Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS)

Multiple reaction monitoring (MRM) mass spectrometry coupled with stable isotope dilution (SID) and liquid chromatography (LC) is increasingly used in biological and clinical studies for precise and reproducible quantification of peptides and proteins in complex sample matrices. Robust LC-SID-MRM-MS-based assays that can be replicated across laboratories and ultimately in clinical laboratory settings require standardized protocols to demonstrate that the analysis platforms are performing adequately. We developed a system suitability protocol (SSP), which employs a predigested mixture of six proteins, to facilitate performance evaluation of LC-SID-MRM-MS instrument platforms, configured with nanoflow-LC systems interfaced to triple quadrupole mass spectrometers. The SSP was designed for use with low multiplex analyses as well as high multiplex approaches when software-driven scheduling of data acquisition is required. Performance was assessed by monitoring of a range of chromatographic and mass spectrometric metrics including peak width, chromatographic resolution, peak capacity, and the variability in peak area and analyte retention time (RT) stability. The SSP, which was evaluated in 11 laboratories on a total of 15 different instruments, enabled early diagnoses of LC and MS anomalies that indicated suboptimal LC-MRM-MS performance. The observed range in variation of each of the metrics scrutinized serves to define the criteria for optimized LC-SID-MRM-MS platforms for routine use, with pass/fail criteria for system suitability performance measures defined as peak area coefficient of variation <0.15, peak width coefficient of variation <0.15, standard deviation of RT <0.15 min (9 s), and the RT drift <0.5min (30 s). The deleterious effect of a marginally performing LC-SID-MRM-MS system on the limit of quantification (LOQ) in targeted quantitative assays illustrates the use and need for a SSP to establish robust and reliable system performance. Use of a SSP helps to ensure that analyte quantification measurements can be replicated with good precision within and across multiple laboratories and should facilitate more widespread use of MRM-MS technology by the basic biomedical and clinical laboratory research communities.

Label-free quantitation of protein modifications by pseudo selected reaction monitoring with internal reference peptides

Liquid chromatography tandem mass spectrometry (LC–MS/MS) based methods provide powerful tools for the quantitative analysis of modified proteins. We have developed a label-free approach using internal reference peptides (IRP) from the target protein for signal normalization without the need for isotope labeling. Ion-trap mass spectrometry and pseudo-selected reaction monitoring (pSRM) were used to acquire full MS/MS and MS³ spectra from target peptides. Skyline, a widely used software for SRM experiments, was used for chromatographic ion extraction. Phosphopeptides spiked into a BSA background yielded concentration response curves with high correlation coefficients (typically >0.9) and low coefficients of variation (≤15%) over a 200-fold concentration range. Stable isotope dilution (SID) and IRP methods were compared for quantitation of six site-specific phosphorylations in the epidermal growth factor receptor (EGFR) in epidermal growth factor-stimulated A431 cells with or without the addition of EGFR inhibitors cetuximab and gefitinib. Equivalent responses were observed with both IRP and SID methods, although analyses using the IRP method typically had higher median CVs (22–31%) than SID (10–20%). Analyses using both methods were consistent with immunoblot using site-selective antibodies. The ease of implementation and the suitability for targeted quantitative comparisons make this method suitable for broad application in protein biochemistry.

Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry

Proteomics experiments based on Selected Reaction Monitoring (SRM, also referred to as Multiple Reaction Monitoring or MRM) are being used to target large numbers of protein candidates in complex mixtures. At present, instrument parameters are often optimized for each peptide, a time and resource intensive process. Large SRM experiments are greatly facilitated by having the ability to predict MS instrument parameters that work well with the broad diversity of peptides they target. For this reason, we investigated the impact of using simple linear equations to predict the collision energy (CE) on peptide signal intensity and compared it with the empirical optimization of the CE for each peptide and transition individually. Using optimized linear equations, the difference between predicted and empirically derived CE values was found to be an average gain of only 7.8% of total peak area. We also found that existing commonly used linear equations fall short of their potential, and should be recalculated for each charge state and when introducing new instrument platforms. We provide a fully automated pipeline for calculating these equations and individually optimizing CE of each transition on SRM instruments from Agilent, Applied Biosystems, Thermo-Scientific and Waters in the open source Skyline software tool ( http://proteome.gs.washington.edu/software/skyline ).

Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development

Selected reaction monitoring (SRM) is a powerful tandem mass spectrometry method that can be used to monitor target peptides within a complex protein digest. The specificity and sensitivity of the approach, as well as its capability to multiplex the measurement of many analytes in parallel, has made it a technology of particular promise for hypothesis driven proteomics. An underappreciated step in the development of an assay to measure many peptides in parallel is the time and effort necessary to establish a usable assay. Here we report the use of shotgun proteomics data to expedite the selection of SRM transitions for target peptides of interest. The use of tandem mass spectrometry data acquired on an LTQ ion trap mass spectrometer can accurately predict which fragment ions will produce the greatest signal in an SRM assay using a triple quadrupole mass spectrometer. Furthermore, we present a scoring routine that can compare the targeted SRM chromatogram data with an MS/MS spectrum acquired by data-dependent acquisition and stored in a library. This scoring routine is invaluable in determining which signal in the chromatogram from a complex mixture best represents the target peptide. These algorithmic developments have been implemented in a software package that is available from the authors upon request.

Precursor-ion mass re-estimation improves peptide identification on hybrid instruments

Mass spectrometry-based proteomics experiments have become an important tool for studying biological systems. Identifying the proteins in complex mixtures by assigning peptide fragmentation spectra to peptide sequences is an important step in the proteomics process. The 1-2 ppm mass-accuracy of hybrid instruments, like the LTQ-FT, has been cited as a key factor in their ability to identify a larger number of peptides with greater confidence than competing instruments. However, in replicate experiments of an 18-protein mixture, we note parent masses deviate 171 ppm, on average, for ion-trap data directed identifications and 8 ppm, on average, for preview Fourier transform (FT) data directed identifications. These deviations are neither caused by poor calibration nor by excessive ion-loading and are most likely due to errors in parent mass estimation. To improve these deviations, we introduce msPrefix, a program to re-estimate a peptide's parent mass from an associated high-accuracy full-scan survey spectrum. In 18-protein mixture experiments, msPrefix parent mass estimates deviate only 1 ppm, on average, from the identified peptides. In a cell lysate experiment searched with a tolerance of 50 ppm, 2295 peptides were confidently identified using native data and 4560 using msPrefixed data. Likewise, in a plasma experiment searched with a tolerance of 50 ppm, 326 peptides were identified using native data and 1216 using msPrefixed data. msPrefix is also able to determine which MS/MS spectra were possibly derived from multiple precursor ions. In complex mixture experiments, we demonstrate that more than 50% of triggered MS/MS may have had multiple precursor ions and note that spectra with multiple candidate ions are less likely to result in an identification using TANDEM. These results demonstrate integration of msPrefix into traditional shotgun proteomics workflows significantly improves identification results.

Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments

The open-source Computational Proteomics Analysis System (CPAS) contains an entire data analysis and management pipeline for Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) proteomics, including experiment annotation, protein database searching and sequence management, and mining LC-MS/MS peptide and protein identifications. CPAS architecture and features, such as a general experiment annotation component, installation software, and data security management, make it useful for collaborative projects across geographical locations and for proteomics laboratories without substantial computational support.

Women 35 years of age or younger have higher locoregional relapse rates after undergoing breast conservation therapy

BACKGROUND

The use of breast conservation therapy (BCT) in young women with invasive breast cancer is controversial. To examine this important issue, rates of locoregional recurrence and overall survival after BCT were compared in two subsets of women--those < or = 35 years of age at time of surgery and their older counterparts.

STUDY DESIGN

We examined records of 290 women with invasive breast cancer treated with BCT (local excision and axillary dissection) at Memorial Sloan-Kettering Cancer Center between 1984 and 1993. These included 87 patients < or = 35 years of age at time of surgery and 203 randomly selected patients > 35 years of age. Followup was obtained from physician charts or patient interviews, or both. Complete data on clinicopathologic factors, recurrence, and survival were available on 280 patients.

RESULTS

Median followup from time of operation was 8.0 years for the entire group. Mean tumor size was 2.0 cm for women < or = 35 years and 1.8 cm for those > 35 (p = 0.07). Involved nodes were found in 48% of the young patients and 36% of the older patients (p = 0.08). Within our study group (n = 280), 274 patients received radiotherapy. Women < or = 35 years of age had significantly higher rates of locoregional recurrence and lower rates of overall survival than their older counterparts (p < 0.05). On multivariate analysis, these results were independent of tumor size and nodal status. A history of locoregional relapse, however, was not associated with a higher rate of death from disease in the entire cohort or in either age group.

CONCLUSIONS

Patients < or = 35 years of age undergoing BCT for invasive breast cancer are at higher risk for locoregional recurrence and death from disease. The higher mortality rate, however, does not appear to be a direct result of locoregional relapse. Additional study is required to verify these findings. Currently, young age does not exclude patients from BCT in our practice. But, we include this data as part of the informed consent process.

Biostatistical basis of elective node dissection for malignant melanoma

During the years 1954 through 1964, 259 individuals with primary malignant melanoma had an elective node dissection. Microscopic metastases were found in 15% of these patients. The presence of only a microscopic focus of involvement gave a 10-year cure rate of 67%; metastasis larger than a microscopic focus in a single node, 50%; and more than one node, 15%. One hundred forty-five individuals were treated by wide excision alone with 18% subsequently requiring a therapeutic lymphadenectomy with a ten-year cure of only 6%. A prospective study was then initiated which was concerned with efficacy of selection of patients for elective node dissection. Clark's level of invasion was determined for 258 patients treated since January 1972. The depth of invasion of the primary lesion was found to correlate directly with the absence of lymph node metastases, extent of nodal involvement, and rate of recurrence. It is concluded that the concept of elective node dissection is valid.

Adverse effect of pregnancy on melanoma: a reappraisal

The influence of pregnancy on the prognosis of cutaneous melanoma in women of childbearing age was examined in a retrospective review of 251 surgically treated cases. There was no statistical difference in survival at five years, free of disease, for Stage I melanoma between nulliparous, parous nonpregnant, and pregnant women. For Stage II melanoma, however, a significantly lower survival rate was observed for pregnant patients (29%) and parous women who had experienced activation of the lesion in a previous pregnancy (22%), as compared with that of nulliparous patients (55%) and other patients in the parous group (51%); p less than 0.05. This discrepancy in survival, together with the observed higher frequencies of Stage II cases, melanomas occurring on the trunk, and symptoms such as bleeding, ulceration, irritation, and elevation of the lesion, strongly suggest an adverse influence of pregnancy on women with Stage II melanoma.