diff --git a/Cargo.lock b/Cargo.lock
index a08e23f..c2d2c63 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1205,6 +1205,12 @@ version = "0.28.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "4271d37baee1b8c7e4b708028c57d816cf9d2434acb33a549475f78c181f6253"
 
+[[package]]
+name = "glob"
+version = "0.3.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d2fabcfbdc87f4758337ca535fb41a6d701b65693ce38287d856d1674551ec9b"
+
 [[package]]
 name = "h2"
 version = "0.3.24"
@@ -2260,6 +2266,7 @@ dependencies = [
  "csv",
  "env_logger",
  "fnv",
+ "glob",
  "itoa",
  "log",
  "num_cpus",
diff --git a/crates/sage-cli/Cargo.toml b/crates/sage-cli/Cargo.toml
index 1ee88d0..368debf 100644
--- a/crates/sage-cli/Cargo.toml
+++ b/crates/sage-cli/Cargo.toml
@@ -23,6 +23,7 @@ csv = "1"
 clap = { version="4.0", features = ["cargo", "unicode"] }
 env_logger = "0.8.4"
 fnv = "1.0"
+glob = "0.3.1"
 log = "0.4.0"
 itoa = "1.0"
 num_cpus = "1.13"
diff --git a/crates/sage-cli/src/input.rs b/crates/sage-cli/src/input.rs
index 4576103..2d337da 100644
--- a/crates/sage-cli/src/input.rs
+++ b/crates/sage-cli/src/input.rs
@@ -8,6 +8,7 @@ use sage_core::{
     tmt::Isobaric,
 };
 use serde::{Deserialize, Serialize};
+use glob::glob;
 
 #[derive(Serialize)]
 /// Actual search parameters - may include overrides or default values not set by user
@@ -176,7 +177,28 @@ impl Input {
             input.database.fasta = Some(fasta.into());
         }
         if let Some(mzml_paths) = matches.get_many::<String>("mzml_paths") {
-            input.mzml_paths = Some(mzml_paths.into_iter().map(|p| p.into()).collect());
+            let mut paths = Vec::new();
+            for path_pattern in mzml_paths {
+                match glob(path_pattern) {
+                    Ok(glob_paths) => {
+                        for entry in glob_paths {
+                            match entry {
+                                Ok(path) => {
+                                    // Convert PathBuf to String, handle potential conversion error
+                                    if let Some(path_str) = path.to_str() {
+                                        paths.push(path_str.to_string());
+                                    } else {
+                                        log::error!("Error converting path to string: {:?}", path);
+                                    }
+                                },
+                                Err(e) => log::error!("Error processing path: {}", e),
+                            }
+                        }
+                    },
+                    Err(e) => log::error!("Glob pattern error: {}", e),
+                }
+            }
+            input.mzml_paths = Some(paths);
         }
 
         if let Some(write_pin) = matches.get_one::<bool>("write-pin").copied() {