Abstract: Methods and systems for improved sample detection in mass spectroscopy are generally described. These are particularly useful, for example, for identifying a protein, a part of a protein, or a peptide when present in a low amount. In some embodiments, these can be useful to allow high-throughput proteomics studies for many samples, e.g., in series or in tandem. For example, certain embodiments are directed to novel approaches for identification of samples at the MS 1 level. In some cases, these improvements can be realized due to improvements in mass spectrometry instrumentation to better than the 1 ppm level for m/z measurements. Examples of improvements include, but are not limited to, improving internal mass standards, super-resolution peak fitting, isotopic labelling, Edman degradation and/or chromatography for proteins or peptides, and/or machine learning to predict peptide behavior, e.g., when exposed to such improvements.