionsTo 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.

Capillary Electrophoresis: A Three-Year Literature Review

“…In peptide analysis, CE has demonstrated strong competitiveness compared to traditional chromatographic techniques. , As an example, the performance of CE-MS, LC-MS, and MALDI-MS was compared in the analysis of CKD273 peptides. Although LC-MS/MS yielded the highest number of identifications, CE-MS/MS provided better identification efficiencies in terms of the number of identifications per unit time and per unit quantity of sample injection, making the latter a preferable option for achieving a balance between identification depth and speed …”

“…Although LC-MS/MS yielded the highest number of identifications, CE-MS/MS provided better identification efficiencies in terms of the number of identifications per unit time and per unit quantity of sample injection, making the latter a preferable option for achieving a balance between identification depth and speed. 165 Benefiting from its strong separation capability, CE has become a routine technique for peptide separations for various biological samples. For example, urine samples were screened for peptides as potential biomarkers of diseases, revealing specific biomarkers associated with prostate cancer, 166 bladder cancer, 167 hepatocellular carcinoma, 168 acute kidney injury, 169 and COVID-19.…”

Recent developments and applications of capillary and microchip electrophoresis in proteomics and peptidomics (mid‐2018–2022)

“…CE-MS, CE-MS/MS, LC-MS/MS, and MALDI-MS methods were employed for the analysis of urine samples of diabetic nephropathy patients applying a urinary proteome classifier for chronic kidney disease (CKD273) [184]. In CE, HPC-coated capillary and 5% (v/v) acetic acid, as BGE were used.…”